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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
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infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6435-%hccV`?$Op-IA_P%]TMTuX-W!3p8MWo/j*l[aEQcB.mhJ*]kR</fs*1^Q/.-A/IOJKn=sPLC<'Yf9](O7/^\e&6-C;*\c45Nd;HU0
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infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6437-%=M.nH?3Nl)`(&:Y\3u0/ja:#Rhn32/oo91IJ-Tr>UlnW3/p(EokMW!a7Dq`9_6+Pa9YSW!P:X;&5cP7Yb%uP`L2V?Dd'+K_cu>J4
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infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6439-%5RaY++Ec+JW/,)G\jT=N(GRMpFTNT$P"UKP"?<-^=p'SLp.+?I?nF.V4Q+>WeBsRuhZTf]8hSf6PCI0fLcjPiQu/rLfI!c:M>ou/
##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6442-%PO4Dd>1njofSQkj2@ESZ[R0;T6QIjY):b%pNt^aD\8#MC?uO"D%#RhXfgMKP:iKGfe!Y4R1H:K+>/Yg<3E*H!=F;f(3\*B-]G+Z+
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##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6449-%89dCmRrP%Y3c/J/KQ%CD^:nSo7cu<W3tU9''N$U7E.'1WU#^jMJgdHDN<sal]8.u5=SgNfXAfodHBp`&n``;,k;oKEpM<P:)]L+d
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##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6455-%YRVPHfR!'Z$EHM?b\U2,Z1O*;7Ukkr;)rK6"Y/X07]>Ja9a_jo7Wep*-/Q)CGT2nf$g5JH)`@1Uk>(]8Q"o!S$aV%CChp3=;OeOd
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infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6459-%X3W=[ne+_V>q="Me9\Y?2C]8M>$#Xe/-7(H7fW=NJLp1'Q7g&scibE/\"7Gtg)k!.W"luAlm%"fKqG!`I^W.'Dh!4b`m9'O^ccJQ
##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6461-%l97(5lcn)6#&LO^pRhueS$DJ!qqHig+/PM;_VR1\B7k.6R^([,mpJHm?lPQ"mn!V)er66Y!mg=Z"6*N+[,L3BDE;srJ01"6Co&!W
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6462:%+5]]P>ArnP]0F'kNX'X;KdY`_Iri2d#&Nhm^,KF1S$AFelq'!VhgeujA$6fTj(@Xp"1HsCrHS2T)m`W=^Ff=C'RnoIV4U+F*a2`n
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6463-%kf?ds++EG$UY[)@oV'0\MuMAhB5[\=0Aeh^^3:W$e:<;qJ)R$tRm6_4J,<#+FmPY,C-M9m&,s]nrn3qDq4IVPYC6!3LZZ)An=q*&
##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6493-%)?c5iA8CIW5;"2`:GtV?Hf#II.S*3Qal.]UB"#WBXbAgrUEnm,b][1#f8F[8,``<HL&XnhAPPdfC?@J:j>S>NjPQlOi$g2MB$07Y
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6494:%$nkg`Y$(AnBrS?n\uNfbTml.]Rg)s^qXBp)`Gcoh\k#Rknmn6kJ.AB>T`ESY#TCS^B!^\(m`jgglfeJZo5eN=Q>R:d-?UHRkkCr!
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6495-%F;8-/#s7aJC;JVDC$&CV+KJ1el(\s[.bj7J:3Mnk^'e0*jjDn5G@Tm"P94!J]Xiii5biX!SH.>aF0s>!l,j>@\%U-7d%m6qeJ\&J
##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6503-%SEknKbB=^lbOGVuHE^c65I#4/$[H(_LWs`&RDIh>>\NQOEO:WeFoURVHZE?FmbR7%od$f4^'/Qh4b.D[_p[h)h8cSV@+I(=Z\]!<
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6504:%I-UoGmO@IfJcml06ls9]DF0Vd:Z%WdM`)]^PI<+$C9J%PD=0[BQa:n/Yo:'^$Ul64emS:,nM/1WmVmgn`EW-1rn>M>OmDtj+VcF5
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6505-%Trk\W\)f?=%+a/RU!TI7[sQ#0Dp`+k3\qVUFb^p\0cKq8p*`YbZ=T0U8oKFp[d-GDI:TS5^"XF+?>j-;oktqB9m]YhPS\5mf]\>L
##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6516-%k<\Zd4G^04DacDC;@l2r^eaOL1T(bDf@g=.j*eO[m`1T'V]NuQ]4G1sLbL`uehb")<IHtkD>2@2A\V<Zh8^91f&i3B^?h,6^`<[&
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6517:%74h83`.0hoY(o5pL]1]Qk,m".DR]Y`IcbPrg@^$'nNGR`T-)j&@rtUOBoGe:9i8;nP]jU=!D7=a(qmZoWWsbH1^43@*0?S'D^%\i
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6518:%9gk$@h'nJ]kB7V$]#T//q*83=_.oDWmWZE6U^%:jJa&sZIV`nPh;i$h5E$r`2breV#qc#m+iWU0bu)6bQ2nF<B#1(;A?0KoS+3dC
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6519-%DZS<]Z'iEEF00$GjAqa]U.:&V2po"H12?P2>q9uc[@1g9Ng5@U]scDebQB0[&)W+g\MNSX^YZ`[3nJiRSf4WteT/!UjedoLl]$>1
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infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6522-%/`0oCgB4NU)S7pL,k,0\SJuaaXg>^#d9nrQ.mEuV%eSOY*EuP`"c5L_aC2")J9,#Y`&f4hq'%&`BdFL\*33":8SrTFS5uPU<mjgd
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6523:%=teW&`HkTD7bh$]l=Es6SU\PBf-[R3V6Y$hb\*A=&&`)/J_4X^+?#]!`&kS/)IDl>R\DWTDf,Q4Hg>d'Et30N=L"DI&TtW?-/qkL
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6524-%^2iQ5CSuRCL%j8]TBW_6q"TD:Y:Ih2[/UL,+$R4]:Up3c@el^_=:V'Olb6gYWeTY&:"*@+@k5PC&R2MtqMki`LgIWMd1p<;6aq7g
##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6548-%NrsS]pFr)(^4lkrG03)3CP29M<c8F/0\GTK\uGBm"dsScKGO80fLrfN9sT)L7HAjnDKeXc?Ff=-W`pr(1ibU\5WsT;c17QM.pUHI
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infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6551-%r:^klT.^bnBO<ns]sFgkB@<8,]_t8)%VT-n7_4)GLJN!SFnfHM=)K2K(VoK'r;S+/^!]D#qT)rf't!t\>?=!%>'0,[6iQJq"j$.V
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6552:%m!.j]MiB_GD9GmrfbD`VR$;GgkfO'mI-cRSeQ4D?i%ssTKT5mD/-uQqrPhp^`k/7Y$5Bma[!.A*>Sq2DQO=b2o"i4&*@MDilfCa(
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6553-%^6P:l$[ENRQ]LWdXd<<ASX$I&<X!rnlK?Lco([$9gK=>7N?/6u\?Rl%c.+Kgk^bU.pfqBlmji@'6:O$0baIin;-B.ThE`Zmi7d?q
##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6565-%e#E7T[T+iF3#3q"[j<p4I++Zj#>Ak*e2gu0^ME.cW@+bKVM*Gl?6u=sS$FI)jb%76kqfC4e$Ge=kP@!8!*nMhV<Y^Pc`4bk=oJ8d
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infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6569:%MHI_hDbFQ<YnP`"@jeJ%)'sXaj>Aqt'V!pk-9#U:[u=d7e[QrFmTs*$9TU=ifIDFMhVAXtKWV,f::cs'VhY&l9Mr*`L+4fU,b,M)
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6570-%QEcY)'C=5Y*LS@#.+>\?V2A`g9p;+pC"(^+mBMc[/)95KWM]@.-p'.ZC=7El;:<Ob8aB*N8>\X0XZ&^D=Dpl#@q2D"F\G1"P:DI7
##############################################
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6573-%hTg7l9'*ZIX6QRZeC85BcK`FF>u*KBl\6r%/!B.qS!m5Od#?;=T@B*;Pk6juW@:OV`F_%dV%).c3CBk(*o9]8@e!U/Xn<(+DL6+5
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps:6574:%^b5)P<<0YDQW=.Ro'WR\TOXGOF\kDanN%6$q'r.-m`T:fUT(!/lZJECCHoZ$FlQY,:V$DRN@SJ>..V[IL"GYX=To3`q#-RW!3UoP
infernal-1.1.3/documentation/userguide/Figures/rna_elements.eps-6575-%Muk+=C2La7TU)]/8].U/jjL\95mcsfHBq8*:1[cOGAh:!E%A?)G.Y-g^qcr#g"E,:7a2e[_oKGoc&#k"W_1*h^bF$1ai"'k29mC`
##############################################
infernal-1.1.3/rmark/rmark-pp.sh-11-# get numbers of false negatives and false positives at E-threshold of 0.1 from rmark-rocplot (after E-value inflation)
infernal-1.1.3/rmark/rmark-pp.sh:12:#ARG=`echo 0.1/$3|bc -l`
infernal-1.1.3/rmark/rmark-pp.sh-13-#echo 0.1/$3|bc -l
##############################################
infernal-1.1.3/rmark/x-blastall-80- $command = "$afetch -o $resultdir/$msaname.sto $msafile $msaname > /dev/null";
infernal-1.1.3/rmark/x-blastall:81: $status = system("$command");
infernal-1.1.3/rmark/x-blastall-82- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastall-85- $command = "$reformat fasta $resultdir/$msaname.sto > $resultdir/$msaname.query";
infernal-1.1.3/rmark/x-blastall:86: $status = system("$command");
infernal-1.1.3/rmark/x-blastall-87- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastall-90- $command = "$blastall $searchopts -p blastn -i $resultdir/$msaname.query -d $fafile -m 8 -a 1 > $resultdir/$msaname.tmp";
infernal-1.1.3/rmark/x-blastall:91: $status = system("$command");
infernal-1.1.3/rmark/x-blastall-92- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastall-124-$command = "sort -g $tmpoutfile > $sorttmpoutfile";
infernal-1.1.3/rmark/x-blastall:125:$status = system("$command");
infernal-1.1.3/rmark/x-blastall-126-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastall-128-$command = "perl $idscript $posfile $sorttmpoutfile > $outfile";
infernal-1.1.3/rmark/x-blastall:129:$status = system("$command");
infernal-1.1.3/rmark/x-blastall-130-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastn-80- $command = "$afetch -o $resultdir/$msaname.sto $msafile $msaname > /dev/null";
infernal-1.1.3/rmark/x-blastn:81: $status = system("$command");
infernal-1.1.3/rmark/x-blastn-82- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastn-85- $command = "$reformat fasta $resultdir/$msaname.sto > $resultdir/$msaname.query";
infernal-1.1.3/rmark/x-blastn:86: $status = system("$command");
infernal-1.1.3/rmark/x-blastn-87- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastn-90- $command = "$blastn -task blastn $searchopts -db $fafile -query $resultdir/$msaname.query -outfmt 7 -num_threads 1 -out $resultdir/$msaname.tmp";
infernal-1.1.3/rmark/x-blastn:91: $status = system("$command");
infernal-1.1.3/rmark/x-blastn-92- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastn-124-$command = "sort -g $tmpoutfile > $sorttmpoutfile";
infernal-1.1.3/rmark/x-blastn:125:$status = system("$command");
infernal-1.1.3/rmark/x-blastn-126-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-blastn-128-$command = "perl $idscript $posfile $sorttmpoutfile > $outfile";
infernal-1.1.3/rmark/x-blastn:129:$status = system("$command");
infernal-1.1.3/rmark/x-blastn-130-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-154- if($do_build_models) {
infernal-1.1.3/rmark/x-cmsearch:155: $status = system("$afetch -o $resultdir/$msaname" . $key . ".sto $msafile $msaname > /dev/null");
infernal-1.1.3/rmark/x-cmsearch-156- if ($status != 0) { die "UH FAILED: $afetch -o $resultdir/$msaname" . $key . ".sto $msafile $msaname > /dev/null"; }
infernal-1.1.3/rmark/x-cmsearch-157-
infernal-1.1.3/rmark/x-cmsearch:158: $status = system("$cmbuild $buildopts $resultdir/$msaname" . $key . ".cm $resultdir/$msaname" . $key . ".sto > /dev/null");
infernal-1.1.3/rmark/x-cmsearch-159- if ($status != 0) { die "FAILED: $cmbuild $buildopts $resultdir/$msaname" . $key . ".cm $resultdir/$msaname" . $key . ".sto > /dev/null"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-162- elsif($do_fetch_models) {
infernal-1.1.3/rmark/x-cmsearch:163: $status = system("$cmfetch -o $resultdir/$msaname" . $key . ".cm $master_model $msaname > /dev/null");
infernal-1.1.3/rmark/x-cmsearch-164- if ($status != 0) { die "FAILED: $cmfetch -o $resultdir/$msaname" . $key . ".cm $master_model > /dev/null"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-175- $command = "grep \"^$msaname\/\" rmark3.ppos | awk \'{ print \$3 }\' > $resultdir/$msaname" . $key . ".sfetch";
infernal-1.1.3/rmark/x-cmsearch:176: $status = system($command);
infernal-1.1.3/rmark/x-cmsearch-177- if ($status != 0) { die "FAILED: $command failed"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-179- $command = "$sfetch -o $resultdir/$msaname" . $key . ".pfa -f $orig_fafile $resultdir/$msaname" . $key . ".sfetch > /dev/null";
infernal-1.1.3/rmark/x-cmsearch:180: $status = system($command);
infernal-1.1.3/rmark/x-cmsearch-181- if ($status != 0) { die "FAILED: $command failed"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-186- $command = "grep \"^$msaname\/\" rmark3.wppos | awk \'{ print \$2 }\' > $resultdir/$msaname" . $key . ".sfetch";
infernal-1.1.3/rmark/x-cmsearch:187: $status = system($command);
infernal-1.1.3/rmark/x-cmsearch-188- if ($status != 0) { die "FAILED: $command failed"; }
infernal-1.1.3/rmark/x-cmsearch-189-
infernal-1.1.3/rmark/x-cmsearch:190: $nl = `wc -l $resultdir/$msaname" . $key . ".sfetch`;
infernal-1.1.3/rmark/x-cmsearch-191- if($nl =~ m/^0\s+/) {
##############################################
infernal-1.1.3/rmark/x-cmsearch-196- $command = "$sfetch -o $resultdir/$msaname" . $key . ".wpfa -f $orig_fafile $resultdir/$msaname" . $key . ".sfetch > /dev/null";
infernal-1.1.3/rmark/x-cmsearch:197: $status = system($command);
infernal-1.1.3/rmark/x-cmsearch-198- if ($status != 0) { die "FAILED: $command failed"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-212- $command = "mpirun -np $mpi_nprocs $cmsearch $bo_opt $to_opt $searchopts $fam_searchopts_H{$msaname} $p7file_opt $tab_opt $extra_opt $cmfile $fafile > $resultdir/$msaname" . $key . ".search";
infernal-1.1.3/rmark/x-cmsearch:213: $status = system($command);
infernal-1.1.3/rmark/x-cmsearch-214- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-217- $command = "$cmsearch $bo_opt $to_opt $searchopts $fam_searchopts_H{$msaname} $p7file_opt $tab_opt $extra_opt $cmfile $fafile > $resultdir/$msaname" . $key . ".search";
infernal-1.1.3/rmark/x-cmsearch:218: $status = system($command);
infernal-1.1.3/rmark/x-cmsearch-219- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-269-
infernal-1.1.3/rmark/x-cmsearch:270: system("grep \"CPU time\" $resultdir/$msaname" . $key . ".search > $resultdir/$msaname" . $key . ".time");
infernal-1.1.3/rmark/x-cmsearch-271- sleep(0.1);
##############################################
infernal-1.1.3/rmark/x-cmsearch-284- $command = "sort -g $tmpoutfile > $sorttmpoutfile";
infernal-1.1.3/rmark/x-cmsearch:285: $status = system("$command");
infernal-1.1.3/rmark/x-cmsearch-286- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-cmsearch-288- $command = "perl $idscript $posfile $sorttmpoutfile > $outfile";
infernal-1.1.3/rmark/x-cmsearch:289: $status = system("$command");
infernal-1.1.3/rmark/x-cmsearch-290- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer-92- if($do_fetch_models) {
infernal-1.1.3/rmark/x-nhmmer:93: $status = system("$hmmfetch -o $resultdir/$msaname.hmm $master_model $msaname > /dev/null");
infernal-1.1.3/rmark/x-nhmmer-94- if ($status != 0) { die "FAILED: $hmmfetch -o $resultdir/$msaname.hmm $master_model > /dev/null"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer-98- $command = "grep \"^$msaname\/\" rmark3.ppos | awk \'{ print \$3 }\' > $resultdir/$msaname.sfetch";
infernal-1.1.3/rmark/x-nhmmer:99: $status = system($command);
infernal-1.1.3/rmark/x-nhmmer-100- if ($status != 0) { die "FAILED: $command failed"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer-102- $command = "$sfetch -o $resultdir/$msaname.pfa -f $orig_fafile $resultdir/$msaname.sfetch > /dev/null";
infernal-1.1.3/rmark/x-nhmmer:103: $status = system($command);
infernal-1.1.3/rmark/x-nhmmer-104- if ($status != 0) { die "FAILED: $command failed"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer-108-
infernal-1.1.3/rmark/x-nhmmer:109: $status = system("$nhmmer $searchopts --tblout $resultdir/$msaname.tmp $modeldir/$msaname.hmm $fafile > $resultdir/$msaname.search");
infernal-1.1.3/rmark/x-nhmmer-110- if ($status != 0) { die "FAILED: $nhmmer $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > $resultdir/$msaname.nhmmer"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer-148-$command = "sort -g $tmpoutfile > $sorttmpoutfile";
infernal-1.1.3/rmark/x-nhmmer:149:$status = system("$command");
infernal-1.1.3/rmark/x-nhmmer-150-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer-152-$command = "perl $idscript $posfile $sorttmpoutfile > $outfile";
infernal-1.1.3/rmark/x-nhmmer:153:$status = system("$command");
infernal-1.1.3/rmark/x-nhmmer-154-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-99-if(! -e "$fafile.ssi") {
infernal-1.1.3/rmark/x-nhmmer2cmsearch:100: $status = system("$sfetch --index $fafile");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-101- if ($status != 0) { die "FAILED: $sfetch --index $fafile"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-106-# greater than the length of the seqs
infernal-1.1.3/rmark/x-nhmmer2cmsearch:107:$output = `$seqstat -a $fafile`;
infernal-1.1.3/rmark/x-nhmmer2cmsearch-108-%falensH = ();
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-126- $command = "$hmmfetch -o $resultdir/$msaname.hmm $master_hmm $msaname > /dev/null";
infernal-1.1.3/rmark/x-nhmmer2cmsearch:127: $status = system("$command");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-128- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-130- $command = "$cmfetch -o $resultdir/$msaname.cm $master_cm $msaname > /dev/null";
infernal-1.1.3/rmark/x-nhmmer2cmsearch:131: $status = system("$command");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-132- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-134- # get W of CM from cmstat
infernal-1.1.3/rmark/x-nhmmer2cmsearch:135: $cmstat_output = `$cmstat $resultdir/$msaname.cm`;
infernal-1.1.3/rmark/x-nhmmer2cmsearch-136- @lines = split(/\n/, $cmstat_output);
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-151- # run nhmmer first
infernal-1.1.3/rmark/x-nhmmer2cmsearch:152: $status = system("$nhmmer $nhmmer_searchopts $fam_searchopts_H{$msaname} --tblout $resultdir/$msaname.tmp $modeldir/$msaname.hmm $fafile > $resultdir/$msaname.search1");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-153- if ($status != 0) { die "FAILED: $nhmmer $nhmmer_searchopts $fam_searchopts_H{$msaname} --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > $resultdir/$msaname.search1"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-195- if(! -e "$fafile.ssi") {
infernal-1.1.3/rmark/x-nhmmer2cmsearch:196: $status = system("$sfetch --index $fafile");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-197- if ($status != 0) { die "FAILED: $sfetch --index $fafile"; }
infernal-1.1.3/rmark/x-nhmmer2cmsearch-198- }
infernal-1.1.3/rmark/x-nhmmer2cmsearch:199: $status = system("$sfetch -Cf $fafile $sfetch_in > $filtered_db");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-200- if ($status != 0) { die "FAILED: $sfetch -Cf $fafile $sfetch_in > $filtered_db"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-204- $command = "mpirun -np $mpi_nprocs $cmsearch --toponly $cmsearch_searchopts --tabfile $resultdir/$msaname.tmp $modeldir/$msaname.cm $filtered_db > $resultdir/$msaname.search";
infernal-1.1.3/rmark/x-nhmmer2cmsearch:205: $status = system("$command");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-206- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-209- $command = "$cmsearch --toponly $cmsearch_searchopts --tabfile $resultdir/$msaname.tmp $modeldir/$msaname.cm $filtered_db > $resultdir/$msaname.search";
infernal-1.1.3/rmark/x-nhmmer2cmsearch:210: $status = system("$command");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-211- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-250- if($at_least_one_hit_survived_the_filter) {
infernal-1.1.3/rmark/x-nhmmer2cmsearch:251: system("grep \"CPU time\" $resultdir/$msaname.search1 > $resultdir/$msaname.time");
infernal-1.1.3/rmark/x-nhmmer2cmsearch:252: system("grep \"CPU time\" $resultdir/$msaname.search >> $resultdir/$msaname.time");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-253- sleep(0.1);
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-267-$command = "sort -g $tmpoutfile > $sorttmpoutfile";
infernal-1.1.3/rmark/x-nhmmer2cmsearch:268:$status = system("$command");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-269-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-nhmmer2cmsearch-271-$command = "perl $idscript $posfile $sorttmpoutfile > $outfile";
infernal-1.1.3/rmark/x-nhmmer2cmsearch:272:$status = system("$command");
infernal-1.1.3/rmark/x-nhmmer2cmsearch-273-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-120-if(! -e "$fafile.ssi") {
infernal-1.1.3/rmark/x-rfamscan:121: $status = system("$sfetch --index $fafile");
infernal-1.1.3/rmark/x-rfamscan-122- if ($status != 0) { die "FAILED: $sfetch --index $fafile"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-127-# greater than the length of the seqs
infernal-1.1.3/rmark/x-rfamscan:128:$output = `$seqstat -a $fafile`;
infernal-1.1.3/rmark/x-rfamscan-129-%falensH = ();
##############################################
infernal-1.1.3/rmark/x-rfamscan-153- if($do_fetch_models) {
infernal-1.1.3/rmark/x-rfamscan:154: $status = system("$cmfetch -o $resultdir/$msaname.cm $master_model $msaname > /dev/null");
infernal-1.1.3/rmark/x-rfamscan-155- if ($status != 0) { die "FAILED: $cmfetch -o $resultdir/$msaname.cm $master_model > /dev/null"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-167- $command = "$afetch $msafile $msaname | $reformat --informat stockholm -o $resultdir/$msaname.sto pfam -";
infernal-1.1.3/rmark/x-rfamscan:168: $status = system("$command");
infernal-1.1.3/rmark/x-rfamscan-169- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-180- $command = "$wublastn $fafile $resultdir/$msaname.query mformat=3 cpus=1 $specsearchopts $fam_searchopts_H{$fam} > $resultdir/$msaname.search1";
infernal-1.1.3/rmark/x-rfamscan:181: $status = system("$command");
infernal-1.1.3/rmark/x-rfamscan-182- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-185- $command = "$wublastn $fafile $resultdir/$msaname.query mformat=3 cpus=1 $senssearchopts $fam_searchopts_H{$fam} >> $resultdir/$msaname.search1";
infernal-1.1.3/rmark/x-rfamscan:186: $status = system("$command");
infernal-1.1.3/rmark/x-rfamscan-187- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-217- $command = "mv $new_sfetch_in $sfetch_in";
infernal-1.1.3/rmark/x-rfamscan:218: $status = system("$command");
infernal-1.1.3/rmark/x-rfamscan-219- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-222- $filtered_db = "$resultdir/$msaname.sub.fa";
infernal-1.1.3/rmark/x-rfamscan:223: $status = system("$sfetch -Cf $fafile $sfetch_in > $filtered_db");
infernal-1.1.3/rmark/x-rfamscan-224- if ($status != 0) { die "FAILED: $sfetch -Cf $fafile $sfetch_in > $filtered_db"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-228- $command = "mpirun -np $mpi_nprocs $cmsearch --noalign --toponly $cmsearchopts --tabfile $resultdir/$msaname.tmp $modeldir/$msaname.cm $filtered_db > $resultdir/$msaname.search";
infernal-1.1.3/rmark/x-rfamscan:229: $status = system("$command");
infernal-1.1.3/rmark/x-rfamscan-230- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-233- $command = "$cmsearch --noalign --toponly $cmsearchopts --tabfile $resultdir/$msaname.tmp $modeldir/$msaname.cm $filtered_db > $resultdir/$msaname.search";
infernal-1.1.3/rmark/x-rfamscan:234: $status = system("$command");
infernal-1.1.3/rmark/x-rfamscan-235- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-293-$command = "sort -g $tmpoutfile > $sorttmpoutfile";
infernal-1.1.3/rmark/x-rfamscan:294:$status = system("$command");
infernal-1.1.3/rmark/x-rfamscan-295-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-rfamscan-297-$command = "perl $idscript $posfile $sorttmpoutfile > $outfile";
infernal-1.1.3/rmark/x-rfamscan:298:$status = system("$command");
infernal-1.1.3/rmark/x-rfamscan-299-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-wublast-88- $command = "$afetch -o $resultdir/$msaname.sto $msafile $msaname > /dev/null";
infernal-1.1.3/rmark/x-wublast:89: $status = system("$command");
infernal-1.1.3/rmark/x-wublast-90- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-wublast-93- $command = "$reformat fasta $resultdir/$msaname.sto > $resultdir/$msaname.query";
infernal-1.1.3/rmark/x-wublast:94: $status = system("$command");
infernal-1.1.3/rmark/x-wublast-95- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-wublast-99- $command = "$blastn $fafile $resultdir/$msaname.query cpus=1 $searchopts $fam_searchopts_H{$fam} topcomboN=100000 mformat=3 > $resultdir/$msaname.tmp";
infernal-1.1.3/rmark/x-wublast:100: $status = system("$command");
infernal-1.1.3/rmark/x-wublast-101- if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-wublast-178-$command = "sort -g $tmpoutfile > $sorttmpoutfile";
infernal-1.1.3/rmark/x-wublast:179:$status = system("$command");
infernal-1.1.3/rmark/x-wublast-180-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/x-wublast-182-$command = "perl $idscript $posfile $sorttmpoutfile > $outfile";
infernal-1.1.3/rmark/x-wublast:183:$status = system("$command");
infernal-1.1.3/rmark/x-wublast-184-if ($status != 0) { die "FAILED: $command"; }
##############################################
infernal-1.1.3/rmark/rmark-master.pl-165- if ($do_force && (-e $resultdir)) {
infernal-1.1.3/rmark/rmark-master.pl:166: system("rm -rf $resultdir");
infernal-1.1.3/rmark/rmark-master.pl-167- }
##############################################
infernal-1.1.3/rmark/rmark-master.pl-170- }
infernal-1.1.3/rmark/rmark-master.pl:171: system("mkdir $resultdir");
infernal-1.1.3/rmark/rmark-master.pl-172-}
##############################################
infernal-1.1.3/rmark/rmark-master.pl-267- #printf("qsub -V -cwd -b y -N $resultdir.$i -j y -o $resultdir/tbl$i.sge -R y -l excl=true '$rmark_script $posonly_opt $debug_opt $build_opt $c_opt -M $mpi_nprocs $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.out'\n");
infernal-1.1.3/rmark/rmark-master.pl:268: system("qsub -V -cwd -b y -N $resultdir.$i -j y -o $resultdir/tbl$i.sge -R y -l excl=true '$rmark_script $posonly_opt $poswindowonly_opt $debug_opt $build_opt $c_opt $x_opt_to_pass $z_opt_to_pass $h_opt_to_pass -M $mpi_nprocs $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.out'");
infernal-1.1.3/rmark/rmark-master.pl-269- }
##############################################
infernal-1.1.3/rmark/rmark-master.pl-271- #print("qsub -V -cwd -b y -N $resultdir.$i -j y -o $resultdir/tbl$i.sge -R y -l excl=true '$rmark_script $posonly_opt $poswindowonly_opt $debug_opt $build_opt $c_opt $x_opt_to_pass $z_opt_to_pass $h_opt_to_pass $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.out'");
infernal-1.1.3/rmark/rmark-master.pl:272: system("qsub -V -cwd -b y -N $resultdir.$i -j y -o $resultdir/tbl$i.sge -R y -l excl=true '$rmark_script $posonly_opt $poswindowonly_opt $debug_opt $build_opt $c_opt $x_opt_to_pass $z_opt_to_pass $h_opt_to_pass $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.out'");
infernal-1.1.3/rmark/rmark-master.pl-273- }
##############################################
infernal-1.1.3/rmark/rmark-master.pl-285- #printf("qsub -V -cwd -b y -N $resultdir.$i.$j.B -j y -o $resultdir/tbl$i.$j.B.sge -l excl=true '$rmark_script -K $j.B -B $posonly_opt $debug_opt $build_opt $c_opt -M $mpi_nprocs $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.$j.B.out'\n");
infernal-1.1.3/rmark/rmark-master.pl:286: system("qsub -V -cwd -b y -N $resultdir.$i.$j.T -j y -o $resultdir/tbl$i.$j.T.sge -l excl=true '$rmark_script -K $j.T -T $posonly_opt $poswindowonly_opt $debug_opt $build_opt $c_opt $x_opt_to_pass $z_opt_to_pass $h_opt_to_pass -M $mpi_nprocs $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl$i $msafile $posfile $fafile $resultdir/tbl$i.$j.T.out'");
infernal-1.1.3/rmark/rmark-master.pl:287: system("qsub -V -cwd -b y -N $resultdir.$i.$j.B -j y -o $resultdir/tbl$i.$j.B.sge -l excl=true '$rmark_script -K $j.B -B $posonly_opt $poswindowonly_opt $debug_opt $build_opt $c_opt $x_opt_to_pass $z_opt_to_pass $h_opt_to_pass -M $mpi_nprocs $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl$i $msafile $posfile $fafile $resultdir/tbl$i.$j.B.out'");
infernal-1.1.3/rmark/rmark-master.pl-288- }
##############################################
infernal-1.1.3/rmark/rmark-master.pl-292- #printf("qsub -V -cwd -b y -N $resultdir.$i.$j.B -j y -o $resultdir/tbl$i.$j.B.sge '$rmark_script -K $j.B -B $posonly_opt $debug_opt $build_opt $c_opt $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.$j.B.out'\n");
infernal-1.1.3/rmark/rmark-master.pl:293: system("qsub -V -cwd -b y -N $resultdir.$i.$j.T -j y -o $resultdir/tbl$i.$j.T.sge -R y -l excl=true '$rmark_script -K $j.T -T $posonly_opt $poswindowonly_opt $debug_opt $build_opt $c_opt $x_opt_to_pass $z_opt_to_pass $h_opt_to_pass $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.$j.T.out'");
infernal-1.1.3/rmark/rmark-master.pl:294: system("qsub -V -cwd -b y -N $resultdir.$i.$j.B -j y -o $resultdir/tbl$i.$j.B.sge -R y -l excl=true '$rmark_script -K $j.B -B $posonly_opt $poswindowonly_opt $debug_opt $build_opt $c_opt $x_opt_to_pass $z_opt_to_pass $h_opt_to_pass $execdir $scriptdir $modeldir $resultdir $optsfile $resultdir/tbl.$i $msafile $posfile $fafile $resultdir/tbl$i.$j.B.out'");
infernal-1.1.3/rmark/rmark-master.pl-295- }
##############################################
infernal-1.1.3/src/impl_sse/cmsearch_dual-50-# Read cmsearch results
infernal-1.1.3/src/impl_sse/cmsearch_dual:51:@cms_hit_lines = `grep -v "^#" $tbl_out`;
infernal-1.1.3/src/impl_sse/cmsearch_dual-52-$num_hits = 0;
##############################################
infernal-1.1.3/src/impl_sse/cmsearch_dual-85-# Read sse_cmsearch results
infernal-1.1.3/src/impl_sse/cmsearch_dual:86:@sse_hit_lines = `cat $glbf`;
infernal-1.1.3/src/impl_sse/cmsearch_dual-87-foreach $line (@sse_hit_lines) {
##############################################
infernal-1.1.3/src/impl_sse/cmsearch_dual-110-$fa2 =~ s/2\.log/hits/;
infernal-1.1.3/src/impl_sse/cmsearch_dual:111:if (-e $fa2) { system("rm $fa2"); }
infernal-1.1.3/src/impl_sse/cmsearch_dual-112-unless (-e "$fafile\.ssi") {
infernal-1.1.3/src/impl_sse/cmsearch_dual:113: system("$sfetch --index $fafile");
infernal-1.1.3/src/impl_sse/cmsearch_dual-114-}
##############################################
infernal-1.1.3/src/Makefile.in-208-${UTESTS}: libinfernal.a ${HDRS} config.h
infernal-1.1.3/src/Makefile.in:209: @BASENAME=`echo $@ | sed -e 's/_utest//' | sed -e 's/^cm_//'` ;\
infernal-1.1.3/src/Makefile.in:210: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/src/Makefile.in-211- DFLAG=CM_$${DFLAG}_TESTDRIVE ;\
##############################################
infernal-1.1.3/src/Makefile.in-223-${BENCHMARKS}: libinfernal.a ${HDRS} config.h
infernal-1.1.3/src/Makefile.in:224: @BASENAME=`echo $@ | sed -e 's/_benchmark//' | sed -e 's/^cm_//'` ;\
infernal-1.1.3/src/Makefile.in:225: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/src/Makefile.in-226- DFLAG=CM_$${DFLAG}_BENCHMARK ;\
##############################################
infernal-1.1.3/testsuite/bug-i1.pl-54-if ($ok) {
infernal-1.1.3/testsuite/bug-i1.pl:55: system("$cmbuild i1.tmp.1 i1.1 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i1.pl-56- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i1.pl-58-if ($ok) {
infernal-1.1.3/testsuite/bug-i1.pl:59: system("$cmalign -o i1.tmp.2 i1.tmp.1 i1.2 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i1.pl-60- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i1.pl-62-if ($ok) {
infernal-1.1.3/testsuite/bug-i1.pl:63: system("$cmbuild -F i1.tmp.1 i1.tmp.2 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i1.pl-64- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i11.pl-44-if ($ok) {
infernal-1.1.3/testsuite/bug-i11.pl:45: system("$cmbuild -F --hand i11.cm i11.1 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i11.pl-46- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i11.pl-48-if ($ok) {
infernal-1.1.3/testsuite/bug-i11.pl:49: system("$cmalign --notrunc i11.cm i11.2 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i11.pl-50- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i12.pl-49-if ($ok) {
infernal-1.1.3/testsuite/bug-i12.pl:50: system("$cmbuild -F --hand i12.cm i12.1 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i12.pl-51- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i12.pl-53-if ($ok) {
infernal-1.1.3/testsuite/bug-i12.pl:54: system("$cmalign --notrunc i12.cm i12.2 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i12.pl-55- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i13.pl-68-if ($ok) {
infernal-1.1.3/testsuite/bug-i13.pl:69: system("$cmbuild -F --hand i13.cm i13.1 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i13.pl-70- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i13.pl-72-if ($ok) {
infernal-1.1.3/testsuite/bug-i13.pl:73: system("$cmalign -g --sub --notrunc i13.cm i13.2 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i13.pl-74- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i14.pl-43-if ($ok) {
infernal-1.1.3/testsuite/bug-i14.pl:44: system("$cmbuild --wnone --enone -F i14.cm $alifile > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i14.pl-45- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i14.pl-47-if ($ok) {
infernal-1.1.3/testsuite/bug-i14.pl:48: system("$cmalign --notrunc i14.cm $seqfile > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i14.pl-49- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i15.pl-35-if ($ok) {
infernal-1.1.3/testsuite/bug-i15.pl:36: system("$cmbuild --hand --wgsc --enone -F i15.cm $alifile > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i15.pl-37- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i15.pl-39-if ($ok) {
infernal-1.1.3/testsuite/bug-i15.pl:40: system("$cmalign -g --sub --notrunc i15.cm $seqfile > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i15.pl-41- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i28.pl-38-if ($ok) {
infernal-1.1.3/testsuite/bug-i28.pl:39: system("$cmsearch $cmfile $seqfile > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i28.pl-40- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i29.pl-23-if ($ok) {
infernal-1.1.3/testsuite/bug-i29.pl:24: system("$cmconvert $cmfile > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i29.pl-25- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i30.pl-48-if ($ok) {
infernal-1.1.3/testsuite/bug-i30.pl:49: system("$cmbuild -F --hand i30.cm i30.1 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i30.pl-50- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i30.pl-53- # need to use --hmmonly so we don't have to calibrate model
infernal-1.1.3/testsuite/bug-i30.pl:54: system("$cmsearch --hmmonly i30.cm i30.2 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i30.pl-55- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i31.pl-23-if ($ok) {
infernal-1.1.3/testsuite/bug-i31.pl:24: system("$cmsearch --tblout i31.tbl -Z 5000 $cmfile $seqfile > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i31.pl-25- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i32.pl-34-if ($ok) {
infernal-1.1.3/testsuite/bug-i32.pl:35: system("$cmbuild -F --hand --refine i32.2 i32.cm i32.1 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i32.pl-36- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i33.pl-31-if ($ok) {
infernal-1.1.3/testsuite/bug-i33.pl:32: system("$cmsearch -A i33.2 $cmfile i33.1 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i33.pl-33- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i33.pl-37-if ($ok) {
infernal-1.1.3/testsuite/bug-i33.pl:38: system("$cmbuild -F i33.3 i33.2 > /dev/null 2> /dev/null");
infernal-1.1.3/testsuite/bug-i33.pl-39- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i34.pl-40-if ($ok) {
infernal-1.1.3/testsuite/bug-i34.pl:41: $output = `$cmalign $cmfile i34.1`;
infernal-1.1.3/testsuite/bug-i34.pl-42- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i36.pl-39-if ($ok) {
infernal-1.1.3/testsuite/bug-i36.pl:40: $output = `$cmsearch --tau 1E-5 --toponly --cyk --cpu 0 --notrunc --rfam $cmfile i36.1`;
infernal-1.1.3/testsuite/bug-i36.pl-41- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i36.pl-46-
infernal-1.1.3/testsuite/bug-i36.pl:47: $output = `$cmsearch --cpu 0 $cmfile i36.2`;
infernal-1.1.3/testsuite/bug-i36.pl-48- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i37.pl-28-if ($ok) {
infernal-1.1.3/testsuite/bug-i37.pl:29: $output = `$cmsearch --cpu 0 --cyk --notrunc -g --toponly $cmfile i37.1`;
infernal-1.1.3/testsuite/bug-i37.pl-30- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i38.pl-35-if ($ok) {
infernal-1.1.3/testsuite/bug-i38.pl:36: $output = `$cmbuild -F --noss i38.cm i38.1`;
infernal-1.1.3/testsuite/bug-i38.pl-37- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i38.pl-45-if ($ok) {
infernal-1.1.3/testsuite/bug-i38.pl:46: $output = `$cmalign --noss --mapali i38.1 -o i38.3 i38.cm i38.2`;
infernal-1.1.3/testsuite/bug-i38.pl-47- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i39.pl-28-if ($ok) {
infernal-1.1.3/testsuite/bug-i39.pl:29: $output = `$cmbuild --noss -O i39.2 -F i39.cm i39.1`;
infernal-1.1.3/testsuite/bug-i39.pl-30- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i39.pl-38-if ($ok) {
infernal-1.1.3/testsuite/bug-i39.pl:39: $output = `$cmbuild --noss -F i39.2.cm i39.2`;
infernal-1.1.3/testsuite/bug-i39.pl-40- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i43.pl-23-if ($ok) {
infernal-1.1.3/testsuite/bug-i43.pl:24: $output = `$cmsearch --cpu 0 --mxsize 512.0 --toponly $cmfile $seqfile`;
infernal-1.1.3/testsuite/bug-i43.pl-25- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i44.pl-39-if ($ok) {
infernal-1.1.3/testsuite/bug-i44.pl:40: $output = `$cmbuild -F i44.cm i44.1`;
infernal-1.1.3/testsuite/bug-i44.pl-41- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i44.pl-49-if ($ok) {
infernal-1.1.3/testsuite/bug-i44.pl:50: $output = `$cmalign --mapali i44.1 --mapstr -o i44.3 i44.cm i44.2`;
infernal-1.1.3/testsuite/bug-i44.pl-51- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-20-
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl:21:system("$eslreformat -u --rename foo fasta $testsuitedir/Vault.sto > $tmppfx.fa");
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-22-if ($? != 0) { print "FAIL: esl-reformat failed unexpectedly\n"; exit 1; }
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-23-
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl:24:system("$cmalign -o $tmppfx.sto --mapali $testsuitedir/Vault.sto $testsuitedir/Vault.c.cm $tmppfx.fa");
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-25-if ($? != 0) { print "FAIL: cmalign failed unexpectedly\n"; exit 1; }
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-26-
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl:27:system("$eslreformat -u fasta $tmppfx.sto > $tmppfx.2.fa");
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-28-if ($? != 0) { print "FAIL: esl-reformat failed unexpectedly\n"; exit 1; }
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-29-
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl:30:system("$eslreformat -u fasta $testsuitedir/Vault.sto > $tmppfx.3.fa");
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-31-if ($? != 0) { print "FAIL: esl-reformat failed unexpectedly\n"; exit 1; }
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-32-
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl:33:system("cat $tmppfx.fa >> $tmppfx.3.fa");
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-34-if ($? != 0) { print "FAIL: cat failed unexpectedly\n"; exit 1; }
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-35-
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl:36:system("diff $tmppfx.2.fa $tmppfx.3.fa");
infernal-1.1.3/testsuite/itest1-cmalign-mapali.pl-37-if ($? != 0) { print "FAIL: --mapali doesn't produce expected sequences\n"; exit 1; }
##############################################
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-30- # homologous sequence fragments: generated from local profile
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:31: `$builddir/src/cmemit -o $tmppfx.fa -N $n $profile`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-32- if ($? != 0) { die "FAIL: cmemit"; }
##############################################
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-37- # random sequences
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:38: `$builddir/easel/miniapps/esl-shuffle --rna -G -N $n -L 50 -o $tmppfx.fa`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-39- if ($? != 0) { die "FAIL: esl-shuffle"; }
##############################################
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-59-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:60: `$builddir/src/cmalign -o $tmppfx.sto $cmfile $fafile > /dev/null 2>&1`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-61- if ($? != 0) { die "FAIL: cmalign failed"; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-62-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:63: `$builddir/easel/miniapps/esl-reformat -r -u fasta $tmppfx.sto > $tmppfx.fa1 2>/dev/null`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-64- if ($? != 0) { die "FAIL: first esl-reformat failed"; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-65-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:66: `$builddir/easel/miniapps/esl-reformat -r -u fasta $fafile > $tmppfx.fa2 2>/dev/null`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-67- if ($? != 0) { die "FAIL: second esl-reformat failed"; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-68-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:69: `diff -b $tmppfx.fa1 $tmppfx.fa2 > /dev/null 2>&1`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-70- if ($? != 0) { die "FAIL: cmalign alignment corrupted\n"; }
##############################################
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-80- # need report = include threshold to have same hits in .sto, .tbl
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:81: `$builddir/src/cmsearch -E 1 --incE 1 --tblout $tmppfx.tbl -A $tmppfx.sto $cmfile $fafile > /dev/null 2>&1`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-82- if ($? != 0) { die "FAIL: cmsearch failed"; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-83-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:84: $nlines = `cat $tmppfx.tbl | grep -v "^#" | wc -l`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-85- if ($nlines == 0) { return 0; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-86-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:87: `$builddir/easel/miniapps/esl-sfetch --index $fafile > /dev/null 2>&1`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-88- if ($? != 0) { die "FAIL: esl-sfetch --index failed"; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-89-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:90: `cat $tmppfx.tbl | grep -v "^#" | awk '{print \$1, \$8, \$9, \$1}' > $tmppfx.gdf`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-91- if ($? != 0) { die "FAIL: gdf table"; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-92-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:93: `$builddir/easel/miniapps/esl-sfetch -Cf $fafile $tmppfx.gdf > $tmppfx.fa3`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-94- if ($? != 0) { die "FAIL: esl-sfetch failed"; }
##############################################
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-96- # Grep out name/desc lines because they'll differ: esl-sfetch adds descline.
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:97: `$builddir/easel/miniapps/esl-reformat -r -u fasta $tmppfx.sto | grep -v "^>" > $tmppfx.fa1 2>/dev/null`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-98- if ($? != 0) { die "FAIL: first esl-reformat failed"; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-99-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:100: `$builddir/easel/miniapps/esl-reformat -r -u fasta $tmppfx.fa3 | grep -v "^>" > $tmppfx.fa2 2>/dev/null`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-101- if ($? != 0) { die "FAIL: second esl-reformat failed"; }
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-102-
infernal-1.1.3/testsuite/itest3-msa-integrity.pl:103: `diff -b $tmppfx.fa1 $tmppfx.fa2 > /dev/null 2>&1`;
infernal-1.1.3/testsuite/itest3-msa-integrity.pl-104- if ($? != 0) { die "FAIL: cmsearch alignment corrupted"; }
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-54-# Create the test CM file
infernal-1.1.3/testsuite/itest9-overlaps.pl:55:`cat $srcdir/testsuite/$model1.c.cm $srcdir/testsuite/$model2.c.cm $srcdir/testsuite/$model3.c.cm > $tmppfx.cm`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest9-overlaps.pl-56-
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-74-
infernal-1.1.3/testsuite/itest9-overlaps.pl:75:`$builddir/src/cmpress $tmppfx.cm`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest9-overlaps.pl-76-
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-78-# trial 1, --fmt 2 only option, should mark up all overlaps
infernal-1.1.3/testsuite/itest9-overlaps.pl:79:$output = `$builddir/src/cmscan --fmt 2 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest9-overlaps.pl-80-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-94-# trial 2, --fmt 2 with --clanin, but no --oskip or --oclan, so should be same result as trial 1
infernal-1.1.3/testsuite/itest9-overlaps.pl:95:$output = `$builddir/src/cmscan --fmt 2 --clanin $tmppfx.clanin1 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest9-overlaps.pl-96-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-110-# trial 3, --fmt 2 with --oskip, so only top scoring hits should print
infernal-1.1.3/testsuite/itest9-overlaps.pl:111:$output = `$builddir/src/cmscan --fmt 2 --oskip -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest9-overlaps.pl-112-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-123-# trial 4, --fmt 2 with --clanin and --oclan using clan file with only tRNA, so no within clan overlaps
infernal-1.1.3/testsuite/itest9-overlaps.pl:124:$output = `$builddir/src/cmscan --fmt 2 --clanin $tmppfx.clanin2 --oclan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest9-overlaps.pl-125-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-140-# be same results as trial 4
infernal-1.1.3/testsuite/itest9-overlaps.pl:141:$output = `$builddir/src/cmscan --fmt 2 --clanin $tmppfx.clanin2 --oclan --oskip -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest9-overlaps.pl-142-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-156-# trial 6, bogus name in clan input file, cmscan should fail
infernal-1.1.3/testsuite/itest9-overlaps.pl:157:$output = `$builddir/src/cmscan --fmt 2 --clanin $tmppfx.clanin3 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest9-overlaps.pl-158-if ($? == 0) { die "FAIL: cmscan did not fail when it should have\n"; }
##############################################
infernal-1.1.3/testsuite/itest9-overlaps.pl-172- print "$cmd\n" if $verbose;
infernal-1.1.3/testsuite/itest9-overlaps.pl:173: return `$cmd`;
infernal-1.1.3/testsuite/itest9-overlaps.pl-174-}
##############################################
infernal-1.1.3/testsuite/bug-i45.pl-31-if ($ok) {
infernal-1.1.3/testsuite/bug-i45.pl:32: $output = `$cmsearch --cpu 0 --onepass --5trunc --rfam --notextw $cmfile $seqfileA`;
infernal-1.1.3/testsuite/bug-i45.pl-33- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i45.pl-51-if ($ok) {
infernal-1.1.3/testsuite/bug-i45.pl:52: $output = `$cmsearch --cpu 0 --onepass --3trunc --rfam --notextw $cmfile $seqfileB`;
infernal-1.1.3/testsuite/bug-i45.pl-53- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i47.pl-37-if ($ok) {
infernal-1.1.3/testsuite/bug-i47.pl:38: $output = `$cmbuild -F i47.1.cm i47.1`;
infernal-1.1.3/testsuite/bug-i47.pl-39- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i47.pl-51-if ($ok) {
infernal-1.1.3/testsuite/bug-i47.pl:52: $output = `$cmbuild -F --p7ml i47.2.cm i47.1`;
infernal-1.1.3/testsuite/bug-i47.pl-53- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/bug-i49.pl-16-if ($ok) {
infernal-1.1.3/testsuite/bug-i49.pl:17: $output = `$cmsearch --cpu 0 --toponly --tblout i49.tbl $cmfile $seqfile > /dev/null`;
infernal-1.1.3/testsuite/bug-i49.pl-18- if ($? != 0) { $ok = 0; }
##############################################
infernal-1.1.3/testsuite/itest2-duplicate-names.pl-70-# cmpress will fail; it uses an SSI index, which does care about dup names.
infernal-1.1.3/testsuite/itest2-duplicate-names.pl:71:@output = `$builddir/src/cmbuild -F $tmppfx.cm $tmppfx.sto 2>&1`; if ($? != 0) { die "FAIL: cmbuild failed\n"; }
infernal-1.1.3/testsuite/itest2-duplicate-names.pl:72:@output = `$builddir/src/cmcalibrate -L 0.05 $tmppfx.cm 2>&1`; if ($? != 0) { die "FAIL: cmcalibrate failed\n"; }
infernal-1.1.3/testsuite/itest2-duplicate-names.pl:73:@output = `$builddir/src/cmpress -F $tmppfx.cm 2>&1`; if ($? == 0) { die "FAIL: cmpress should have detected dup names and failed, but it didn't\n"; }
infernal-1.1.3/testsuite/itest2-duplicate-names.pl-74-
infernal-1.1.3/testsuite/itest2-duplicate-names.pl-75-# cmsearch should show four results
infernal-1.1.3/testsuite/itest2-duplicate-names.pl:76:$output = `$builddir/src/cmsearch --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest2-duplicate-names.pl-77-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-59-
infernal-1.1.3/testsuite/itest4-stdin.pl:60:`cat $srcdir/testsuite/$model1.c.cm $srcdir/testsuite/$model2.c.cm $srcdir/testsuite/$model3.c.cm > $tmppfx.cm`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-61-if(-e "$tmppfx.cm.i1m") { unlink "$tmppfx.cm.i1m"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-65-if(-e "$tmppfx.cm.ssi") { unlink "$tmppfx.cm.ssi"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:66:`$builddir/src/cmpress $tmppfx.cm`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-67-
infernal-1.1.3/testsuite/itest4-stdin.pl:68:`cat $srcdir/testsuite/$model1.sto $srcdir/testsuite/$model2.sto $srcdir/testsuite/$model3.sto > $tmppfx.sto`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-69-
infernal-1.1.3/testsuite/itest4-stdin.pl:70:`$builddir/src/cmemit -c $srcdir/testsuite/$model1.c.cm > $tmppfx.fa1`; if ($?) { die "FAIL: cmemit -c\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:71:`cat $tmppfx.fa1 > $tmppfx.fa2`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:72:`$builddir/src/cmemit -c $srcdir/testsuite/$model2.c.cm >> $tmppfx.fa2`; if ($?) { die "FAIL: cmemit -c\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:73:`$builddir/src/cmemit -c $srcdir/testsuite/$model3.c.cm >> $tmppfx.fa2`; if ($?) { die "FAIL: cmemit -c\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-74-
infernal-1.1.3/testsuite/itest4-stdin.pl:75:`$builddir/src/cmemit -N10 $srcdir/testsuite/$model1.c.cm > $tmppfx.fa10`; if ($?) { die "FAIL: cmemit\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-76-
infernal-1.1.3/testsuite/itest4-stdin.pl:77:`$builddir/src/cmemit -N10 $srcdir/testsuite/$model1.c.cm > $tmppfx.db`; if ($?) { die "FAIL: cmemit\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:78:`$builddir/src/cmemit -N10 $srcdir/testsuite/$model2.c.cm >> $tmppfx.db`; if ($?) { die "FAIL: cmemit\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:79:`$builddir/src/cmemit -N10 $srcdir/testsuite/$model3.c.cm >> $tmppfx.db`; if ($?) { die "FAIL: cmemit\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:80:`$builddir/easel/miniapps/esl-shuffle -G -N100 -L 80 --rna >> $tmppfx.db`; if ($?) { die "FAIL: esl-shuffle\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-81-
infernal-1.1.3/testsuite/itest4-stdin.pl:82:`echo $model1 > $tmppfx.key`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:83:`echo $model2 >> $tmppfx.key`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-84-
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-94-
infernal-1.1.3/testsuite/itest4-stdin.pl:95:`$prog $arg1 $arg2 | grep -v "^#DEBUG" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:96:`cat $arg1 | $prog - $arg2 | grep -v "^#DEBUG" > $tmppfx.out2`; if ($?) { die "FAIL: $tag - $tag2\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:97:`cat $arg2 | $prog $arg1 - | grep -v "^#DEBUG" > $tmppfx.out3`; if ($?) { die "FAIL: $tag $tag1 -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-98-
infernal-1.1.3/testsuite/itest4-stdin.pl:99:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:100:`diff -b $tmppfx.out1 $tmppfx.out3 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag2 comes through stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-101-
infernal-1.1.3/testsuite/itest4-stdin.pl:102:$output = `cat $arg1 $arg2 | $prog - - 2>&1`;
infernal-1.1.3/testsuite/itest4-stdin.pl-103-if (!$?) { die "FAIL: $tag should fail on double - -\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-115-
infernal-1.1.3/testsuite/itest4-stdin.pl:116:`$prog -F $tmppfx.cm.out1 $arg1 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag <cmfile> $tag1 \n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:117:`cat $arg1 | $prog -F --informat stockholm $tmppfx.cm.out2 - | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag <cmfile> -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:118:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-119-
infernal-1.1.3/testsuite/itest4-stdin.pl:120:$output = `$prog - $arg1`;
infernal-1.1.3/testsuite/itest4-stdin.pl-121-if (!$?) { die "FAIL: $tag should reject - for <cmfile_out>\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-131-# need to remove COM lines, they will differ due to different cmdline usage, differs from hmmer version
infernal-1.1.3/testsuite/itest4-stdin.pl:132:`$prog $arg1 | grep -v "^COM" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:133:`cat $arg1 | $prog - | grep -v "^COM" > $tmppfx.out2`; if ($?) { die "FAIL: $tag -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-134-
infernal-1.1.3/testsuite/itest4-stdin.pl:135:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`;
infernal-1.1.3/testsuite/itest4-stdin.pl-136-if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-146-
infernal-1.1.3/testsuite/itest4-stdin.pl:147:`$prog --seed 42 $arg1 > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:148:`cat $arg1 | $prog --seed 42 - > $tmppfx.out2`; if ($?) { die "FAIL: $tag -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-149-
infernal-1.1.3/testsuite/itest4-stdin.pl:150:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`;
infernal-1.1.3/testsuite/itest4-stdin.pl-151-if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-168-
infernal-1.1.3/testsuite/itest4-stdin.pl:169:`$prog $arg1 snR75 > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:170:`cat $arg1 | $prog - snR75 > $tmppfx.out2`; if ($?) { die "FAIL: $tag -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:171:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-172-
infernal-1.1.3/testsuite/itest4-stdin.pl:173:`$prog -f $arg1 $arg2 > $tmppfx.out1`; if ($?) { die "FAIL: $tag -f $tag1 $tag2\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:174:`cat $arg1 | $prog -f - $arg2 > $tmppfx.out2`; if ($?) { die "FAIL: $tag -f - $tag2\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:175:`cat $arg2 | $prog -f $arg1 - > $tmppfx.out3`; if ($?) { die "FAIL: $tag -f $tag1 -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:176:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag -f results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:177:`diff -b $tmppfx.out1 $tmppfx.out3 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag -f results differ if $tag2 comes through stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-178-
infernal-1.1.3/testsuite/itest4-stdin.pl:179:$output = `cat $arg1 $arg2 | $prog -f - - 2>&1`;
infernal-1.1.3/testsuite/itest4-stdin.pl-180-if (! $?) { die "FAIL: $tag should have failed on double - -\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-187-if(-e "$arg1.ssi") { unlink "$arg1.ssi"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:188:`$prog --index $arg1 > $tmppfx.out1`; if ($?) { die "FAIL: $tag --index $tag1\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:189:$output = `cat $arg1 | $prog --index - 2>&1`; if (! $?) { die "FAIL: $tag should reject - for <cmfile> when using --index\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-190-if ($output !~ /^Can't use - with --index/) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-200-
infernal-1.1.3/testsuite/itest4-stdin.pl:201:$output = `cat $arg1 | $prog - 2>&1`; if (! $?) { die "FAIL: $tag should reject - for <cmfile>\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-202-if ($output !~ /^\nError: Can't use - for <cmfile>/) { die "FAIL: $tag didn't give expected error message.\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-214-# need to repress $tmppfx.cm, we deleted pressed files above
infernal-1.1.3/testsuite/itest4-stdin.pl:215:`$builddir/src/cmpress $arg1`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:216:`$prog $arg1 $arg2 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:217:`cat $arg2 | $prog $arg1 - | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag $tag1 -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-218-
infernal-1.1.3/testsuite/itest4-stdin.pl:219:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`;
infernal-1.1.3/testsuite/itest4-stdin.pl-220-if ($?) { die "FAIL: $tag results differ if $arg2 comes from stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-221-
infernal-1.1.3/testsuite/itest4-stdin.pl:222:$output = `cat $arg1 | $prog - $arg2 2>&1`;
infernal-1.1.3/testsuite/itest4-stdin.pl-223-if (! $?) { die "FAIL: $tag should reject - for $tag1\n"; }
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-239-
infernal-1.1.3/testsuite/itest4-stdin.pl:240:`$prog $arg1 $arg2 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:241:`cat $arg1 | $prog - $arg2 | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag - $tag2\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-242-
infernal-1.1.3/testsuite/itest4-stdin.pl:243:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $prog results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-244-
infernal-1.1.3/testsuite/itest4-stdin.pl:245:$output = `cat $arg2 | $prog $arg1 - 2>&1`; if (! $?) { die "FAIL: $prog should fail on stdin $tag2.\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:246:$output = `cat $arg1 $arg2 | $prog - - 2>&1`; if (! $?) { die "FAIL: $prog should have failed on double - -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-247-
##############################################
infernal-1.1.3/testsuite/itest4-stdin.pl-255-
infernal-1.1.3/testsuite/itest4-stdin.pl:256:`$prog $arg1 > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl:257:`cat $arg1 | $prog - > $tmppfx.out2`; if ($?) { die "FAIL: $tag -\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-258-
infernal-1.1.3/testsuite/itest4-stdin.pl:259:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/testsuite/itest4-stdin.pl-260-
##############################################
infernal-1.1.3/testsuite/itest5-pipeline.pl-48-# Create the test CM files
infernal-1.1.3/testsuite/itest5-pipeline.pl:49:`cat $srcdir/testsuite/$model1.c.cm > $tmppfx.cm`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest5-pipeline.pl:50:`cat $srcdir/testsuite/$model2.c.cm $srcdir/testsuite/$model1.c.cm > $tmppfx.cm2`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest5-pipeline.pl-51-
##############################################
infernal-1.1.3/testsuite/itest5-pipeline.pl-60-# cmsearch, single CM file
infernal-1.1.3/testsuite/itest5-pipeline.pl:61:$output = `$builddir/src/cmsearch -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest5-pipeline.pl-62-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest5-pipeline.pl-73-# cmsearch, multi-CM file
infernal-1.1.3/testsuite/itest5-pipeline.pl:74:$output = `$builddir/src/cmsearch -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest5-pipeline.pl-75-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest5-pipeline.pl-96-if(-e "$tmppfx.cm2.ssi") { unlink "$tmppfx.cm2.ssi"; }
infernal-1.1.3/testsuite/itest5-pipeline.pl:97:`$builddir/src/cmpress $tmppfx.cm`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest5-pipeline.pl:98:`$builddir/src/cmpress $tmppfx.cm2`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest5-pipeline.pl-99-
infernal-1.1.3/testsuite/itest5-pipeline.pl-100-# cmscan, single CM file
infernal-1.1.3/testsuite/itest5-pipeline.pl:101:$output = `$builddir/src/cmscan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest5-pipeline.pl-102-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest5-pipeline.pl-113-# cmscan, multi-CM file
infernal-1.1.3/testsuite/itest5-pipeline.pl:114:$output = `$builddir/src/cmscan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest5-pipeline.pl-115-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest5-pipeline.pl-136- print "$cmd\n" if $verbose;
infernal-1.1.3/testsuite/itest5-pipeline.pl:137: return `$cmd`;
infernal-1.1.3/testsuite/itest5-pipeline.pl-138-}
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-91-# Create the test CM files
infernal-1.1.3/testsuite/itest6-sensitivity.pl:92:`cat $srcdir/testsuite/$model1.c.cm > $tmppfx.cm1`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl:93:`cat $srcdir/testsuite/$model2.c.cm > $tmppfx.cm2`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl:94:`cat $srcdir/testsuite/$model3.c.cm > $tmppfx.cm3`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl-95-
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-103-######################
infernal-1.1.3/testsuite/itest6-sensitivity.pl:104:`cat $srcdir/testsuite/mito-ascaris.fa > $tmppfx.fa`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl-105-
infernal-1.1.3/testsuite/itest6-sensitivity.pl-106-# cmsearch
infernal-1.1.3/testsuite/itest6-sensitivity.pl:107:$output = `$builddir/src/cmsearch -E 1E-3 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest6-sensitivity.pl-108-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-121-if(-e "$tmppfx.cm1.ssi") { unlink "$tmppfx.cm1.ssi"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl:122:`$builddir/src/cmpress $tmppfx.cm1`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl:123:$output = `$builddir/src/cmscan -E 1E-3 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest6-sensitivity.pl-124-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-140-######################
infernal-1.1.3/testsuite/itest6-sensitivity.pl:141:`cat $srcdir/testsuite/ffs-frag.fa > $tmppfx.fa`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl:142:`cat $srcdir/testsuite/ffs-ecoli.fa > $tmppfx.fa2`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl-143-
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-145-# larger subseq
infernal-1.1.3/testsuite/itest6-sensitivity.pl:146:$output = `$builddir/src/cmsearch -E 0.01 --nohmm --fbeta 1E-2 --beta 1E-4 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest6-sensitivity.pl-147-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-153-# shorter subseq
infernal-1.1.3/testsuite/itest6-sensitivity.pl:154:$output = `$builddir/src/cmsearch -E 0.01 --nohmm --fbeta 1E-2 --beta 1E-4 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest6-sensitivity.pl-155-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-167-if(-e "$tmppfx.cm2.ssi") { unlink "$tmppfx.cm2.ssi"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl:168:`$builddir/src/cmpress $tmppfx.cm2`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl-169-
infernal-1.1.3/testsuite/itest6-sensitivity.pl-170-# shorter subseq (we don't search longer subseq)
infernal-1.1.3/testsuite/itest6-sensitivity.pl:171:$output = `$builddir/src/cmscan -E 0.01 --nohmm --fbeta 1E-2 --beta 1E-4 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest6-sensitivity.pl-172-
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-185-######################
infernal-1.1.3/testsuite/itest6-sensitivity.pl:186:`cat $srcdir/testsuite/rnaseP-frag.fa > $tmppfx.fa`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl:187:`cat $srcdir/testsuite/rnaseP-bsu.fa > $tmppfx.fa2`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl-188-
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-190-# longer subseq
infernal-1.1.3/testsuite/itest6-sensitivity.pl:191:$output = `$builddir/src/cmsearch -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm3 $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest6-sensitivity.pl-192-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-199-# shorter subseq
infernal-1.1.3/testsuite/itest6-sensitivity.pl:200:$output = `$builddir/src/cmsearch -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm3 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest6-sensitivity.pl-201-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest6-sensitivity.pl-214-if(-e "$tmppfx.cm3.ssi") { unlink "$tmppfx.cm3.ssi"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl:215:`$builddir/src/cmpress $tmppfx.cm3`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest6-sensitivity.pl-216-
infernal-1.1.3/testsuite/itest6-sensitivity.pl-217-# shorter subseq (we don't search longer subseq)
infernal-1.1.3/testsuite/itest6-sensitivity.pl:218:$output = `$builddir/src/cmscan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm3 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest6-sensitivity.pl-219-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-47-# Create the test CM files and sequence files
infernal-1.1.3/testsuite/itest7-trunc.pl:48:`cat $srcdir/testsuite/$model1.c.cm > $tmppfx.cm1`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest7-trunc.pl:49:`cat $srcdir/testsuite/$model2.c.cm > $tmppfx.cm2`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest7-trunc.pl:50:`cat $srcdir/testsuite/tremitted-Vault.fa > $tmppfx.fa1`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest7-trunc.pl:51:`cat $srcdir/testsuite/tremitted-Plant_SRP.fa > $tmppfx.fa2`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest7-trunc.pl-52-
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-56-# cmsearch, default, finds 2 hits E < 0.01
infernal-1.1.3/testsuite/itest7-trunc.pl:57:$output = `$builddir/src/cmsearch -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-58-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-69-# cmsearch --notrunc, finds 0 hits E < 10
infernal-1.1.3/testsuite/itest7-trunc.pl:70:$output = `$builddir/src/cmsearch --notrunc --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-71-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-76-# cmsearch --anytrunc, finds 3 hits E < 0.01
infernal-1.1.3/testsuite/itest7-trunc.pl:77:$output = `$builddir/src/cmsearch --anytrunc -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-78-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-89-if(-e "$tmppfx.cm1.ssi") { unlink "$tmppfx.cm1.ssi"; }
infernal-1.1.3/testsuite/itest7-trunc.pl:90:`$builddir/src/cmpress $tmppfx.cm1`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest7-trunc.pl-91-
infernal-1.1.3/testsuite/itest7-trunc.pl-92-# cmscan, default, finds 3 hits (not 2) E < 0.01
infernal-1.1.3/testsuite/itest7-trunc.pl:93:$output = `$builddir/src/cmscan -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-94-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-105-# cmscan --notrunc, finds 0 hits E < 10
infernal-1.1.3/testsuite/itest7-trunc.pl:106:$output = `$builddir/src/cmscan --notrunc --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-107-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-112-# cmscan --anytrunc, finds 3 hits E < 0.01
infernal-1.1.3/testsuite/itest7-trunc.pl:113:$output = `$builddir/src/cmscan --anytrunc -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm1 $tmppfx.fa1 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-114-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-122-# cmsearch, default, finds 3 hits E < 0.01
infernal-1.1.3/testsuite/itest7-trunc.pl:123:$output = `$builddir/src/cmsearch -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-124-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-138-# cmsearch --notrunc, finds 0 hits E < 10
infernal-1.1.3/testsuite/itest7-trunc.pl:139:$output = `$builddir/src/cmsearch --notrunc --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-140-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-145-# cmsearch --anytrunc, finds 3 hits E < 0.01
infernal-1.1.3/testsuite/itest7-trunc.pl:146:$output = `$builddir/src/cmsearch --anytrunc -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-147-if ($? != 0) { die "FAIL: cmsearch failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-158-if(-e "$tmppfx.cm2.ssi") { unlink "$tmppfx.cm2.ssi"; }
infernal-1.1.3/testsuite/itest7-trunc.pl:159:`$builddir/src/cmpress $tmppfx.cm2`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest7-trunc.pl-160-
infernal-1.1.3/testsuite/itest7-trunc.pl-161-# cmscan, default, finds 3 hits E < 0.01
infernal-1.1.3/testsuite/itest7-trunc.pl:162:$output = `$builddir/src/cmscan -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-163-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-178-# cmscan --notrunc, finds 0 hits E < 10
infernal-1.1.3/testsuite/itest7-trunc.pl:179:$output = `$builddir/src/cmscan --notrunc --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-180-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest7-trunc.pl-185-# cmscan --anytrunc, finds 3 hits E < 0.01
infernal-1.1.3/testsuite/itest7-trunc.pl:186:$output = `$builddir/src/cmscan --anytrunc -E 0.01 --tblout $tmppfx.tbl $tmppfx.cm2 $tmppfx.fa2 2>&1`;
infernal-1.1.3/testsuite/itest7-trunc.pl-187-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest8-glist.pl-48-# Create the test CM file
infernal-1.1.3/testsuite/itest8-glist.pl:49:`cat $srcdir/testsuite/$model2.c.cm $srcdir/testsuite/$model1.c.cm > $tmppfx.cm`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/testsuite/itest8-glist.pl-50-
##############################################
infernal-1.1.3/testsuite/itest8-glist.pl-70-
infernal-1.1.3/testsuite/itest8-glist.pl:71:`$builddir/src/cmpress $tmppfx.cm`; if ($?) { die "FAIL: cmpress\n"; }
infernal-1.1.3/testsuite/itest8-glist.pl-72-
##############################################
infernal-1.1.3/testsuite/itest8-glist.pl-74-# trial one, no --glist, all hits should be local
infernal-1.1.3/testsuite/itest8-glist.pl:75:$output = `$builddir/src/cmscan -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest8-glist.pl-76-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest8-glist.pl-82-# trial two, tRNA in --glist, tRNA hit should be glocal, Plant_SRP hit should be local
infernal-1.1.3/testsuite/itest8-glist.pl:83:$output = `$builddir/src/cmscan --glist $tmppfx.list1 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest8-glist.pl-84-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest8-glist.pl-90-# trial three, tRNA and Plant_SRP in --glist, both hits should be glocal
infernal-1.1.3/testsuite/itest8-glist.pl:91:$output = `$builddir/src/cmscan --glist $tmppfx.list2 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest8-glist.pl-92-if ($? != 0) { die "FAIL: cmscan failed\n"; }
##############################################
infernal-1.1.3/testsuite/itest8-glist.pl-98-# trial four, bogus name in glist, cmscan should fail
infernal-1.1.3/testsuite/itest8-glist.pl:99:$output = `$builddir/src/cmscan --glist $tmppfx.list3 -E 0.1 --tblout $tmppfx.tbl $tmppfx.cm $tmppfx.fa 2>&1`;
infernal-1.1.3/testsuite/itest8-glist.pl-100-if ($? == 0) { die "FAIL: cmscan did not fail when it should have\n"; }
##############################################
infernal-1.1.3/testsuite/itest8-glist.pl-115- print "$cmd\n" if $verbose;
infernal-1.1.3/testsuite/itest8-glist.pl:116: return `$cmd`;
infernal-1.1.3/testsuite/itest8-glist.pl-117-}
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-309-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:310:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-311- + +L +VL GT FL+WL + G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-469-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:470:Query: 55 LVLNLPLQE---AAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-471- + ++ ++L G+ + W+ + G G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-502-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:503:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-504- + + +L +VL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-535-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:536:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-537- + + +L +VL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-663-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:664:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-665- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-696-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:697:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-698- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-729-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:730:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-731- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-761-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:762:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-763- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-794-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:795:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-796- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-826-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:827:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-828- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-859-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:860:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-861- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-891-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:892:Query: 55 LVLNLPLQE---AAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-893- + ++ +L G+ + W+ + G G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-1180-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:1181:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-1182- + +L +VL AGT FL+WL + + G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-1244-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:1245:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-1246- + + ++ LVL GT FL+WL + + G+G +I+ A +
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-1792-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:1793:Query: 55 LVLNLPLQE----AAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGSIMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-1794- + ++LP + + + L+ GT FL+WL +L G+G I I++ S
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-1825-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:1826:Query: 55 LVLNLPL----QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGSIMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-1827- + + LP + ++ + L+ T FL+WL +L G+G I I++
##############################################
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-3898-
infernal-1.1.3/easel/demotic/examples/example.psiblast.out:3899:Query: 58 NL------PLQEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/easel/demotic/examples/example.psiblast.out-3900- L GV I L + L G ++++ ++ + G+G + ++A +
##############################################
infernal-1.1.3/easel/devkit/autodoc-64-
infernal-1.1.3/easel/devkit/autodoc:65:$text = `cat $cfile`;
infernal-1.1.3/easel/devkit/autodoc-66-$nfuncs = &parse_function_documentation($text);
##############################################
infernal-1.1.3/easel/devkit/autodoc.md-143-3. An unindented closing brace followed by a blank line.
infernal-1.1.3/easel/devkit/autodoc.md:144: The regex fragment for this is `^\}\s*$^\s*$`.
infernal-1.1.3/easel/devkit/autodoc.md-145-
##############################################
infernal-1.1.3/easel/devkit/sedition-53-
infernal-1.1.3/easel/devkit/sedition:54:system("cp $filename $filename.sed.tmp");
infernal-1.1.3/easel/devkit/sedition-55-if ($? != 0) {die "failed to make tmp copy"; }
infernal-1.1.3/easel/devkit/sedition-56-if (! $writable) {
infernal-1.1.3/easel/devkit/sedition:57: system("chmod +w $filename");
infernal-1.1.3/easel/devkit/sedition-58- if ($? != 0) { choke "failed to make $filename temporarily writable"; }
infernal-1.1.3/easel/devkit/sedition-59-}
infernal-1.1.3/easel/devkit/sedition:60:system("sed $sedargs $filename.sed.tmp > $filename");
infernal-1.1.3/easel/devkit/sedition-61-if ($? != 0) {choke "sed failed"; }
infernal-1.1.3/easel/devkit/sedition-62-if (! $writable) {
infernal-1.1.3/easel/devkit/sedition:63: system("chmod -w $filename");
infernal-1.1.3/easel/devkit/sedition-64- if ($? != 0) { choke "failed to make $filename temporarily writable"; }
##############################################
infernal-1.1.3/easel/devkit/sedition-pp-87-unlink $sourcefile;
infernal-1.1.3/easel/devkit/sedition-pp:88:system("mv /tmp/tmp.pp.sedition $sourcefile");
infernal-1.1.3/easel/devkit/sedition-pp-89-chmod $mode, $sourcefile;
##############################################
infernal-1.1.3/easel/devkit/sqc-414- #
infernal-1.1.3/easel/devkit/sqc:415: # The `(true; $cmd)` stuff is because a segfault gets reported by shell,
infernal-1.1.3/easel/devkit/sqc-416- # not the process itself; we want to redirect that output too.
##############################################
infernal-1.1.3/easel/devkit/sqc-419- print "sqc: running cmd: $cmd\n" if $verbose;
infernal-1.1.3/easel/devkit/sqc:420: `(true; $cmd) 2> /dev/null > /dev/null`;
infernal-1.1.3/easel/devkit/sqc-421- $status1 = $?;
##############################################
infernal-1.1.3/easel/devkit/sqc-423- if ($testtype eq "regression") {
infernal-1.1.3/easel/devkit/sqc:424: `(true; $cmd2) 2> /dev/null > /dev/null`;
infernal-1.1.3/easel/devkit/sqc-425- $status2 = $?;
##############################################
infernal-1.1.3/easel/devkit/sqc-467- {
infernal-1.1.3/easel/devkit/sqc:468: system("diff $tmp.REGRESSION.old.$i $tmp.REGRESSION.new.$i > /dev/null");
infernal-1.1.3/easel/devkit/sqc-469- if ($? != 0) { $nregress_failed++; }
##############################################
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infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11277-%Xq&SrT@EW`7@me5F+=2OgT-6<mI0gsm:`?a+l*ng!lF<hEVrc&CqI^dIR&FeYAR^6.\FI#F%8`BGOstbh<jOQkMMlG!>m-_V(6fs
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11293-%Mp7T<TP?QdDo)\@i)cdO.K5fl,&f/88PX4oo#8Z4(K]5?n(qs=^AI3SMT"!VGi]eT^%kL;*odC>Bk(W+O2d?tb=7$&lL<:V4[s8=
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11294:%pq)8cCRAJM?1am[0QLR#7Oio_VglCmrpK@9lJd1IT2BWO`*Ih"$KgFt0ZR`jn16_F'kJ3tpV8"._2Cfr>M#C"\U,!0I1B=X$n+d#
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11295-%'YU>u!E0),pV7Y4_jp@n<Sn,LWdh^TUrR$Rg][/Wl8=@(.Ohf["@t3Uh#I/bGMc^d$UqLgS`.'H4!Z86\G.uf`hsBbc&SEK``4N,
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11296-%S\cB'WPr`,!rI@"39tO='_t:]pi.XKI"W=NJbM@VF(24qhKqjWcsP6eVp,ICd8th;Lqi^O`dS9D^%gZUF_GCp\rS\NLo1=+f\\Ud
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11297:%I.>0!9\GKac?LNP\*`Z?(/jb[$p[F.%r<3ulJ[*,>L%E3]4/8eViV9c_dthjf[Yj&.R(kdTaHq]W+#qiJTfhpD+t`Lca]+lH5+F(
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11298-%,>)Y"65B%EcuON1g:o1aB^U,$)"%,ec/VanfQ+5QDOTN"-+t543IX#^=^N,i(D1EBUZ8)VEPgXUofQM,fS"W2KPEHe#2D#U9Nbi[
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11303-%OcKUqE2$tFoBN>!-eWY8>o_S49q7rTQr6+BCSQ=g9uO9ai@!5h7Y*2TobD(uO<>Y'mJ_rb9$^CY(o.6-%^K7C5P-'?AWNr6%!dHg
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11304:%iUk7]%WJ`S:6]f,R>-)'Y;S9>q!M\8Vm[0\J+$(W)qSPjXf&>$%T56[#,LTq8C1>*Eh#_6lVSc@N2e"$McJhR;p-o`g;0X7QM;\G
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11305-%oRhAo+1FqMd\l+g"n(D6S$Ua'5;_glI1)NH]T6P:OhZ*rk!p?LPEfOF_mZ5>^qG@oiCB%Scf"Cfm+rZcWPH3"S<:D*g:r3p^ns\W
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11314-%=BZC1T"K"0m?u.=3/qY8^aGpAmrOHspDJu:9LQtVj@/mtF!IG4]-G"sGVouWiCm?sG*SJVFOs"%3l#$Z7t@1D63Fn`*t5N3<Fu-M
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11315:%7c=HhMo#KR2W0`ZD3Y)]3^X2Z;M=Z+L4O/H$LE(ll*b2f>Bgea31-QNQu;iVOnEbU(@5?ZnQ88VBJu5[#4hSXVDQ'tLrZ.T?FB`&
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11316-%>j7NQ#psT+!s"+Yr8Y^<*m;FDD(mU&4KiU'GR8.X-[#OL1;aV'f5Y&da%%Oq>lo)`.@.#XAR/=A5]1E%Xd3dhec;e!k]-5frf7QA
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11320-%>$<dUNoW,t`fK<4p8d:FZ5I^<mjdYdM8r=TSL2a(%Q<8;4QhP4?[g/(BFaj+jpL*o_UF^Eo&SsHDMd0o_<m:]4gJ')7'Z)m/or#k
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11321:%M&Rc_$`.\c9Pq\c1Oldl.I_WaCc[M9c[?d`]O.cA=4I9XkQMLnI7FUaZCp0TL4D2sf)rgL?._mhRs[`la/$aM/"_Z`7\OS,;ko2l
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11322-%E6eUB.h9('TnZMKQ9!9O7DI*0!&RJ_Mo;`-f-%T)9]8;joYhI#Bs'$FJFlA).^3#jU%HgA"Eu-J;f3T_";Mk^>-+F#9l5l/8'J$]
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11324-%I8b:<5%/%\NU`n;\qPEGX+d\>8`u3/3\QOeXHFd>g<-4]`AF\pi$a.c1A$Wd<q0jr?),26*-cSF4^if_<g6X=el5%+Y"Ic;@So74
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11325:%7.KnS_U\j\`u34?Y&4Y<DE!jrC(^P]h0!h8`\V&<cR]aYH<el)\k,MT;;gL;$1Dumn>O$)j1`pOHQ9SiN>QK"fEe^*5!"A;<2,IR
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11326:%Z3;"Q2[gC7)4J'qS[_]N\qegQT`Cq2%bUXJX0/$:2et`:Hc=uS@u@:7i=1'4#biee$7&U$>n_6;cjEH`TG#d>^q+Ejo!\EFl^7C$
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11327-%(`qr+;c]C0Zb<q8N\h&]OaJX"1h/84*+oZ@RC?!&X^Ge2<sgGHH3*A<Ki/q(,fT6lr.hn8IXMFU`*+MD(6$RMOc]6l#p?!*T5*Uk
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11330-%!`M%X8TFD*:eL-YL@nE+_@C+RVecf3%hbWP$$X9P7TG#k$_U)r_afQNWd+Te86:=W1;qOJU.Jpr'$K?KYsS4L;\E99##cPQ=CC,+
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11331:%RXr!;o%%fMZO)b8+r6p@'1\*9_4l!]]QkKZWNE77Rb%`p$p)^X",NL\=!1&S<q[dPI5,\gBTNU$/<`S6D8g<'\_d'T<J^9<'g#gs
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11332-%L%JYLL#\)chY/F[$V",-X2VX^8Q3eemdb/sALY5M[cgR95b-K5&Le*]/<g3HOeBMU"gG:^i>/ELZsj\\=ZpOc'a\*>o'H=laS0O$
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11333-%O0*k'"ThZ:j1[4G+F-U1n9P+OW*6;e2;qVe4OQ*[dU[,i0$@5)H1.\l>Q(e]9JNK?%o6VajTIOQLl2;^E;cBV-c\4j@,RDO-D0(^
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11334:%o9reMNo,k4+4`p7SnK23m+0)_>TrOB'0]?2Q%UA0n?8J/)SJ!Mk7GMa-g1Ee8>f9%)<,c_m/OSu<$+'D$.GCO]rW`9DtWndjS9pX
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11335-%$hI)4/nSs9)P'VnFohS<;)[8g7NE"FO$'q*7l"QcG+\6mjJXeHHq!pq4n6'LN$sJ;*-c5Me\\5O()DqQ9Y-pih-(?L@QW!i"V5fH
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11336-%(N*SFh&$uNUd#;4C%c!M\Fh0;KU;kf/BZPfEs;&A40__h]]ba:XNAnQr("=raomW>2oTF@X\&%n(>c3gEDQ,8i_shlJqFpP@o]ct
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11337:%-#!8<AKB^/LANpm1E0C5le'9E8F3(3@\>W^?M+a)g<`FX)CZMPIVaUn$.CK;j15LmKm];k\a63`R7nAU=,Y0%2eF\EY1iWhr6?:3
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11338-%E+/sT"6.\^%u??.+ec:bYKsqR1!X+<H#nmD7:7eS]$ARBg&\,6%%JP4\dksIT@L`b=l%A;YM8lKMt9I%E'h@C$Qqe$U4O+<o*I8/
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11352-%k';Q]LK#mI`]Xua$h^a!pS1Lq>V>;hJ5]qMk3>n5b@fNAO@LW5%4XNip#)?oIn96:NQ(FAEU!;XIMQTRMt_L$<qB)i;O6_pcZq%9
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11353:%C!Nig>3;T@5$A`Vi<4XVB$aX9K6DMGA!\'4,F>l;bL*l"jWlUBV$>bm>k>sLlM*PIr$TO%o4a@]1N%+LR$3`HP>RC95J63LVU_=J
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11354-%@?$it5!%,^PSB"^5*J'Eoc,7Z4C,B_+9:s=-*p(BUHHrI/oUt"GN*%\Ut&N[7Qpah;'>JuqQ7\G>=GWEkL;RlZ>8MC`T(r1@n(!l
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11355:%&"L]mXe*3j`S+(n`*r$$@QKA:D6`K+dE.;`mPAAARG$V6''3EK7p8('&r:rWki]id>Ff_EGVu`H[e(4X?dM4s`EY[._EIXKU&L[!
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11356:%8Ofa0Kd-;'[>0t+Na.7I62DZ+0;R.n@,5K#K6#ai^A+H#It-A4`3\ecB,I3Q3U[o'()$e3ZBZ[7CgrpI$"pEBrW]nu`I`*Fqd6Im
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11357-%4.BN!I8^K8%]Nb>.rqB^;HkWj@SC?][LO$m_3cuaX]RM'BkfB>*I_mjTdq3KS%WeLa)-<jq&`1:F5!*^ogIKmlf/56fpdNP..tL<
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11359-%iA<V-n)/0)B"DTfRSmhK6B39/4KZ-f9(N]t6Rn\c61f8Q"d0';kjth&r.GKB^-0*gpMnfa&!/\hKPPXKrFXr,X\'E?19sV/4d37G
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11360:%FP>,)f'7A*>WTHV0gFCgZ)TLr:JjnN7J>$mr_7a>E,ZN:(a#Tsagu4LA1CAT.`'pq4YtK$X3`KNANi+A%OF.WB]dnL.:nOP]J7TL
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11361-%FTl))JG$1NH'27FquDp^_,c)7%SQIIe-F+b0ENW8Di$e$Jote*#VAPL"4H:*m745G"Er>)Sg5P@YUhR'\O;JPj,ABQqOt!F*?K>?
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11378-%Ol;g%kTbi4Rn0Gg7Q`]bVC`lpr<W^8<^2VTaaOV>5;e/FRiY@^=>YlpcQ+k+YSr.?lAbci*"a^8r`m:%PXkG/64Vdq[;e(VmKo6&
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11379:%f`MBOhYo.)PNLCm0":UXj2XW=+eYOqbE'&WjOnB46gj`i)EmX22P"C^q*&l#Pir$c!ZX.#_4N`$rm+5<+4#i+St<REM%dK\pd*o>
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11380-%VKm1b+<i('ld4+tF+kULr3YB9QrmeIr-Uj/Y<s3Z$R)l!nP^ZF*V*06g'RJ^IiA#Wr[a(H*[1EC8b\;_g#qOh9FFkBL<!L]q?ebd
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11382-%9?[ZT3e4r&#i$ZrqZf.QGQdn6>CH-[2fRV+*4XT+ef\*6.o<B]s*iS@o[pH]H?(!NaZ$oT?BN_3G)i3UfZh$65[2P7!MhEI&Qh-c
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11383:%'aT<Xj6,(*khKnof5p9c1j]"g@G,1Ca8pE\)B`Q)5j-9Ga$t9Lb-i+Fl!(/!gDsg+T[Vrag6C26C@0Al#MBio>,n<'>?[%`%^PiS
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11384-%*00mJDOjuc*Iu]?e=R`/%<=E)/mc!g?$CTVK7i1cfQG\qF8u6q+e20%'@ACAZqg$Y<hSR/;Lhm8),fhH5ec;gU"T^5X,:nOp>1Zq
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11393-%^XAn_eumLP)1c'`]sQ/k@S<aqXos3X]VSW:Zd)nD*hVkOm:dVi9;Dgd*OYkeMkNgIb4Y!k(Ia[i5]#U/m2S>j\eE^O_ZroJhZLKN
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11394:%f&$cmHJ[fY`F48kVcQqYQZ#+`m-a$6G(Y^h3GcjBCs`SSYW+O!Ro`rqBr(9nF>PsZqspf^htutSJg7m"pn.S5R`nVe2Ic<?%i2'+
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11395-%HgX"`N22P<4XR>t#N<[j%Qn'a^\lD*gYtY`ZJDYAC%C88!+TY48a,"<YXQ$L:.gsBe-0F_R^,OR31!dKR&UFk0O,X!G?;1m%oi43
##############################################
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11398-%\Ad5P&p"l/,j$^2K"4Iu`D4XjpiJ\.7iu^FI?kM3Mu48;<#0"..luh"qC:"s6,jDPVPRo?]/7nMVhSM=%)%Vo((+AZqkSa7r]s@B
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11399:%"a8QcNQu_?-Jc+X?lT?h7_a460HW9pdEOp19Lt&:56u!JU8[<"`R;D)h(b3@"K>G$B`#KEP<EM=N%<ZYas9SFR.ah=3)I3SfOtNN
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11400:%%O:+p&>ZY"Gg>P$""f[Vbd/H-b,shoh'OF(A6*Mp,GcFDgDm`%Zb^*>`$!;dr=gY4,g@e.1EDZ`N>:9HWFMCND48n(CPV!rHOLN6
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11401-%ZN:t[B0pg^<O77W-"X[^*gbEr0OH^\XU5;e_6Oha1S!TBj4N0N4_+5/:p*`S45bpngO`!]^9`u+8*u##eW'e2StmBG#>..`l_sQ8
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11402-%m$uLaVTgB2@fJNeAG`VY;;/8QmWkr(A@YQ^r1K%]`RQ)c//=-j(\H2A,oU]@i?1"GFRV2[Z-/H0D@tMMs!8L%D3PqX6/lcFGPLkY
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps:11403:%c<JYc\+Uru`KV'ine<%c#B$!Hcn:`DYbXE&56XY,7<"O-UZm@j>XTSlI9U5GBHPdH1^:EB/aIS,&f,ok),U7_bNnUL+0I6A2m?\I
infernal-1.1.3/easel/documentation/figures/rnaseP-bsu-alignment.eps-11404-%;0:r^^Z,E?k5:HE<"F'b2Qo:nSPH$)o$<VOYPun>ErXOOD>*\^5E?1YcKuXSII@gIZ"O?^[S8Y#hHhmEhZ\QIIk2!'fXC=#$=+Lu
##############################################
infernal-1.1.3/easel/esl_gumbel.tex-476-We start with the same likelihood equation that arises in censored
infernal-1.1.3/easel/esl_gumbel.tex:477:data for a \emph{known} total number of samples $N$ (where $N=n+z$),
infernal-1.1.3/easel/esl_gumbel.tex-478-but since $N$ is unknown, we need to integrate over all possible $N$
##############################################
infernal-1.1.3/easel/esl_scorematrix.c-352- *
infernal-1.1.3/easel/esl_scorematrix.c:353: * $P(b \mid a) = P(ab) / P(a)$, where $P(a) = \sum_b P(ab)$.
infernal-1.1.3/easel/esl_scorematrix.c-354- *
##############################################
infernal-1.1.3/easel/install-sh-97- case $1 in
infernal-1.1.3/easel/install-sh:98: -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
infernal-1.1.3/easel/install-sh-99- shift
##############################################
infernal-1.1.3/easel/install-sh-130-
infernal-1.1.3/easel/install-sh:131: -t=*) transformarg=`echo $1 | sed 's/-t=//'`
infernal-1.1.3/easel/install-sh-132- shift
##############################################
infernal-1.1.3/easel/install-sh-190- if test -d "$dst"; then
infernal-1.1.3/easel/install-sh:191: dst=$dst/`basename "$src"`
infernal-1.1.3/easel/install-sh-192- fi
##############################################
infernal-1.1.3/easel/install-sh-195-# This sed command emulates the dirname command.
infernal-1.1.3/easel/install-sh:196:dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
infernal-1.1.3/easel/install-sh-197-
##############################################
infernal-1.1.3/easel/install-sh-208- IFS='%'
infernal-1.1.3/easel/install-sh:209: set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
infernal-1.1.3/easel/install-sh-210- IFS=$oIFS
##############################################
infernal-1.1.3/easel/install-sh-231- if test -z "$transformarg"; then
infernal-1.1.3/easel/install-sh:232: dstfile=`basename "$dst"`
infernal-1.1.3/easel/install-sh-233- else
##############################################
infernal-1.1.3/easel/install-sh-238- # don't allow the sed command to completely eliminate the filename.
infernal-1.1.3/easel/install-sh:239: test -z "$dstfile" && dstfile=`basename "$dst"`
infernal-1.1.3/easel/install-sh-240-
##############################################
infernal-1.1.3/easel/m4/ax_compiler_vendor.m4-76- *:) vendor=$ventest; continue ;;
infernal-1.1.3/easel/m4/ax_compiler_vendor.m4:77: *) vencpp="defined("`echo $ventest | sed 's/,/) || defined(/g'`")" ;;
infernal-1.1.3/easel/m4/ax_compiler_vendor.m4-78- esac
##############################################
infernal-1.1.3/easel/m4/ax_compiler_vendor.m4-84- done
infernal-1.1.3/easel/m4/ax_compiler_vendor.m4:85: ax_cv_[]_AC_LANG_ABBREV[]_compiler_vendor=`echo $vendor | cut -d: -f1`
infernal-1.1.3/easel/m4/ax_compiler_vendor.m4-86- ])
##############################################
infernal-1.1.3/easel/m4/ax_pthread.m4-296- ax_pthread_sed='s/conftest\.\$ac_ext/conftest.$ac_objext/g'
infernal-1.1.3/easel/m4/ax_pthread.m4:297: ax_pthread_link_step=`$as_echo "$ac_link" | sed "$ax_pthread_sed"`
infernal-1.1.3/easel/m4/ax_pthread.m4-298- ax_pthread_2step_ac_link="($ac_compile) && (echo ==== >&5) && ($ax_pthread_link_step)"
##############################################
infernal-1.1.3/easel/m4/esl_pic_flags.m4-96- linux*|k*bsd*-gnu)
infernal-1.1.3/easel/m4/esl_pic_flags.m4:97: case `basename "$CC"` in
infernal-1.1.3/easel/m4/esl_pic_flags.m4-98- icc*|ecc*|ifort*)
##############################################
infernal-1.1.3/easel/m4/esl_pic_flags.m4-113- *)
infernal-1.1.3/easel/m4/esl_pic_flags.m4:114: case `$CC -V 2>&1 | sed 5q` in
infernal-1.1.3/easel/m4/esl_pic_flags.m4-115- *Sun\ C*|*Sun\ F*)
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-58-#
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:59:@output = `$esl_afetch $tmppfx.sto baz`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-60-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-64-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:65:@output = `$esl_afetch $tmppfx.sto XX00003.3`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-66-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-71-# Without SSI, when fetching from a list, MSAs are in order of .sto file, not .list file
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:72:@output = `$esl_afetch -f $tmppfx.sto $tmppfx.list`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-73-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-77-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:78:@output = `$esl_afetch -O $tmppfx.sto $tmppfx.name`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:79:@output = `$esl_afetch $tmppfx.sto $tmppfx.name > $tmppfx.tmp`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-80-system "diff $tmppfx.name $tmppfx.tmp > /dev/null 2>&1"; if ($? != 0) { die "FAIL: esl-afetch bad diff"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-81-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:82:@output = `$esl_afetch -f -o $tmppfx.tmp $tmppfx.sto $tmppfx.list`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:83:@output = `$esl_afetch -f $tmppfx.sto $tmppfx.list > $tmppfx.tmp2`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-84-system "diff $tmppfx.tmp $tmppfx.tmp2 > /dev/null 2>&1"; if ($? != 0) { die "FAIL: esl-afetch bad diff"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-85-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:86:@output = `$esl_afetch --informat stockholm $tmppfx.sto baz`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-87-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-88-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:89:@output = `$esl_afetch --outformat clustal $tmppfx.sto XX00003.3`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-90-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-95-#
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:96:@output = `$esl_afetch --index $tmppfx.sto`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-97-if ($? != 0) { die "FAIL: esl-afetch indexing failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-103-# so the test alignments are fetched with no blank line between #=GF AC line and first seq.
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:104:@output = `$esl_afetch $tmppfx.sto baz`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-105-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-109-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:110:@output = `$esl_afetch $tmppfx.sto XX00003.3`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-111-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-116-# With SSI, when fetching from a list, MSAs are in order of .list file, not .sto file
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:117:@output = `$esl_afetch -f $tmppfx.sto $tmppfx.list`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-118-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-122-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:123:@output = `$esl_afetch -O $tmppfx.sto $tmppfx.name`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:124:@output = `$esl_afetch $tmppfx.sto $tmppfx.name > $tmppfx.tmp`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-125-system "diff $tmppfx.name $tmppfx.tmp > /dev/null 2>&1"; if ($? != 0) { die "FAIL: esl-afetch bad diff"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-126-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:127:@output = `$esl_afetch -f -o $tmppfx.tmp $tmppfx.sto $tmppfx.list`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:128:@output = `$esl_afetch -f $tmppfx.sto $tmppfx.list > $tmppfx.tmp2`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-129-system "diff $tmppfx.tmp $tmppfx.tmp2 > /dev/null 2>&1"; if ($? != 0) { die "FAIL: esl-afetch bad diff"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-130-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:131:@output = `$esl_afetch --informat stockholm $tmppfx.sto baz`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-132-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-133-
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl:134:@output = `$esl_afetch --outformat clustal $tmppfx.sto XX00003.3`;
infernal-1.1.3/easel/miniapps/esl-afetch.itest.pl-135-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-118-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:119:$output = `$eslalimanip -h`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-120-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-122-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:123:$output = `$eslalimanip --devhelp`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-124-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-127-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:128:$output = `$eslalimanip --rna $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-129-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-131-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:132:system("$eslalimanip -o $tmppfx.o.stk --rna $tmppfx.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-133-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:134:$output = `cat $tmppfx.o.stk`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-135-if ($output !~ /\#=GR seq1 PP 5789\*\*..\*\*88...\*9.9\*\*\*\*88.7..776543210/) { die "FAIL: alignment manipulated incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-136-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:137:$output = `$eslalimanip --dna $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-138-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-140-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:141:$output = `$eslalimanip --amino $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-142-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-144-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:145:$output = `$eslalimanip --rna --informat stockholm $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-146-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-148-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:149:$output = `$eslalimanip --rna --informat pfam $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-150-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-152-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:153:$output = `$eslalimanip --rna --informat afa $tmppfx.afa 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-154-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-156-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:157:$output = `$eslalimanip --rna --outformat afa $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-158-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-160-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:161:$output = `$eslalimanip --rna --outformat psiblast $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-162-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-164-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:165:$output = `$eslalimanip --rna --outformat a2m $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-166-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-168-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:169:$output = `$eslalimanip --rna --lnfract 0.9 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-170-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-172-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:173:$output = `$eslalimanip --rna --lnfract 0.9 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-174-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-179-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:180:$output = `$eslalimanip --rna --lxfract 1.02 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-181-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-186-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:187:$output = `$eslalimanip --rna --lmin 30 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-188-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-193-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:194:$output = `$eslalimanip --rna --lmax 29 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-195-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-200-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:201:$output = `$eslalimanip --rna --rffract 0.953 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-202-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-207-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:208:$output = `$eslalimanip --rna --detrunc 1 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-209-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-214-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:215:$output = `$eslalimanip --rna --xambig 0 $tmppfx.stk2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-216-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-221-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:222:$output = `$eslalimanip --rna --seq-k $tmppfx.list $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-223-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-228-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:229:$output = `$eslalimanip --rna --seq-k $tmppfx.list --informat pfam --small $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-230-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-235-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:236:$output = `$eslalimanip --rna --k-reorder --seq-k $tmppfx.list $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-237-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-242-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:243:$output = `$eslalimanip --rna --seq-r $tmppfx.list $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-244-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-249-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:250:$output = `$eslalimanip --rna --seq-r $tmppfx.list --informat pfam --small $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-251-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-256-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:257:$output = `$eslalimanip --rna --seq-ins 9 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-258-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-263-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:264:$output = `$eslalimanip --rna --seq-ins 9 --seq-ni 3 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-265-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-270-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:271:$output = `$eslalimanip --rna --seq-ins 9 --seq-xi 2 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-272-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-277-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:278:$output = `$eslalimanip --rna --trim $tmppfx.trim.fa $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-279-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-282-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:283:$output = `$eslalimanip --rna --minpp 0.9 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-284-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-287-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:288:$output = `$eslalimanip --rna --reorder $tmppfx.list2 $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-289-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-294-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:295:$output = `$eslalimanip --rna --mask2rf $tmppfx.rfmask $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-296-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-298-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:299:$output = `$eslalimanip --rna --m-keeprf --mask2rf $tmppfx.rfmask $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-300-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-302-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:303:$output = `$eslalimanip --rna --mask2rf $tmppfx.amask $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-304-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-306-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:307:$output = `$eslalimanip --rna --m-keeprf --mask2rf $tmppfx.amask $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-308-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-310-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:311:$output = `$eslalimanip --rna --num-all $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-312-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-315-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:316:$output = `$eslalimanip --rna --num-rf $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-317-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-320-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:321:$output = `$eslalimanip --rna --rm-gc RF $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-322-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-324-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:325:$output = `$eslalimanip --rna --rm-gc SS_cons $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-326-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-328-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:329:$output = `$eslalimanip --rna --rm-gc PP_cons $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-330-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-332-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:333:$output = `$eslalimanip --rna --sindi $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-334-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-337-
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl:338:$output = `$eslalimanip --rna --post2pp $tmppfx.post.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimanip.itest.pl-339-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-92-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:93:$output = `$eslalimap -h`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-94-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-96-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:97:$output = `$eslalimap $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-98-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-101-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:102:$output = `$eslalimap --dna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-103-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-106-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:107:$output = `$eslalimap $tmppfx.1 $tmppfx.3 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-108-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-111-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:112:system("$eslalimap --mask-a2a $tmppfx.a2a --mask-a2rf $tmppfx.a2rf --mask-rf2a $tmppfx.rf2a --mask-rf2rf $tmppfx.rf2rf $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-113-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:114:$output = `cat $tmppfx.a2a`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-115-if ($output !~ /111111111111111111011111111/) { die "FAIL: alignments mapped incorrectly."; }
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-116-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:117:$output = `cat $tmppfx.a2rf`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-118-if ($output !~ /001111111111111111011111111/) { die "FAIL: alignments mapped incorrectly."; }
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-119-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:120:$output = `cat $tmppfx.rf2a`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-121-if ($output !~ /111111111111111101111111/) { die "FAIL: alignments mapped incorrectly."; }
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-122-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:123:$output = `cat $tmppfx.rf2rf`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-124-if ($output !~ /111111111111111101111111/) { die "FAIL: alignments mapped incorrectly."; }
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-125-
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:126:system("$eslalimap --rna --submap $tmppfx.submask $tmppfx.4 $tmppfx.5 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-127-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl:128:$output = `cat $tmppfx.submask`;
infernal-1.1.3/easel/miniapps/esl-alimap.itest.pl-129-if ($output !~ /0011001100111/) { die "FAIL: alignments mapped incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-84-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:85:$output = `$eslalimask -h`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-86-if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-91-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:92: $output = `$eslalimask $smallA[$pass] --rna $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-93- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-100- if($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:101: $output = `$eslalimask $smallA[$pass] --dna $afileA[$pass] $tmppfx.rfmask 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-102- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-106- }
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:107: system("$eslalimask $smallA[$pass] --amino -o $tmppfx.out $afileA[$pass] $tmppfx.fullmask > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:108: $output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-109- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-115-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:116: system("$eslalimask $smallA[$pass] --rna -q -o $tmppfx.out $afileA[$pass] $tmppfx.fullmask > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:117: $output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-118- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-124-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:125: $output = `$eslalimask $smallA[$pass] --amino --informat pfam $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-126- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-132-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:133: $output = `$eslalimask $smallA[$pass] --rna --outformat pfam $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-134- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-141- if($smallA[$pass] eq "") {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:142: $output = `$eslalimask $smallA[$pass] --rna --outformat a2m $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-143- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-150-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:151: $output = `$eslalimask $smallA[$pass] --rna --outformat psiblast $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-152- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-159-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:160: $output = `$eslalimask $smallA[$pass] --rna --outformat afa $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-161- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-164-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:165: $output = `$eslalimask $smallA[$pass] --rna -t $afileA[$pass] 12-23 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-166- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-173- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:174: $output = `$eslalimask $smallA[$pass] --rna -t --t-rf $afileA[$pass] 18: 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-175- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-181- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:182: $output = `$eslalimask $smallA[$pass] --rna -t --t-rmins --t-rf $afileA[$pass] 18: 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-183- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-189- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:190: $output = `$eslalimask $smallA[$pass] --rna -t --t-rmins --t-rf $afileA[$pass] 18: 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-191- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-196-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:197: $output = `$eslalimask $smallA[$pass] --rna -g $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-198- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-209- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:210: $output = `$eslalimask $smallA[$pass] --rna -g --keepins $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-211- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-217- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:218: $output = `$eslalimask $smallA[$pass] --rna -g --keepins --gapthresh 0.3 $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-219- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-225- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:226: $output = `$eslalimask $smallA[$pass] --rna -g --keepins --gapthresh 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-227- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-233- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:234: $output = `$eslalimask $smallA[$pass] --rna -g --keepins --gapthresh 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-235- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-240-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:241: $output = `$eslalimask $smallA[$pass] --gmask-all $tmppfx.gmaskall --rna -g --gapthresh 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-242- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:243: $output = `cat $tmppfx.gmaskall`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-244- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-245- if ($output !~ /00111100111100010001111110100111110000/) { die "FAIL: alignment masked incorrectly on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:246: $output = `$eslalimask $smallA[$pass] --gmask-rf $tmppfx.gmaskrf --rna -g --gapthresh 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-247- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:248: $output = `cat $tmppfx.gmaskrf`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-249- if ($output !~ /111111111111111111111/) { die "FAIL: alignment masked incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-254-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:255: $output = `$eslalimask $smallA[$pass] -p --rna $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-256- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-266-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:267: $output = `$eslalimask $smallA[$pass] --pavg 0.73 -p --rna $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-268- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-279- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:280: $output = `$eslalimask $smallA[$pass] --ppcons 0.85 -p --rna $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-281- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-285-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:286: $output = `$eslalimask $smallA[$pass] --pthresh 0.85 --pfract 0.5 --rna -p $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-287- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-296-
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:297: $output = `$eslalimask $smallA[$pass] --pmask-all $tmppfx.pmaskall --rna -p --pthresh 0.75 --pfract 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-298- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:299: $output = `cat $tmppfx.pmaskall`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-300- if ($have_rfA[$pass]) {
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-301- if ($output !~ /00000000010000000001111110000000000000/) { die "FAIL: alignment masked incorrectly on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:302: $output = `$eslalimask $smallA[$pass] --pmask-rf $tmppfx.pmaskrf --rna -p --pthresh 0.75 --pfract 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-303- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl:304: $output = `cat $tmppfx.pmaskrf`;
infernal-1.1.3/easel/miniapps/esl-alimask.itest.pl-305- if ($output !~ /000001000111111000000/) { die "FAIL: alignment masked incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-73-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:74:$output = `$eslalimerge -h`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-75-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-77-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:78:$output = `$eslalimerge --rna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-79-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-83-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:84:$output = `$eslalimerge --dna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-85-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-89-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:90:$output = `$eslalimerge --amino $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-91-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-95-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:96:$output = `$eslalimerge --rna --list $tmppfx.list 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-97-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-100-if ($output !~ /\.\.AAAA\.AaaAAAaccccC\.\.\.\-CccCCCCccc\.cccgGggGGggGGg\.\.\./) { die "FAIL: alignments merged incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:101:system("$eslalimerge --rna -o $tmppfx.out $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-102-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:103:$output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-104-if ($output !~ /sequence 3 is the best/) { die "FAIL: alignments merged incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-107-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:108:system("$eslalimerge --rna -v -o $tmppfx.out $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-109-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-110-# don't worry about checking verbose output printed to stdout
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:111:$output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-112-if ($output !~ /sequence 3 is the best/) { die "FAIL: alignments merged incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-114-if ($output !~ /\.\.AAAA\.AaaAAAaccccC\.\.\.\-CccCCCCccccccgGggGGggGGg\.\.\./) { die "FAIL: alignments merged incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:115:$output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-116-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:117:$output = `$eslalimerge --rna --outformat pfam $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-118-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-122-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:123:$output = `$eslalimerge --rna --outformat a2m $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-124-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-127-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:128:$output = `$eslalimerge --rna --outformat psiblast $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-129-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-132-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:133:$output = `$eslalimerge --rna --outformat afa $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-134-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-137-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:138:$output = `$eslalimerge --rna --rfonly $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-139-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-144-# test that hmmer3 fragment annotation is correctly handled (this WILL NOT WORK currently with --small!)
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:145:$output = `$eslalimerge --rna $tmppfx.4 $tmppfx.5 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-146-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-149-# repeat all the same tests (except a2m and psiblast output) but now in small memory mode
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:150:$output = `$eslalimerge --small --rna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-151-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-155-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:156:$output = `$eslalimerge --small --dna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-157-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-161-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:162:$output = `$eslalimerge --small --amino $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-163-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-167-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:168:$output = `$eslalimerge --small --rna --list $tmppfx.list 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-169-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-173-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:174:system("$eslalimerge --small --rna -o $tmppfx.out $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-175-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:176:$output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-177-if ($output !~ /sequence 3 is the best/) { die "FAIL: alignments merged incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-180-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:181:system("$eslalimerge --small --rna -v -o $tmppfx.out $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-182-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-183-# don't worry about checking verbose output printed to stdout
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:184:$output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-185-if ($output !~ /sequence 3 is the best/) { die "FAIL: alignments merged incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-187-if ($output !~ /\.\.AAAA\.AaaAAAaccccC\.\.\.\-CccCCCCccccccgGggGGggGGg\.\.\./) { die "FAIL: alignments merged incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:188:$output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-189-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:190:$output = `$eslalimerge --small --rna --outformat pfam $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-191-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-195-
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl:196:$output = `$eslalimerge --small --rna --rfonly $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alimerge.itest.pl-197-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-68-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:69:$output = `$eslalistat -h`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-70-if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-79-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:80: $output = `$eslalistat $smallA[$pass] --rna $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-81- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-91-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:92: $output = `$eslalistat $smallA[$pass] --dna $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-93- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-103-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:104: $output = `$eslalistat $smallA[$pass] --amino $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-105- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-116- if($pass == 0) {
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:117: $output = `$eslalistat $smallA[$pass] --informat afa --rna $tmppfx.afa 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-118- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-124-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:125: $output = `$eslalistat $smallA[$pass] -1 --rna $tmppfx.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-126- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-134- # test a file with 2 alignments
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:135: $output = `$eslalistat $smallA[$pass] --rna $tmppfx.dbl.stk 2>&1`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-136- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-149- # test output file options
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:150: system("$eslalistat --icinfo $tmppfx.ic $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-151- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:152: $output = `cat $tmppfx.ic`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-153- if($output !~ /5 9 1.0\d+ 2.0\d+/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-155-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:156: system("$eslalistat --rinfo $tmppfx.r $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-157- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:158: $output = `cat $tmppfx.r`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-159- if($output !~ /21 34 2.0 0.66\d+ 1.0 0.33\d+/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-161-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:162: system("$eslalistat --pcinfo $tmppfx.pc $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-163- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:164: $output = `cat $tmppfx.pc`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-165- if($output !~ /31\s+18\s+3.0\s+0.0\s+0.0\s+0.0\s+0.0\s+0.0\s+0.0\s+0.0\s+1.0\s+1.0\s+0.0\s+1.0\s+0.0\s+0.82\d+/) {
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-169-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:170: system("$eslalistat --list $tmppfx.list $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-171- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:172: $output = `cat $tmppfx.list`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-173- if($output !~ /seq2.+seq2/s) { die "FAIL: alignment lists created incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-176- if($pass == 0) { # these are incompatible with --small
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:177: system("$eslalistat --psinfo $tmppfx.ps $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-178- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:179: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-180- if($output !~ /seq3 20 0 0 0 1 3 4 0 0 9 2 1 0.67\d+/) {
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-186-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:187: system("$eslalistat --iinfo $tmppfx.i $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-188- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:189: $output = `cat $tmppfx.i`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-190- if($output !~ /16\s+1.0\s+0.33\d+\s+2.0/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-192-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:193: system("$eslalistat --cinfo $tmppfx.c --noambig $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-194- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:195: $output = `cat $tmppfx.c`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-196- if($output !~ /3\s+3\.\d+\s+0\.\d+\s+0\.\d+\s+0/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-198-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:199: system("$eslalistat --bpinfo $tmppfx.bp $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-200- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:201: $output = `cat $tmppfx.bp`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-202- if($output !~ /16\s+34\s+0\s+0\s+0\s+0\s+0\s+0\s+2\s+0\s+0\s+0\s+0\s+0\s+0\s+0\s+0\s+0\s+/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-204-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:205: system("$eslalistat --weight --cinfo $tmppfx.c $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-206- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:207: $output = `cat $tmppfx.c`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-208- if($output !~ /2\s+1\.5\s+0\.\d+\s+0\.\d+\s+0/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-211-
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:212: system("$eslalistat --cinfo $tmppfx.c $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-213- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl:214: $output = `cat $tmppfx.c`;
infernal-1.1.3/easel/miniapps/esl-alistat.itest.pl-215- if($output !~ /3\s+3\.\d+\s+0\.\d+\s+0\.\d+\s+0/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-71-
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl:72:$output = `$eslcompalign -h`;
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-73-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-75-
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl:76:$output = `$eslcompalign --rna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-77-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-80-
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl:81:$output = `$eslcompalign -c $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-82-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-84-
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl:85:$output = `$eslcompalign -p $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-86-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-88-
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl:89:$output = `$eslcompalign --p-mask $tmppfx.mask -p $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-90-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-92-
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl:93:system("$eslcompalign -c --c2dfile $tmppfx.dfile $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-94-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl:95:$output = `cat $tmppfx.dfile`;
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-96-if ($output !~ /^0.000 0.33\d+ 0.000 0.000/) { die "FAIL: alignments compared incorrectly."; }
##############################################
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-98-#Test that esl-compalign can handle '~' characters annotating fragments, a la hmmbuild -O in hmmer3.
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl:99:$output = `$eslcompalign --rna $tmppfx.1 $tmppfx.3 2>&1`;
infernal-1.1.3/easel/miniapps/esl-compalign.itest.pl-100-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly";}
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-60-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:61:$output = `$eslconstruct -h`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-62-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-64-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:65:$output = `$eslconstruct $tmppfx.1 2>&1`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-66-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-70-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:71:$output = `$eslconstruct $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-72-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-74-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:75:$output = `$eslconstruct $tmppfx.3 3>&1`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-76-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-79-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:80:$output = `$eslconstruct -a $tmppfx.1 2>&1`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-81-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-86-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:87:$output = `$eslconstruct -v $tmppfx.1 2>&1`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-88-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-94-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:95:system("$eslconstruct -o $tmppfx.stk -x $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-96-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:97:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-98-if ($output !~ /\#=GC SS_cons ::::::::::::::::<<_______>>/) { die "FAIL: consensus structure calculated incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-99-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:100:system("$eslconstruct -o $tmppfx.stk -r $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-101-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:102:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-103-if ($output !~ /\#=GC SS_cons :::::<_______>::<<_______>>/) { die "FAIL: consensus structure calculated incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-104-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:105:system("$eslconstruct -o $tmppfx.stk -c $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-106-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:107:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-108-if ($output !~ /#=GC SS_cons ::::<<<____>->>:<<-<____>>>/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-109-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:110:system("$eslconstruct -o $tmppfx.stk -c --rfc $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-111-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:112:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-113-if ($output !~ /#=GC SS_cons ::::<<<____>->>:<<-<____>>>/) { die "FAIL: consensus stucture calculated incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-115-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:116:system("$eslconstruct -o $tmppfx.stk --indi simpex-2 $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-117-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:118:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-119-if ($output !~ /\#=GC SS_cons ::::<<<____>->>::<--<___>>:/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-120-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:121:system("$eslconstruct -o $tmppfx.stk --indi simpex-2 --rfindi $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-122-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:123:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-124-if ($output !~ /\#=GC SS_cons ::::<<<____>->>::<--<___>>:/) { die "FAIL: consensus stucture calculated incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-126-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:127:system("$eslconstruct -o $tmppfx.stk --ffreq 0.6 $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-128-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:129:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-130-if ($output !~ /#=GC SS_cons ::::<<<____>->>:<<-<____>>>/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-131-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:132:system("$eslconstruct -o $tmppfx.stk --ffreq 0.7 $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-133-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:134:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-135-if ($output !~ /#=GC SS_cons :::::::::::::::::<_______>:/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-136-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:137:system("$eslconstruct -o $tmppfx.stk --fmin $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-138-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:139:$output = `cat $tmppfx.stk`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-140-if ($output !~ /#=GC SS_cons ::::<<<____>->>:<<-<____>>>/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-141-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:142:system("$eslconstruct -l $tmppfx.list -o $tmppfx.stk --fmin $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-143-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:144:$output = `cat $tmppfx.list`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-145-if ($output !~ /simpex-1/) { die "FAIL: consensus stucture calculated incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-147-
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:148:system("$eslconstruct --lmax 1 -l $tmppfx.list -o $tmppfx.stk --fmin $tmppfx.1 > /dev/null");
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-149-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl:150:$output = `cat $tmppfx.list`;
infernal-1.1.3/easel/miniapps/esl-construct.itest.pl-151-if ($output !~ /simpex-1/) { die "FAIL: consensus stucture calculated incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-32-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:33:$output = `$eslmask -h`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-34-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-36-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:37:$output = `$eslmask $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-38-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-41-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:42:$output = `$eslmask -r $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-43-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-46-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:47:system("$eslmask -o $tmppfx.out $tmppfx.1 $tmppfx.2 2>&1");
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-48-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:49:$output = `cat $tmppfx.out`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-50-if ($output !~ /aaAAAAAAAAXXXXXXXXXXCCCCCCCCcc/) { die "FAIL: seq masked incorrectly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-52-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:53:$output = `$eslmask -l $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-54-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-57-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:58:$output = `$eslmask -lr $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-59-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-62-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:63:$output = `$eslmask -m N $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-64-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-67-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:68:$output = `$eslmask -x 2 $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-69-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-72-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:73:$output = `$eslmask -x 7 $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-74-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-77-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:78:$output = `$eslmask -rx 2 $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-79-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-82-
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl:83:$output = `$eslmask -rx 7 $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/easel/miniapps/esl-mask.itest.pl-84-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-83-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:84:$output = `$eslseqrange -h`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-85-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-89-if(-e "$tmppfx.fa.ssi") { unlink "$tmppfx.fa.ssi"; } # erase the index if it exists
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:90:$output = `$eslsfetch --index $tmppfx.fa 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-91-if ($? != 0) { die "FAIL: esl-sfetch --index failed unexpectedly"; }
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-92-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:93:$output = `$eslseqrange $tmppfx.fa 1 31 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-94-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-97-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:98:$output = `$eslseqrange $tmppfx.fa 1 31 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-99-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-101-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:102:$output = `$eslseqrange $tmppfx.fa 17 31 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-103-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-105-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:106:$output = `$eslseqrange $tmppfx.fa 1 13 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-107-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-109-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:110:$output = `$eslseqrange $tmppfx.fa 1 3 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-111-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-113-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:114:$output = `$eslseqrange $tmppfx.fa 2 3 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-115-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-117-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:118:$output = `$eslseqrange $tmppfx.fa 3 3 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-119-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-122-# test --informat
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:123:$output = `$eslseqrange --informat fasta $tmppfx.fa 3 3 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-124-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-127-# test cases we expect to fail
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:128:$output = `$eslseqrange $tmppfx.fa 1 32 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-129-if ($? == 0) { die "FAIL: esl-seqrange did not fail when expected"; }
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-130-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:131:$output = `$eslseqrange $tmppfx.fa 31 1 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-132-if ($? == 0) { die "FAIL: esl-seqrange did not fail when expected"; }
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-133-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:134:$output = `$eslseqrange $tmppfx.fa -1 1 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-135-if ($? == 0) { die "FAIL: esl-seqrange did not fail when expected"; }
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-136-
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl:137:$output = `$eslseqrange $tmppfx.fa 1 -1 2>&1`;
infernal-1.1.3/easel/miniapps/esl-seqrange.itest.pl-138-if ($? == 0) { die "FAIL: esl-seqrange did not fail when expected"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-344-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:345:$output = `$eslssdraw -h`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-346-if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-360-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:361: system("$eslssdraw $smallA[$pass] $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-362- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:363: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-364- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-368-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:369: system("$eslssdraw $smallA[$pass] -d $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-370- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:371: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-372- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-376-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:377: system("$eslssdraw $smallA[$pass] --prob $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-378- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:379: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-380- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-383-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:384: system("$eslssdraw $smallA[$pass] --ifreq $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-385- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:386: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-387- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-390-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:391: system("$eslssdraw $smallA[$pass] --iavglen $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-392- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:393: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-394- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-398-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:399: system("$eslssdraw $smallA[$pass] --dall $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-400- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:401: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-402- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-405-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:406: system("$eslssdraw $smallA[$pass] --dint $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-407- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:408: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-409- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-412-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:413: system("$eslssdraw $smallA[$pass] --mutinfo $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-414- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:415: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-416- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-419-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:420: system("$eslssdraw $smallA[$pass] --span $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-421- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:422: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-423- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-426-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:427: system("$eslssdraw $smallA[$pass] --span $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-428- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:429: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-430- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-433-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:434: system("$eslssdraw $smallA[$pass] --info --prob --ifreq --dall --dint --mutinfo --span --tabfile $tmppfx.tab $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-435- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:436: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-437- if($output !~ /setcmykcolor \(g\).+moveto show/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:438: $output = `cat $tmppfx.tab`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-439- if($output !~ /Information content data/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-453-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:454: system("$eslssdraw $smallA[$pass] --rf $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-455- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:456: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-457- if($output !~ /\(\*REFERENCE\* \(\"#=GC RF\"\)\) 212.49 418.24 moveto show/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-460- if($pass == 0) {
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:461: system("$eslssdraw $smallA[$pass] --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-462- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:463: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-464- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-474-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:475: system("$eslssdraw $smallA[$pass] --mask-col --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-476- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:477: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-478- if($output !~ /\%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.00\d* 1.00\d* 0.00\d* 0.00\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-479-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:480: system("$eslssdraw $smallA[$pass] --mask-diff $tmppfx.mask2 --mask-col --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-481- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:482: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-483- if($output !~ /\%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.00\d* 0.00\d* 0.00\d* 0.20\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-484-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:485: system("$eslssdraw $smallA[$pass] --mask-diff $tmppfx.mask2 --mask-col --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-486- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:487: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-488- if($output !~ /\%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.00\d* 0.00\d* 0.00\d* 0.20\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-489-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:490: system("$eslssdraw $smallA[$pass] --no-leg $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-491- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:492: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-493- if($output =~ /\(LEGEND\) 134.00 216.00 moveto show/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-494-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:495: system("$eslssdraw $smallA[$pass] --no-head $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-496- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:497: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-498- if($output =~ /\(tRNA 71 21\) 96.98 418.24 moveto show/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-499-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:500: system("$eslssdraw $smallA[$pass] --no-foot $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-501- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:502: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-503- if($output =~ /\(Created by 'esl-ssdraw'. Copyright \(C\) 2010 Howard Hughes Medical Institute.\) 12.00 12.00 moveto show/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-506- if($pass == 0) {
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:507: system("$eslssdraw $smallA[$pass] --no-pp --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-508- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:509: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-510- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-521-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:522: system("$eslssdraw $smallA[$pass] --no-bp --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-523- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:524: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-525- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-536-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:537: system("$eslssdraw $smallA[$pass] --no-ol --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-538- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:539: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-540- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-552- # NOTE: for --no-ntpp we don't actually check that residues are not drawn on PP diagrams
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:553: system("$eslssdraw $smallA[$pass] --no-ntpp --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-554- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:555: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-556- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-568-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:569: system("$eslssdraw $smallA[$pass] --no-cnt --info $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-570- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:571: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-572- if($output =~ /setcmykcolor (g)\s+168\.\d+\s+392\.\d+\s+moveto show/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-573-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:574: system("$eslssdraw $smallA[$pass] --cthresh 0.4 --info $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-575- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:576: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-577- if($output =~ /setcmykcolor (G)\s+168\.\d+\s+392\.\d+\s+moveto show/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-578-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:579: system("$eslssdraw $smallA[$pass] --cambig --info $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-580- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:581: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-582- if($output =~ /setcmykcolor (K)\s+168\.\d+\s+392\.\d+\s+moveto show/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-583-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:584: system("$eslssdraw $smallA[$pass] --cambig --cthresh 0.4 --info $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-585- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:586: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-587- if($output =~ /setcmykcolor (C)\s+168\.\d+\s+376\.\d+\s+moveto show/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-588-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:589: system("$eslssdraw $smallA[$pass] --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-590- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:591: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-592- if($output !~ /\%nucleotide 3\nnewpath\n 171.00 379.00 3.0 0 360 arc closepath\n 0.0\d*0 0.63\d* 1.0\d*0 0.0\d*0 setcmykcolor\n stroke/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-593-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:594: system("$eslssdraw $smallA[$pass] --mask-x --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-595- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:596: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-597- if($output !~ /stroke\n 175.00 375.00 moveto -8.0 8.0 rlineto closepath/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-598-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:599: system("$eslssdraw $smallA[$pass] --mask-u --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-600- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:601: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-602- if($output !~ /\%nucleotide 3\nnewpath\n 168.00 376.00 moveto 0 6.0 rlineto 6.0 0 rlineto 0 -6.0 rlineto closepath\n 0.00\d* 0.63\d* 1.00\d* 0.00\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-603-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:604: system("$eslssdraw $smallA[$pass] --mask-a --mask-x --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-605- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:606: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-607- if($output !~ /%nucleotide 3\nnewpath\n 0.00\d* 0.63\d* 1.00\d* 0.00\d* setcmykcolor\n 167.00 375.00 moveto 8.0 8.0 rlineto closepath\n stroke/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-608-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:609: system("$eslssdraw $smallA[$pass] --mask-a --mask-u --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-610- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:611: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-612- if($output !~ /\%nucleotide 3\nnewpath\n 168.50 376.50 moveto 0 5.0 rlineto 5.0 0 rlineto 0 -5.0 rlineto closepath\n 0.00\d* 0.63\d* 1.00\d* 0.00\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-613-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:614: system("$eslssdraw $smallA[$pass] --dfile $tmppfx.dfile $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:615: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-616- if($output !~ /%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.92\d* 0.84\d* 0.00\d* 0.08\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-617-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:618: system("$eslssdraw $smallA[$pass] --mask $tmppfx.mask1 --dfile $tmppfx.dfile $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:619: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-620- if($output !~ /%nucleotide 3\nnewpath\n 171.00 379.00 3.0 0 360 arc closepath\n 0.9200 0.8400 0.00\d* 0.0800 setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-621-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:622: system("$eslssdraw $smallA[$pass] --efile $tmppfx.efile $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:623: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-624- if($output !~ /\%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.03 0.17 0.20 0.14 setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-625-
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:626: system("$eslssdraw $smallA[$pass] --ifreq --ifile $tmppfx.ifile $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-627- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl:628: $output = `cat $tmppfx.ps`;
infernal-1.1.3/easel/miniapps/esl-ssdraw.itest.pl-629- if($output !~ /\%nucleotide 45\nnewpath\n 198.40 312.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.00\d* 0.94\d* 1.00\d* 0.00\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-28-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:29:$output = `$builddir/miniapps/esl-translate -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-30-if ($output !~ / coords=1\.\.192\s+length=64\s+frame=1/) { die "FAIL: standard genetic code mistranslated? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-32-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:33:$output = `$builddir/miniapps/esl-translate -c 3 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-34-if ($output !~ / coords=1\.\.195\s+length=65\s+frame=1/) { die "FAIL: yeast mito genetic code mistranslated? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-36-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:37:$output = `$builddir/miniapps/esl-translate -c 14 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-38-if ($output !~ / coords=1\.\.198\s+length=66\s+frame=1/) { die "FAIL: alt flatworm genetic code mistranslated? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-43-# Initiator is always M.
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:44:$output = `$builddir/miniapps/esl-translate -M -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-45-if ($output !~ / coords=1\.\.192\s+length=64\s+frame=1/) { die "FAIL: standard genetic code initiators mishandled w/ -M? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-47-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:48:$output = `$builddir/miniapps/esl-translate -M -c 3 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-49-if ($output !~ / coords=4\.\.195\s+length=64\s+frame=1/) { die "FAIL: yeast mito genetic code initiators mishandled w/ -M? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-51-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:52:$output = `$builddir/miniapps/esl-translate -M -c 14 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-53-if ($output !~ / coords=7\.\.198\s+length=64\s+frame=1/) { die "FAIL: alt flatworm genetic code initiators mishandled w/ -M? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-56-# Use only AUG initiator, -m option.
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:57:$output = `$builddir/miniapps/esl-translate -m -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-58-if ($output !~ / coords=7\.\.192\s+length=62\s+frame=1/) { die "FAIL: standard genetic code AUG starts mishandled w/ -m? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-60-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:61:$output = `$builddir/miniapps/esl-translate -m -c 3 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-62-if ($output !~ / coords=7\.\.195\s+length=63\s+frame=1/) { die "FAIL: yeast mito genetic code AUG starts mishandled w/ -m? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-64-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:65:$output = `$builddir/miniapps/esl-translate -m -c 14 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-66-if ($output !~ / coords=7\.\.198\s+length=64\s+frame=1/) { die "FAIL: alt flatworm genetic code AUG starts mishandled w/ -m? unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-86-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:87:$output = `$builddir/miniapps/esl-translate -l 25 --watson $tmppfx.fa`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-88-if ($output !~ / coords=4\.\.81\s+length=26\s+frame=1/) { die "FAIL: ambiguity codes mishandled by translation - unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-90-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:91:$output = `$builddir/miniapps/esl-translate -M -l 25 --watson $tmppfx.fa`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-92-if ($output !~ / coords=4\.\.81\s+length=26\s+frame=1/) { die "FAIL: ambiguity codes mishandled by translation - unexpected desc line"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-99-#
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:100:system("$builddir/miniapps/esl-shuffle -G --dna -N 2 -L 10000 > $tmppfx.fa");
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:101:$out1 = `$builddir/miniapps/esl-translate $tmppfx.fa`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:102:$out2 = `$builddir/miniapps/esl-translate -W $tmppfx.fa`;;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-103-if ($out1 ne $out2) { die "FAIL: default vs. windowed (-W) give different results"; }
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-108-#
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:109:system("$builddir/miniapps/esl-sfetch --index $tmppfx.fa > /dev/null");
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:110:@output = `$builddir/miniapps/esl-translate -l 100 $tmppfx.fa`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-111-foreach $line (@output)
##############################################
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-136-
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl:137: $out2 = `$builddir/miniapps/esl-sfetch -c $start..$end $tmppfx.fa $source | $builddir/miniapps/esl-translate -l $aalen -`;
infernal-1.1.3/easel/miniapps/esl-translate.itest.pl-138- if ($has_leading_stop) { $expected_start = 4; } else { $expected_start = 1; }
##############################################
infernal-1.1.3/easel/testsuite/coverage_report.pl-73- # one way to fail: there isn't a test driver at all
infernal-1.1.3/easel/testsuite/coverage_report.pl:74: `grep $flag $module`;
infernal-1.1.3/easel/testsuite/coverage_report.pl-75- if ($? != 0) { printf("%40s[NO DRIVER]\n", ""); push @nodriverlist, $module; next; }
##############################################
infernal-1.1.3/easel/testsuite/coverage_report.pl-81-
infernal-1.1.3/easel/testsuite/coverage_report.pl:82: `$top_builddir/$progname > /dev/null 2>&1`;
infernal-1.1.3/easel/testsuite/coverage_report.pl-83- if ($? != 0) { printf("%40s[UTEST FAILED ]\n", ""); next; };
##############################################
infernal-1.1.3/easel/testsuite/coverage_report.pl-85-
infernal-1.1.3/easel/testsuite/coverage_report.pl:86: $output = `(cd $top_builddir; gcov $basecfile)`;
infernal-1.1.3/easel/testsuite/coverage_report.pl-87- if ($output =~ /File.*$basecfile.*\nLines executed:\s*(\d+\.\d+)% of\s+(\d+)/) {
##############################################
infernal-1.1.3/easel/testsuite/coverage_report.pl-100- foreach $badmodule (@nodriverlist) {
infernal-1.1.3/easel/testsuite/coverage_report.pl:101: $output = `sloccount $badmodule`;
infernal-1.1.3/easel/testsuite/coverage_report.pl-102- if ($output =~ /ansic:\s+(\d+)/) { $nlines_nodrivers += $1; }
##############################################
infernal-1.1.3/easel/testsuite/e2.sh-13-
infernal-1.1.3/easel/testsuite/e2.sh:14:output=`cat $alifile | $prog - 2>&1 | head -n 1 | grep -c "^Format of seqfile - unrecognized."`
infernal-1.1.3/easel/testsuite/e2.sh-15-if test "$output" = 0
##############################################
infernal-1.1.3/easel/testsuite/e2.sh-20-
infernal-1.1.3/easel/testsuite/e2.sh:21:output=`cat $alifile | $prog --informat stockholm - 2>&1`
infernal-1.1.3/easel/testsuite/e2.sh-22-if test $? -gt 0
##############################################
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-45-# esl-reformat tests
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:46:system("$reformat fasta $tmppfx.dna > $tmppfx.out 2>&1"); if ($? != 0) { print "FAIL: reformat failed on .dna test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:47:system("diff $tmppfx.dna $tmppfx.out > /dev/null 2>&1"); if ($? != 0) { print "FAIL: reformat changed .dna test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-48-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:49:system("$reformat fasta $tmppfx.aa > $tmppfx.out 2>&1"); if ($? != 0) { print "FAIL: reformat failed on .aa test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:50:system("diff $tmppfx.aa $tmppfx.out > /dev/null 2>&1"); if ($? != 0) { print "FAIL: reformat changed .aa test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-51-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:52:$output = `$reformat fasta $tmppfx.bad 2>&1`; if ($? == 0) { print "FAIL: reformat should have failed on .bad test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-53-if (! $output =~ /Illegal character %/) { print "FAIL: reformat should have found illegal % in .bad test\n"; exit 1; }
##############################################
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-55-# esl-seqstat tests
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:56:$output = `$seqstat --dna $tmppfx.dna 2>&1`; if ($? != 0) { print "FAIL: seqstat failed on .dna test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-57-($n) = $output =~ /Total # residues:\s+(\d+)/; if ($n != 32) { print "FAIL: seqstat sees wrong residue count ($n) in .dna test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-58-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:59:$output = `$seqstat $tmppfx.aa 2>&1`; if ($? != 0) { print "FAIL: seqstat failed on .aa test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-60-($n) = $output =~ /Total # residues:\s+(\d+)/; if ($n != 53) { print "FAIL: seqstat sees wrong residue count ($n) in .aa test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-61-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:62:$output = `$seqstat $tmppfx.bad 2>&1`; if ($? == 0) { print "FAIL: seqstat should have failed on .bad test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-63-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-64-# esl-shuffle tests
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:65:system("$shuffle $tmppfx.dna > $tmppfx.out 2>&1"); if ($? != 0) { print "FAIL: shuffle failed on .dna test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:66:system("$seqstat --dna -c $tmppfx.out > $tmppfx.out2 2>&1"); if ($? != 0) { print "FAIL: seqstat -c failed on shuffled .dna\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:67:system("$seqstat --dna -c $tmppfx.dna > $tmppfx.out3 2>&1"); if ($? != 0) { print "FAIL: seqstat -c failed on .dna test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:68:system("diff $tmppfx.out2 $tmppfx.out3 > /dev/null 2>&1"); if ($? != 0) { print "FAIL: shuffle changed .dna composition\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-69-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:70:system("$shuffle $tmppfx.aa > $tmppfx.out 2>&1"); if ($? != 0) { print "FAIL: shuffle failed on .aa test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:71:system("$seqstat -c $tmppfx.out > $tmppfx.out2 2>&1"); if ($? != 0) { print "FAIL: seqstat -c failed on shuffled .aa\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:72:system("$seqstat -c $tmppfx.aa > $tmppfx.out3 2>&1"); if ($? != 0) { print "FAIL: seqstat -c failed on .aa test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:73:system("diff $tmppfx.out2 $tmppfx.out3 > /dev/null 2>&1"); if ($? != 0) { print "FAIL: shuffle changed .aa composition\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-74-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:75:$output = `$shuffle $tmppfx.bad 2>&1`; if ($? == 0) { print "FAIL: shuffle should have failed on .bad test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-76-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-77-# esl-sfetch tests
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:78:system("$sfetch --index $tmppfx.aa >/dev/null 2>&1"); if ($? != 0) { print "FAIL: sfetch --index failed on .aa test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:79:$output = `$sfetch -c 27..27 $tmppfx.aa test 2>&1 | grep -v "^>"`; if ($? != 0) { print "FAIL: sfetch failed on .aa test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-80-if (! $output =~ /^\*/) { print "FAIL: sfetch didn't retrieve * on .aa test ($output)\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-81-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:82:system("$sfetch --index $tmppfx.dna >/dev/null 2>&1"); if ($? != 0) { print "FAIL: sfetch --index failed on .dna test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:83:$output = `$sfetch -c 16..16 $tmppfx.aa test 2>&1 | grep -v "^>"`; if ($? != 0) { print "FAIL: sfetch failed on .dna test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-84-if (! $output =~ /^\*/) { print "FAIL: sfetch didn't retrieve * on .dna test ($output)\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-85-
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl:86:$output = `$sfetch --index $tmppfx.bad 2>&1`; if ($? == 0) { print "FAIL: sfetch --index should have failed on .bad test\n"; exit 1; }
infernal-1.1.3/easel/testsuite/i1-degen-residues.pl-87-
##############################################
infernal-1.1.3/easel/testsuite/i2-ncbi-indices.pl-35-#
infernal-1.1.3/easel/testsuite/i2-ncbi-indices.pl:36:$output = `$top_builddir/miniapps/esl-seqstat -a $tmppfx.fa 2>&1`;
infernal-1.1.3/easel/testsuite/i2-ncbi-indices.pl-37-if ($? != 0) { die "FAIL: esl-seqstat fails to read BLAST-formatted FASTA file\n"; }
##############################################
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl-76-
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl:77:$output = `$builddir/miniapps/esl-reformat stockholm $tmppfx.sto1 2>&1`;
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl-78-if ($? == 0) { die "FAIL: blank AC,DE lines should be invalid Stockholm format (bug #e5) (1)\n"; }
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl-79-
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl:80:$output = `$builddir/miniapps/esl-reformat stockholm $tmppfx.sto2 2>&1`;
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl-81-if ($? == 0) { die "FAIL: blank AC,DE lines should be invalid Stockholm format (bug #e5) (2)\n"; }
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl-82-
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl:83:$output = `$builddir/miniapps/esl-reformat stockholm $tmppfx.sto3`;
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl-84-if ($? != 0) { die "FAIL: blank CC line should be valid Stockholm format (1)\n"; }
##############################################
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl-86-
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl:87:$output = `$builddir/miniapps/esl-reformat stockholm $tmppfx.sto4`;
infernal-1.1.3/easel/testsuite/i3-blank-gf.pl-88-if ($? != 0) { die "FAIL: blank CC line should be valid Stockholm format (2)\n"; }
##############################################
infernal-1.1.3/easel/testsuite/valgrind_report.pl-55- # one way to fail: there isn't a test driver at all
infernal-1.1.3/easel/testsuite/valgrind_report.pl:56: `grep $flag $module`;
infernal-1.1.3/easel/testsuite/valgrind_report.pl-57- if ($? != 0) { printf(" [NO DRIVER]\n"); next; }
##############################################
infernal-1.1.3/easel/testsuite/valgrind_report.pl-64-
infernal-1.1.3/easel/testsuite/valgrind_report.pl:65: $output = `valgrind $top_builddir/$progname 2>&1`;
infernal-1.1.3/easel/testsuite/valgrind_report.pl-66- if ($? != 0) { printf(" [VALGRIND FAILED]\n"); next; };
##############################################
infernal-1.1.3/easel/config.guess-34-
infernal-1.1.3/easel/config.guess:35:me=`echo "$0" | sed -e 's,.*/,,'`
infernal-1.1.3/easel/config.guess-36-
##############################################
infernal-1.1.3/easel/config.guess-102-: ${TMPDIR=/tmp} ;
infernal-1.1.3/easel/config.guess:103: { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
infernal-1.1.3/easel/config.guess-104- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
##############################################
infernal-1.1.3/easel/config.guess-151- EOF
infernal-1.1.3/easel/config.guess:152: eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`"
infernal-1.1.3/easel/config.guess-153-
##############################################
infernal-1.1.3/easel/config.guess-188- earmv*)
infernal-1.1.3/easel/config.guess:189: arch=`echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
infernal-1.1.3/easel/config.guess:190: endian=`echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p'`
infernal-1.1.3/easel/config.guess-191- machine="${arch}${endian}"-unknown
##############################################
infernal-1.1.3/easel/config.guess-220- expr='s/^earmv[0-9]/-eabi/;s/eb$//'
infernal-1.1.3/easel/config.guess:221: abi=`echo "$UNAME_MACHINE_ARCH" | sed -e "$expr"`
infernal-1.1.3/easel/config.guess-222- ;;
##############################################
infernal-1.1.3/easel/config.guess-233- *)
infernal-1.1.3/easel/config.guess:234: release=`echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2`
infernal-1.1.3/easel/config.guess-235- ;;
##############################################
infernal-1.1.3/easel/config.guess-280- *4.0)
infernal-1.1.3/easel/config.guess:281: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
infernal-1.1.3/easel/config.guess-282- ;;
infernal-1.1.3/easel/config.guess-283- *5.*)
infernal-1.1.3/easel/config.guess:284: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
infernal-1.1.3/easel/config.guess-285- ;;
##############################################
infernal-1.1.3/easel/config.guess-290- # types through head -n 1, so we only detect the type of CPU 0.
infernal-1.1.3/easel/config.guess:291: ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
infernal-1.1.3/easel/config.guess-292- case "$ALPHA_CPU_TYPE" in
##############################################
infernal-1.1.3/easel/config.guess-328- # 1.2 uses "1.2" for uname -r.
infernal-1.1.3/easel/config.guess:329: echo "$UNAME_MACHINE"-dec-osf"`echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`"
infernal-1.1.3/easel/config.guess-330- # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
##############################################
infernal-1.1.3/easel/config.guess-379- s390x:SunOS:*:*)
infernal-1.1.3/easel/config.guess:380: echo "$UNAME_MACHINE"-ibm-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
infernal-1.1.3/easel/config.guess-381- exit ;;
infernal-1.1.3/easel/config.guess-382- sun4H:SunOS:5.*:*)
infernal-1.1.3/easel/config.guess:383: echo sparc-hal-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/easel/config.guess-384- exit ;;
infernal-1.1.3/easel/config.guess-385- sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
infernal-1.1.3/easel/config.guess:386: echo sparc-sun-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
infernal-1.1.3/easel/config.guess-387- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-404- fi
infernal-1.1.3/easel/config.guess:405: echo "$SUN_ARCH"-pc-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/easel/config.guess-406- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-410- # it's likely to be more like Solaris than SunOS4.
infernal-1.1.3/easel/config.guess:411: echo sparc-sun-solaris3"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/easel/config.guess-412- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-419- # Japanese Language versions have a version number like `4.1.3-JL'.
infernal-1.1.3/easel/config.guess:420: echo sparc-sun-sunos"`echo "$UNAME_RELEASE"|sed -e 's/-/_/'`"
infernal-1.1.3/easel/config.guess-421- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-425- sun*:*:4.2BSD:*)
infernal-1.1.3/easel/config.guess:426: UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
infernal-1.1.3/easel/config.guess-427- test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3
##############################################
infernal-1.1.3/easel/config.guess-507- $CC_FOR_BUILD -o "$dummy" "$dummy.c" &&
infernal-1.1.3/easel/config.guess:508: dummyarg=`echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p'` &&
infernal-1.1.3/easel/config.guess:509: SYSTEM_NAME=`"$dummy" "$dummyarg"` &&
infernal-1.1.3/easel/config.guess-510- { echo "$SYSTEM_NAME"; exit; }
##############################################
infernal-1.1.3/easel/config.guess-563- *:IRIX*:*:*)
infernal-1.1.3/easel/config.guess:564: echo mips-sgi-irix"`echo "$UNAME_RELEASE"|sed -e 's/-/_/g'`"
infernal-1.1.3/easel/config.guess-565- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-593-EOF
infernal-1.1.3/easel/config.guess:594: if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"`
infernal-1.1.3/easel/config.guess-595- then
##############################################
infernal-1.1.3/easel/config.guess-606- *:AIX:*:[4567])
infernal-1.1.3/easel/config.guess:607: IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
infernal-1.1.3/easel/config.guess-608- if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then
##############################################
infernal-1.1.3/easel/config.guess-642- 9000/[34678]??:HP-UX:*:*)
infernal-1.1.3/easel/config.guess:643: HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
infernal-1.1.3/easel/config.guess-644- case "$UNAME_MACHINE" in
##############################################
infernal-1.1.3/easel/config.guess-696-EOF
infernal-1.1.3/easel/config.guess:697: (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"`
infernal-1.1.3/easel/config.guess-698- test -z "$HP_ARCH" && HP_ARCH=hppa
##############################################
infernal-1.1.3/easel/config.guess-724- ia64:HP-UX:*:*)
infernal-1.1.3/easel/config.guess:725: HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
infernal-1.1.3/easel/config.guess-726- echo ia64-hp-hpux"$HPUX_REV"
##############################################
infernal-1.1.3/easel/config.guess-754-EOF
infernal-1.1.3/easel/config.guess:755: $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` &&
infernal-1.1.3/easel/config.guess-756- { echo "$SYSTEM_NAME"; exit; }
##############################################
infernal-1.1.3/easel/config.guess-825- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
infernal-1.1.3/easel/config.guess:826: FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'`
infernal-1.1.3/easel/config.guess-827- echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
infernal-1.1.3/easel/config.guess-830- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
infernal-1.1.3/easel/config.guess:831: FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
infernal-1.1.3/easel/config.guess-832- echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
infernal-1.1.3/easel/config.guess-850- esac
infernal-1.1.3/easel/config.guess:851: echo "$UNAME_PROCESSOR"-unknown-freebsd"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
infernal-1.1.3/easel/config.guess-852- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-886- prep*:SunOS:5.*:*)
infernal-1.1.3/easel/config.guess:887: echo powerpcle-unknown-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/easel/config.guess-888- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-890- # the GNU system
infernal-1.1.3/easel/config.guess:891: echo "`echo "$UNAME_MACHINE"|sed -e 's,[-/].*$,,'`-unknown-$LIBC`echo "$UNAME_RELEASE"|sed -e 's,/.*$,,'`"
infernal-1.1.3/easel/config.guess-892- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-894- # other systems with GNU libc and userland
infernal-1.1.3/easel/config.guess:895: echo "$UNAME_MACHINE-unknown-`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"``echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`-$LIBC"
infernal-1.1.3/easel/config.guess-896- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-988-EOF
infernal-1.1.3/easel/config.guess:989: eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU'`"
infernal-1.1.3/easel/config.guess-990- test "x$CPU" != x && { echo "$CPU-unknown-linux-$LIBC"; exit; }
##############################################
infernal-1.1.3/easel/config.guess-1088- i*86:*:4.*:*)
infernal-1.1.3/easel/config.guess:1089: UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'`
infernal-1.1.3/easel/config.guess-1090- if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
##############################################
infernal-1.1.3/easel/config.guess-1291- fi
infernal-1.1.3/easel/config.guess:1292: if test "`echo "$UNAME_RELEASE" | sed -e 's/\..*//'`" -le 10 ; then
infernal-1.1.3/easel/config.guess-1293- if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
##############################################
infernal-1.1.3/easel/config.guess-1389- *:DragonFly:*:*)
infernal-1.1.3/easel/config.guess:1390: echo "$UNAME_MACHINE"-unknown-dragonfly"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
infernal-1.1.3/easel/config.guess-1391- exit ;;
##############################################
infernal-1.1.3/easel/config.guess-1402- i*86:skyos:*:*)
infernal-1.1.3/easel/config.guess:1403: echo "$UNAME_MACHINE"-pc-skyos"`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'`"
infernal-1.1.3/easel/config.guess-1404- exit ;;
##############################################
infernal-1.1.3/easel/config.sub-52-
infernal-1.1.3/easel/config.sub:53:me=`echo "$0" | sed -e 's,.*/,,'`
infernal-1.1.3/easel/config.sub-54-
##############################################
infernal-1.1.3/easel/config.sub-114-# Here we must recognize all the valid KERNEL-OS combinations.
infernal-1.1.3/easel/config.sub:115:maybe_os=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
infernal-1.1.3/easel/config.sub-116-case $maybe_os in
##############################################
infernal-1.1.3/easel/config.sub-122- os=-$maybe_os
infernal-1.1.3/easel/config.sub:123: basic_machine=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
infernal-1.1.3/easel/config.sub-124- ;;
##############################################
infernal-1.1.3/easel/config.sub-126- os=-linux-android
infernal-1.1.3/easel/config.sub:127: basic_machine=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
infernal-1.1.3/easel/config.sub-128- ;;
infernal-1.1.3/easel/config.sub-129- *)
infernal-1.1.3/easel/config.sub:130: basic_machine=`echo "$1" | sed 's/-[^-]*$//'`
infernal-1.1.3/easel/config.sub-131- if [ "$basic_machine" != "$1" ]
infernal-1.1.3/easel/config.sub:132: then os=`echo "$1" | sed 's/.*-/-/'`
infernal-1.1.3/easel/config.sub-133- else os=; fi
##############################################
infernal-1.1.3/easel/config.sub-180- os=-sco5v6
infernal-1.1.3/easel/config.sub:181: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-182- ;;
##############################################
infernal-1.1.3/easel/config.sub-184- os=-sco3.2v5
infernal-1.1.3/easel/config.sub:185: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-186- ;;
##############################################
infernal-1.1.3/easel/config.sub-188- os=-sco3.2v4
infernal-1.1.3/easel/config.sub:189: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-190- ;;
infernal-1.1.3/easel/config.sub-191- -sco3.2.[4-9]*)
infernal-1.1.3/easel/config.sub:192: os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
infernal-1.1.3/easel/config.sub:193: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-194- ;;
##############################################
infernal-1.1.3/easel/config.sub-196- # Don't forget version if it is 3.2v4 or newer.
infernal-1.1.3/easel/config.sub:197: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-198- ;;
##############################################
infernal-1.1.3/easel/config.sub-200- # Don't forget version if it is 3.2v4 or newer.
infernal-1.1.3/easel/config.sub:201: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-202- ;;
##############################################
infernal-1.1.3/easel/config.sub-204- os=-sco3.2v2
infernal-1.1.3/easel/config.sub:205: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-206- ;;
infernal-1.1.3/easel/config.sub-207- -udk*)
infernal-1.1.3/easel/config.sub:208: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-209- ;;
##############################################
infernal-1.1.3/easel/config.sub-211- os=-isc2.2
infernal-1.1.3/easel/config.sub:212: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-213- ;;
##############################################
infernal-1.1.3/easel/config.sub-217- -isc*)
infernal-1.1.3/easel/config.sub:218: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/easel/config.sub-219- ;;
##############################################
infernal-1.1.3/easel/config.sub-229- -ptx*)
infernal-1.1.3/easel/config.sub:230: basic_machine=`echo "$1" | sed -e 's/86-.*/86-sequent/'`
infernal-1.1.3/easel/config.sub-231- ;;
##############################################
infernal-1.1.3/easel/config.sub-364- *-*-*)
infernal-1.1.3/easel/config.sub:365: echo Invalid configuration \`"$1"\': machine \`"$basic_machine"\' not recognized 1>&2
infernal-1.1.3/easel/config.sub-366- exit 1
##############################################
infernal-1.1.3/easel/config.sub-493- amd64-*)
infernal-1.1.3/easel/config.sub:494: basic_machine=x86_64-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-495- ;;
##############################################
infernal-1.1.3/easel/config.sub-538- blackfin-*)
infernal-1.1.3/easel/config.sub:539: basic_machine=bfin-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-540- os=-linux
##############################################
infernal-1.1.3/easel/config.sub-546- c54x-*)
infernal-1.1.3/easel/config.sub:547: basic_machine=tic54x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-548- ;;
infernal-1.1.3/easel/config.sub-549- c55x-*)
infernal-1.1.3/easel/config.sub:550: basic_machine=tic55x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-551- ;;
infernal-1.1.3/easel/config.sub-552- c6x-*)
infernal-1.1.3/easel/config.sub:553: basic_machine=tic6x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-554- ;;
##############################################
infernal-1.1.3/easel/config.sub-650- e500v[12]-*)
infernal-1.1.3/easel/config.sub:651: basic_machine=powerpc-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-652- os=$os"spe"
##############################################
infernal-1.1.3/easel/config.sub-754- i*86v32)
infernal-1.1.3/easel/config.sub:755: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/easel/config.sub-756- os=-sysv32
##############################################
infernal-1.1.3/easel/config.sub-758- i*86v4*)
infernal-1.1.3/easel/config.sub:759: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/easel/config.sub-760- os=-sysv4
##############################################
infernal-1.1.3/easel/config.sub-762- i*86v)
infernal-1.1.3/easel/config.sub:763: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/easel/config.sub-764- os=-sysv
##############################################
infernal-1.1.3/easel/config.sub-766- i*86sol2)
infernal-1.1.3/easel/config.sub:767: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/easel/config.sub-768- os=-solaris2
##############################################
infernal-1.1.3/easel/config.sub-792- leon-*|leon[3-9]-*)
infernal-1.1.3/easel/config.sub:793: basic_machine=sparc-`echo "$basic_machine" | sed 's/-.*//'`
infernal-1.1.3/easel/config.sub-794- ;;
##############################################
infernal-1.1.3/easel/config.sub-799- m68knommu-*)
infernal-1.1.3/easel/config.sub:800: basic_machine=m68k-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-801- os=-linux
##############################################
infernal-1.1.3/easel/config.sub-833- mips3*-*)
infernal-1.1.3/easel/config.sub:834: basic_machine=`echo "$basic_machine" | sed -e 's/mips3/mips64/'`
infernal-1.1.3/easel/config.sub-835- ;;
infernal-1.1.3/easel/config.sub-836- mips3*)
infernal-1.1.3/easel/config.sub:837: basic_machine=`echo "$basic_machine" | sed -e 's/mips3/mips64/'`-unknown
infernal-1.1.3/easel/config.sub-838- ;;
##############################################
infernal-1.1.3/easel/config.sub-855- ms1-*)
infernal-1.1.3/easel/config.sub:856: basic_machine=`echo "$basic_machine" | sed -e 's/ms1-/mt-/'`
infernal-1.1.3/easel/config.sub-857- ;;
##############################################
infernal-1.1.3/easel/config.sub-980- parisc-*)
infernal-1.1.3/easel/config.sub:981: basic_machine=hppa-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-982- os=-linux
##############################################
infernal-1.1.3/easel/config.sub-996- pc98-*)
infernal-1.1.3/easel/config.sub:997: basic_machine=i386-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-998- ;;
##############################################
infernal-1.1.3/easel/config.sub-1011- pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
infernal-1.1.3/easel/config.sub:1012: basic_machine=i586-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1013- ;;
infernal-1.1.3/easel/config.sub-1014- pentiumpro-* | p6-* | 6x86-* | athlon-*)
infernal-1.1.3/easel/config.sub:1015: basic_machine=i686-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1016- ;;
infernal-1.1.3/easel/config.sub-1017- pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
infernal-1.1.3/easel/config.sub:1018: basic_machine=i686-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1019- ;;
infernal-1.1.3/easel/config.sub-1020- pentium4-*)
infernal-1.1.3/easel/config.sub:1021: basic_machine=i786-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1022- ;;
##############################################
infernal-1.1.3/easel/config.sub-1030- ppc-* | ppcbe-*)
infernal-1.1.3/easel/config.sub:1031: basic_machine=powerpc-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1032- ;;
##############################################
infernal-1.1.3/easel/config.sub-1036- ppcle-* | powerpclittle-*)
infernal-1.1.3/easel/config.sub:1037: basic_machine=powerpcle-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1038- ;;
##############################################
infernal-1.1.3/easel/config.sub-1040- ;;
infernal-1.1.3/easel/config.sub:1041: ppc64-*) basic_machine=powerpc64-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1042- ;;
##############################################
infernal-1.1.3/easel/config.sub-1046- ppc64le-* | powerpc64little-*)
infernal-1.1.3/easel/config.sub:1047: basic_machine=powerpc64le-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1048- ;;
##############################################
infernal-1.1.3/easel/config.sub-1122- strongarm-* | thumb-*)
infernal-1.1.3/easel/config.sub:1123: basic_machine=arm-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/easel/config.sub-1124- ;;
##############################################
infernal-1.1.3/easel/config.sub-1255- xscale-* | xscalee[bl]-*)
infernal-1.1.3/easel/config.sub:1256: basic_machine=`echo "$basic_machine" | sed 's/^xscale/arm/'`
infernal-1.1.3/easel/config.sub-1257- ;;
##############################################
infernal-1.1.3/easel/config.sub-1317- *)
infernal-1.1.3/easel/config.sub:1318: echo Invalid configuration \`"$1"\': machine \`"$basic_machine"\' not recognized 1>&2
infernal-1.1.3/easel/config.sub-1319- exit 1
##############################################
infernal-1.1.3/easel/config.sub-1325- *-digital*)
infernal-1.1.3/easel/config.sub:1326: basic_machine=`echo "$basic_machine" | sed 's/digital.*/dec/'`
infernal-1.1.3/easel/config.sub-1327- ;;
infernal-1.1.3/easel/config.sub-1328- *-commodore*)
infernal-1.1.3/easel/config.sub:1329: basic_machine=`echo "$basic_machine" | sed 's/commodore.*/cbm/'`
infernal-1.1.3/easel/config.sub-1330- ;;
##############################################
infernal-1.1.3/easel/config.sub-1346- -solaris1 | -solaris1.*)
infernal-1.1.3/easel/config.sub:1347: os=`echo $os | sed -e 's|solaris1|sunos4|'`
infernal-1.1.3/easel/config.sub-1348- ;;
##############################################
infernal-1.1.3/easel/config.sub-1355- -gnu/linux*)
infernal-1.1.3/easel/config.sub:1356: os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
infernal-1.1.3/easel/config.sub-1357- ;;
##############################################
infernal-1.1.3/easel/config.sub-1407- -nto*)
infernal-1.1.3/easel/config.sub:1408: os=`echo $os | sed -e 's|nto|nto-qnx|'`
infernal-1.1.3/easel/config.sub-1409- ;;
##############################################
infernal-1.1.3/easel/config.sub-1414- -mac*)
infernal-1.1.3/easel/config.sub:1415: os=`echo "$os" | sed -e 's|mac|macos|'`
infernal-1.1.3/easel/config.sub-1416- ;;
##############################################
infernal-1.1.3/easel/config.sub-1420- -linux*)
infernal-1.1.3/easel/config.sub:1421: os=`echo $os | sed -e 's|linux|linux-gnu|'`
infernal-1.1.3/easel/config.sub-1422- ;;
infernal-1.1.3/easel/config.sub-1423- -sunos5*)
infernal-1.1.3/easel/config.sub:1424: os=`echo "$os" | sed -e 's|sunos5|solaris2|'`
infernal-1.1.3/easel/config.sub-1425- ;;
infernal-1.1.3/easel/config.sub-1426- -sunos6*)
infernal-1.1.3/easel/config.sub:1427: os=`echo "$os" | sed -e 's|sunos6|solaris3|'`
infernal-1.1.3/easel/config.sub-1428- ;;
##############################################
infernal-1.1.3/easel/config.sub-1469- -sinix5.*)
infernal-1.1.3/easel/config.sub:1470: os=`echo $os | sed -e 's|sinix|sysv|'`
infernal-1.1.3/easel/config.sub-1471- ;;
##############################################
infernal-1.1.3/easel/config.sub-1528- # Get rid of the `-' at the beginning of $os.
infernal-1.1.3/easel/config.sub:1529: os=`echo $os | sed 's/[^-]*-//'`
infernal-1.1.3/easel/config.sub:1530: echo Invalid configuration \`"$1"\': system \`"$os"\' not recognized 1>&2
infernal-1.1.3/easel/config.sub-1531- exit 1
##############################################
infernal-1.1.3/easel/config.sub-1788- esac
infernal-1.1.3/easel/config.sub:1789: basic_machine=`echo "$basic_machine" | sed "s/unknown/$vendor/"`
infernal-1.1.3/easel/config.sub-1790- ;;
##############################################
infernal-1.1.3/easel/Makefile.in-567-${ALL_UTESTS}: libeasel.a
infernal-1.1.3/easel/Makefile.in:568: @BASENAME=`echo $@ | sed -e 's/_utest//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/easel/Makefile.in:569: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/easel/Makefile.in-570- DFLAG=esl$${DFLAG}_TESTDRIVE ;\
##############################################
infernal-1.1.3/easel/Makefile.in-581-${ALL_BENCHMARKS}: libeasel.a
infernal-1.1.3/easel/Makefile.in:582: @BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/easel/Makefile.in:583: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/easel/Makefile.in-584- DFLAG=esl$${DFLAG}_BENCHMARK ;\
##############################################
infernal-1.1.3/easel/Makefile.in-595-${ALL_EXPERIMENTS}: libeasel.a
infernal-1.1.3/easel/Makefile.in:596: @BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/easel/Makefile.in:597: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/easel/Makefile.in-598- DFLAG=esl$${DFLAG}_EXPERIMENT ;\
##############################################
infernal-1.1.3/easel/Makefile.in-609-${ALL_EXAMPLES}: libeasel.a
infernal-1.1.3/easel/Makefile.in:610: @BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/easel/Makefile.in:611: DFLAG=esl`echo $@ | sed -e 's/^esl_//' | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/easel/Makefile.in-612- if test $@ = "easel_example"; \
##############################################
infernal-1.1.3/hmmer/config.guess-34-
infernal-1.1.3/hmmer/config.guess:35:me=`echo "$0" | sed -e 's,.*/,,'`
infernal-1.1.3/hmmer/config.guess-36-
##############################################
infernal-1.1.3/hmmer/config.guess-102-: ${TMPDIR=/tmp} ;
infernal-1.1.3/hmmer/config.guess:103: { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
infernal-1.1.3/hmmer/config.guess-104- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
##############################################
infernal-1.1.3/hmmer/config.guess-151- EOF
infernal-1.1.3/hmmer/config.guess:152: eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`"
infernal-1.1.3/hmmer/config.guess-153-
##############################################
infernal-1.1.3/hmmer/config.guess-188- earmv*)
infernal-1.1.3/hmmer/config.guess:189: arch=`echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
infernal-1.1.3/hmmer/config.guess:190: endian=`echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p'`
infernal-1.1.3/hmmer/config.guess-191- machine="${arch}${endian}"-unknown
##############################################
infernal-1.1.3/hmmer/config.guess-220- expr='s/^earmv[0-9]/-eabi/;s/eb$//'
infernal-1.1.3/hmmer/config.guess:221: abi=`echo "$UNAME_MACHINE_ARCH" | sed -e "$expr"`
infernal-1.1.3/hmmer/config.guess-222- ;;
##############################################
infernal-1.1.3/hmmer/config.guess-233- *)
infernal-1.1.3/hmmer/config.guess:234: release=`echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2`
infernal-1.1.3/hmmer/config.guess-235- ;;
##############################################
infernal-1.1.3/hmmer/config.guess-280- *4.0)
infernal-1.1.3/hmmer/config.guess:281: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
infernal-1.1.3/hmmer/config.guess-282- ;;
infernal-1.1.3/hmmer/config.guess-283- *5.*)
infernal-1.1.3/hmmer/config.guess:284: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
infernal-1.1.3/hmmer/config.guess-285- ;;
##############################################
infernal-1.1.3/hmmer/config.guess-290- # types through head -n 1, so we only detect the type of CPU 0.
infernal-1.1.3/hmmer/config.guess:291: ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
infernal-1.1.3/hmmer/config.guess-292- case "$ALPHA_CPU_TYPE" in
##############################################
infernal-1.1.3/hmmer/config.guess-328- # 1.2 uses "1.2" for uname -r.
infernal-1.1.3/hmmer/config.guess:329: echo "$UNAME_MACHINE"-dec-osf"`echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`"
infernal-1.1.3/hmmer/config.guess-330- # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
##############################################
infernal-1.1.3/hmmer/config.guess-379- s390x:SunOS:*:*)
infernal-1.1.3/hmmer/config.guess:380: echo "$UNAME_MACHINE"-ibm-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/config.guess-381- exit ;;
infernal-1.1.3/hmmer/config.guess-382- sun4H:SunOS:5.*:*)
infernal-1.1.3/hmmer/config.guess:383: echo sparc-hal-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/config.guess-384- exit ;;
infernal-1.1.3/hmmer/config.guess-385- sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
infernal-1.1.3/hmmer/config.guess:386: echo sparc-sun-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/config.guess-387- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-404- fi
infernal-1.1.3/hmmer/config.guess:405: echo "$SUN_ARCH"-pc-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/config.guess-406- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-410- # it's likely to be more like Solaris than SunOS4.
infernal-1.1.3/hmmer/config.guess:411: echo sparc-sun-solaris3"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/config.guess-412- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-419- # Japanese Language versions have a version number like `4.1.3-JL'.
infernal-1.1.3/hmmer/config.guess:420: echo sparc-sun-sunos"`echo "$UNAME_RELEASE"|sed -e 's/-/_/'`"
infernal-1.1.3/hmmer/config.guess-421- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-425- sun*:*:4.2BSD:*)
infernal-1.1.3/hmmer/config.guess:426: UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
infernal-1.1.3/hmmer/config.guess-427- test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3
##############################################
infernal-1.1.3/hmmer/config.guess-507- $CC_FOR_BUILD -o "$dummy" "$dummy.c" &&
infernal-1.1.3/hmmer/config.guess:508: dummyarg=`echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p'` &&
infernal-1.1.3/hmmer/config.guess:509: SYSTEM_NAME=`"$dummy" "$dummyarg"` &&
infernal-1.1.3/hmmer/config.guess-510- { echo "$SYSTEM_NAME"; exit; }
##############################################
infernal-1.1.3/hmmer/config.guess-563- *:IRIX*:*:*)
infernal-1.1.3/hmmer/config.guess:564: echo mips-sgi-irix"`echo "$UNAME_RELEASE"|sed -e 's/-/_/g'`"
infernal-1.1.3/hmmer/config.guess-565- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-593-EOF
infernal-1.1.3/hmmer/config.guess:594: if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"`
infernal-1.1.3/hmmer/config.guess-595- then
##############################################
infernal-1.1.3/hmmer/config.guess-606- *:AIX:*:[4567])
infernal-1.1.3/hmmer/config.guess:607: IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
infernal-1.1.3/hmmer/config.guess-608- if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then
##############################################
infernal-1.1.3/hmmer/config.guess-642- 9000/[34678]??:HP-UX:*:*)
infernal-1.1.3/hmmer/config.guess:643: HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
infernal-1.1.3/hmmer/config.guess-644- case "$UNAME_MACHINE" in
##############################################
infernal-1.1.3/hmmer/config.guess-696-EOF
infernal-1.1.3/hmmer/config.guess:697: (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"`
infernal-1.1.3/hmmer/config.guess-698- test -z "$HP_ARCH" && HP_ARCH=hppa
##############################################
infernal-1.1.3/hmmer/config.guess-724- ia64:HP-UX:*:*)
infernal-1.1.3/hmmer/config.guess:725: HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
infernal-1.1.3/hmmer/config.guess-726- echo ia64-hp-hpux"$HPUX_REV"
##############################################
infernal-1.1.3/hmmer/config.guess-754-EOF
infernal-1.1.3/hmmer/config.guess:755: $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` &&
infernal-1.1.3/hmmer/config.guess-756- { echo "$SYSTEM_NAME"; exit; }
##############################################
infernal-1.1.3/hmmer/config.guess-825- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
infernal-1.1.3/hmmer/config.guess:826: FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'`
infernal-1.1.3/hmmer/config.guess-827- echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
infernal-1.1.3/hmmer/config.guess-830- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
infernal-1.1.3/hmmer/config.guess:831: FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
infernal-1.1.3/hmmer/config.guess-832- echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
infernal-1.1.3/hmmer/config.guess-850- esac
infernal-1.1.3/hmmer/config.guess:851: echo "$UNAME_PROCESSOR"-unknown-freebsd"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
infernal-1.1.3/hmmer/config.guess-852- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-886- prep*:SunOS:5.*:*)
infernal-1.1.3/hmmer/config.guess:887: echo powerpcle-unknown-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/config.guess-888- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-890- # the GNU system
infernal-1.1.3/hmmer/config.guess:891: echo "`echo "$UNAME_MACHINE"|sed -e 's,[-/].*$,,'`-unknown-$LIBC`echo "$UNAME_RELEASE"|sed -e 's,/.*$,,'`"
infernal-1.1.3/hmmer/config.guess-892- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-894- # other systems with GNU libc and userland
infernal-1.1.3/hmmer/config.guess:895: echo "$UNAME_MACHINE-unknown-`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"``echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`-$LIBC"
infernal-1.1.3/hmmer/config.guess-896- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-988-EOF
infernal-1.1.3/hmmer/config.guess:989: eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU'`"
infernal-1.1.3/hmmer/config.guess-990- test "x$CPU" != x && { echo "$CPU-unknown-linux-$LIBC"; exit; }
##############################################
infernal-1.1.3/hmmer/config.guess-1088- i*86:*:4.*:*)
infernal-1.1.3/hmmer/config.guess:1089: UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'`
infernal-1.1.3/hmmer/config.guess-1090- if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
##############################################
infernal-1.1.3/hmmer/config.guess-1291- fi
infernal-1.1.3/hmmer/config.guess:1292: if test "`echo "$UNAME_RELEASE" | sed -e 's/\..*//'`" -le 10 ; then
infernal-1.1.3/hmmer/config.guess-1293- if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
##############################################
infernal-1.1.3/hmmer/config.guess-1389- *:DragonFly:*:*)
infernal-1.1.3/hmmer/config.guess:1390: echo "$UNAME_MACHINE"-unknown-dragonfly"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
infernal-1.1.3/hmmer/config.guess-1391- exit ;;
##############################################
infernal-1.1.3/hmmer/config.guess-1402- i*86:skyos:*:*)
infernal-1.1.3/hmmer/config.guess:1403: echo "$UNAME_MACHINE"-pc-skyos"`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'`"
infernal-1.1.3/hmmer/config.guess-1404- exit ;;
##############################################
infernal-1.1.3/hmmer/config.sub-52-
infernal-1.1.3/hmmer/config.sub:53:me=`echo "$0" | sed -e 's,.*/,,'`
infernal-1.1.3/hmmer/config.sub-54-
##############################################
infernal-1.1.3/hmmer/config.sub-114-# Here we must recognize all the valid KERNEL-OS combinations.
infernal-1.1.3/hmmer/config.sub:115:maybe_os=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
infernal-1.1.3/hmmer/config.sub-116-case $maybe_os in
##############################################
infernal-1.1.3/hmmer/config.sub-122- os=-$maybe_os
infernal-1.1.3/hmmer/config.sub:123: basic_machine=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
infernal-1.1.3/hmmer/config.sub-124- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-126- os=-linux-android
infernal-1.1.3/hmmer/config.sub:127: basic_machine=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
infernal-1.1.3/hmmer/config.sub-128- ;;
infernal-1.1.3/hmmer/config.sub-129- *)
infernal-1.1.3/hmmer/config.sub:130: basic_machine=`echo "$1" | sed 's/-[^-]*$//'`
infernal-1.1.3/hmmer/config.sub-131- if [ "$basic_machine" != "$1" ]
infernal-1.1.3/hmmer/config.sub:132: then os=`echo "$1" | sed 's/.*-/-/'`
infernal-1.1.3/hmmer/config.sub-133- else os=; fi
##############################################
infernal-1.1.3/hmmer/config.sub-180- os=-sco5v6
infernal-1.1.3/hmmer/config.sub:181: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-182- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-184- os=-sco3.2v5
infernal-1.1.3/hmmer/config.sub:185: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-186- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-188- os=-sco3.2v4
infernal-1.1.3/hmmer/config.sub:189: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-190- ;;
infernal-1.1.3/hmmer/config.sub-191- -sco3.2.[4-9]*)
infernal-1.1.3/hmmer/config.sub:192: os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
infernal-1.1.3/hmmer/config.sub:193: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-194- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-196- # Don't forget version if it is 3.2v4 or newer.
infernal-1.1.3/hmmer/config.sub:197: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-198- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-200- # Don't forget version if it is 3.2v4 or newer.
infernal-1.1.3/hmmer/config.sub:201: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-202- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-204- os=-sco3.2v2
infernal-1.1.3/hmmer/config.sub:205: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-206- ;;
infernal-1.1.3/hmmer/config.sub-207- -udk*)
infernal-1.1.3/hmmer/config.sub:208: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-209- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-211- os=-isc2.2
infernal-1.1.3/hmmer/config.sub:212: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-213- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-217- -isc*)
infernal-1.1.3/hmmer/config.sub:218: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-219- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-229- -ptx*)
infernal-1.1.3/hmmer/config.sub:230: basic_machine=`echo "$1" | sed -e 's/86-.*/86-sequent/'`
infernal-1.1.3/hmmer/config.sub-231- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-364- *-*-*)
infernal-1.1.3/hmmer/config.sub:365: echo Invalid configuration \`"$1"\': machine \`"$basic_machine"\' not recognized 1>&2
infernal-1.1.3/hmmer/config.sub-366- exit 1
##############################################
infernal-1.1.3/hmmer/config.sub-493- amd64-*)
infernal-1.1.3/hmmer/config.sub:494: basic_machine=x86_64-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-495- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-538- blackfin-*)
infernal-1.1.3/hmmer/config.sub:539: basic_machine=bfin-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-540- os=-linux
##############################################
infernal-1.1.3/hmmer/config.sub-546- c54x-*)
infernal-1.1.3/hmmer/config.sub:547: basic_machine=tic54x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-548- ;;
infernal-1.1.3/hmmer/config.sub-549- c55x-*)
infernal-1.1.3/hmmer/config.sub:550: basic_machine=tic55x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-551- ;;
infernal-1.1.3/hmmer/config.sub-552- c6x-*)
infernal-1.1.3/hmmer/config.sub:553: basic_machine=tic6x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-554- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-650- e500v[12]-*)
infernal-1.1.3/hmmer/config.sub:651: basic_machine=powerpc-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-652- os=$os"spe"
##############################################
infernal-1.1.3/hmmer/config.sub-754- i*86v32)
infernal-1.1.3/hmmer/config.sub:755: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-756- os=-sysv32
##############################################
infernal-1.1.3/hmmer/config.sub-758- i*86v4*)
infernal-1.1.3/hmmer/config.sub:759: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-760- os=-sysv4
##############################################
infernal-1.1.3/hmmer/config.sub-762- i*86v)
infernal-1.1.3/hmmer/config.sub:763: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-764- os=-sysv
##############################################
infernal-1.1.3/hmmer/config.sub-766- i*86sol2)
infernal-1.1.3/hmmer/config.sub:767: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/hmmer/config.sub-768- os=-solaris2
##############################################
infernal-1.1.3/hmmer/config.sub-792- leon-*|leon[3-9]-*)
infernal-1.1.3/hmmer/config.sub:793: basic_machine=sparc-`echo "$basic_machine" | sed 's/-.*//'`
infernal-1.1.3/hmmer/config.sub-794- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-799- m68knommu-*)
infernal-1.1.3/hmmer/config.sub:800: basic_machine=m68k-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-801- os=-linux
##############################################
infernal-1.1.3/hmmer/config.sub-833- mips3*-*)
infernal-1.1.3/hmmer/config.sub:834: basic_machine=`echo "$basic_machine" | sed -e 's/mips3/mips64/'`
infernal-1.1.3/hmmer/config.sub-835- ;;
infernal-1.1.3/hmmer/config.sub-836- mips3*)
infernal-1.1.3/hmmer/config.sub:837: basic_machine=`echo "$basic_machine" | sed -e 's/mips3/mips64/'`-unknown
infernal-1.1.3/hmmer/config.sub-838- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-855- ms1-*)
infernal-1.1.3/hmmer/config.sub:856: basic_machine=`echo "$basic_machine" | sed -e 's/ms1-/mt-/'`
infernal-1.1.3/hmmer/config.sub-857- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-980- parisc-*)
infernal-1.1.3/hmmer/config.sub:981: basic_machine=hppa-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-982- os=-linux
##############################################
infernal-1.1.3/hmmer/config.sub-996- pc98-*)
infernal-1.1.3/hmmer/config.sub:997: basic_machine=i386-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-998- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1011- pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
infernal-1.1.3/hmmer/config.sub:1012: basic_machine=i586-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1013- ;;
infernal-1.1.3/hmmer/config.sub-1014- pentiumpro-* | p6-* | 6x86-* | athlon-*)
infernal-1.1.3/hmmer/config.sub:1015: basic_machine=i686-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1016- ;;
infernal-1.1.3/hmmer/config.sub-1017- pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
infernal-1.1.3/hmmer/config.sub:1018: basic_machine=i686-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1019- ;;
infernal-1.1.3/hmmer/config.sub-1020- pentium4-*)
infernal-1.1.3/hmmer/config.sub:1021: basic_machine=i786-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1022- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1030- ppc-* | ppcbe-*)
infernal-1.1.3/hmmer/config.sub:1031: basic_machine=powerpc-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1032- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1036- ppcle-* | powerpclittle-*)
infernal-1.1.3/hmmer/config.sub:1037: basic_machine=powerpcle-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1038- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1040- ;;
infernal-1.1.3/hmmer/config.sub:1041: ppc64-*) basic_machine=powerpc64-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1042- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1046- ppc64le-* | powerpc64little-*)
infernal-1.1.3/hmmer/config.sub:1047: basic_machine=powerpc64le-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1048- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1122- strongarm-* | thumb-*)
infernal-1.1.3/hmmer/config.sub:1123: basic_machine=arm-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/config.sub-1124- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1255- xscale-* | xscalee[bl]-*)
infernal-1.1.3/hmmer/config.sub:1256: basic_machine=`echo "$basic_machine" | sed 's/^xscale/arm/'`
infernal-1.1.3/hmmer/config.sub-1257- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1317- *)
infernal-1.1.3/hmmer/config.sub:1318: echo Invalid configuration \`"$1"\': machine \`"$basic_machine"\' not recognized 1>&2
infernal-1.1.3/hmmer/config.sub-1319- exit 1
##############################################
infernal-1.1.3/hmmer/config.sub-1325- *-digital*)
infernal-1.1.3/hmmer/config.sub:1326: basic_machine=`echo "$basic_machine" | sed 's/digital.*/dec/'`
infernal-1.1.3/hmmer/config.sub-1327- ;;
infernal-1.1.3/hmmer/config.sub-1328- *-commodore*)
infernal-1.1.3/hmmer/config.sub:1329: basic_machine=`echo "$basic_machine" | sed 's/commodore.*/cbm/'`
infernal-1.1.3/hmmer/config.sub-1330- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1346- -solaris1 | -solaris1.*)
infernal-1.1.3/hmmer/config.sub:1347: os=`echo $os | sed -e 's|solaris1|sunos4|'`
infernal-1.1.3/hmmer/config.sub-1348- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1355- -gnu/linux*)
infernal-1.1.3/hmmer/config.sub:1356: os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
infernal-1.1.3/hmmer/config.sub-1357- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1407- -nto*)
infernal-1.1.3/hmmer/config.sub:1408: os=`echo $os | sed -e 's|nto|nto-qnx|'`
infernal-1.1.3/hmmer/config.sub-1409- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1414- -mac*)
infernal-1.1.3/hmmer/config.sub:1415: os=`echo "$os" | sed -e 's|mac|macos|'`
infernal-1.1.3/hmmer/config.sub-1416- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1420- -linux*)
infernal-1.1.3/hmmer/config.sub:1421: os=`echo $os | sed -e 's|linux|linux-gnu|'`
infernal-1.1.3/hmmer/config.sub-1422- ;;
infernal-1.1.3/hmmer/config.sub-1423- -sunos5*)
infernal-1.1.3/hmmer/config.sub:1424: os=`echo "$os" | sed -e 's|sunos5|solaris2|'`
infernal-1.1.3/hmmer/config.sub-1425- ;;
infernal-1.1.3/hmmer/config.sub-1426- -sunos6*)
infernal-1.1.3/hmmer/config.sub:1427: os=`echo "$os" | sed -e 's|sunos6|solaris3|'`
infernal-1.1.3/hmmer/config.sub-1428- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1469- -sinix5.*)
infernal-1.1.3/hmmer/config.sub:1470: os=`echo $os | sed -e 's|sinix|sysv|'`
infernal-1.1.3/hmmer/config.sub-1471- ;;
##############################################
infernal-1.1.3/hmmer/config.sub-1528- # Get rid of the `-' at the beginning of $os.
infernal-1.1.3/hmmer/config.sub:1529: os=`echo $os | sed 's/[^-]*-//'`
infernal-1.1.3/hmmer/config.sub:1530: echo Invalid configuration \`"$1"\': system \`"$os"\' not recognized 1>&2
infernal-1.1.3/hmmer/config.sub-1531- exit 1
##############################################
infernal-1.1.3/hmmer/config.sub-1788- esac
infernal-1.1.3/hmmer/config.sub:1789: basic_machine=`echo "$basic_machine" | sed "s/unknown/$vendor/"`
infernal-1.1.3/hmmer/config.sub-1790- ;;
##############################################
infernal-1.1.3/hmmer/install-sh-97- case $1 in
infernal-1.1.3/hmmer/install-sh:98: -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
infernal-1.1.3/hmmer/install-sh-99- shift
##############################################
infernal-1.1.3/hmmer/install-sh-130-
infernal-1.1.3/hmmer/install-sh:131: -t=*) transformarg=`echo $1 | sed 's/-t=//'`
infernal-1.1.3/hmmer/install-sh-132- shift
##############################################
infernal-1.1.3/hmmer/install-sh-190- if test -d "$dst"; then
infernal-1.1.3/hmmer/install-sh:191: dst=$dst/`basename "$src"`
infernal-1.1.3/hmmer/install-sh-192- fi
##############################################
infernal-1.1.3/hmmer/install-sh-195-# This sed command emulates the dirname command.
infernal-1.1.3/hmmer/install-sh:196:dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
infernal-1.1.3/hmmer/install-sh-197-
##############################################
infernal-1.1.3/hmmer/install-sh-208- IFS='%'
infernal-1.1.3/hmmer/install-sh:209: set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
infernal-1.1.3/hmmer/install-sh-210- IFS=$oIFS
##############################################
infernal-1.1.3/hmmer/install-sh-231- if test -z "$transformarg"; then
infernal-1.1.3/hmmer/install-sh:232: dstfile=`basename "$dst"`
infernal-1.1.3/hmmer/install-sh-233- else
##############################################
infernal-1.1.3/hmmer/install-sh-238- # don't allow the sed command to completely eliminate the filename.
infernal-1.1.3/hmmer/install-sh:239: test -z "$dstfile" && dstfile=`basename "$dst"`
infernal-1.1.3/hmmer/install-sh-240-
##############################################
infernal-1.1.3/hmmer/profmark/pmark-master.pl-59-if (-e $resultdir) { die("$resultdir exists");}
infernal-1.1.3/hmmer/profmark/pmark-master.pl:60:system("mkdir $resultdir");
infernal-1.1.3/hmmer/profmark/pmark-master.pl-61-
##############################################
infernal-1.1.3/hmmer/profmark/pmark-master.pl-110-$maxi = $ncpu-1;
infernal-1.1.3/hmmer/profmark/pmark-master.pl:111:system("sbatch --array=0-$maxi $resultdir.sh");
infernal-1.1.3/hmmer/profmark/pmark-master.pl-112-
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-fasta-45-
infernal-1.1.3/hmmer/profmark/x-fps-fasta:46: `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-fps-fasta-47- if ($?) { print "FAILED: esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-fasta-49- # Extract a list of individual sequence names from the multiple alignment.
infernal-1.1.3/hmmer/profmark/x-fps-fasta:50: $output = `esl-seqstat -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'`;
infernal-1.1.3/hmmer/profmark/x-fps-fasta-51- if ($?) { print "FAILED: esl-seqstat -a $wrkdir/$msaname.sto\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-fasta-58- {
infernal-1.1.3/hmmer/profmark/x-fps-fasta:59: $output = `esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/profmark/x-fps-fasta-60- if ($?) { print "FAILED: esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast-45-
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast:46: `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast-47- if ($?) { print "FAILED: esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast-49- # Extract a list of individual sequence names from the multiple alignment.
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast:50: $output = `esl-seqstat -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'`;
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast-51- if ($?) { print "FAILED: esl-seqstat -a $wrkdir/$msaname.sto\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast-58- {
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast:59: $output = `esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast-60- if ($?) { print "FAILED: esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+-45-
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+:46: `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+-47- if ($?) { print "FAILED: esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+-49- # Extract a list of individual sequence names from the multiple alignment.
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+:50: $output = `esl-seqstat -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'`;
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+-51- if ($?) { print "FAILED: esl-seqstat -a $wrkdir/$msaname.sto\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+-58- {
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+:59: $output = `esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/profmark/x-fps-ncbiblast+-60- if ($?) { print "FAILED: esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-phmmer-43-
infernal-1.1.3/hmmer/profmark/x-fps-phmmer:44: `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-fps-phmmer-45- if ($?) { print "FAILED: esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-phmmer-47- # Extract a list of individual sequence names from the multiple alignment.
infernal-1.1.3/hmmer/profmark/x-fps-phmmer:48: $output = `esl-seqstat -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'`;
infernal-1.1.3/hmmer/profmark/x-fps-phmmer-49- if ($?) { print "FAILED: esl-seqstat\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-phmmer-56- {
infernal-1.1.3/hmmer/profmark/x-fps-phmmer:57: $output = `esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/profmark/x-fps-phmmer-58- if ($?) { print "FAILED: esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname\n"; next MSA; }
infernal-1.1.3/hmmer/profmark/x-fps-phmmer-59-
infernal-1.1.3/hmmer/profmark/x-fps-phmmer:60: `$phmmer --cpu 1 --tblout $wrkdir/$msaname.tmp $opts $wrkdir/$msaname.query.fa $fafile > /dev/null`;
infernal-1.1.3/hmmer/profmark/x-fps-phmmer-61- if ($?) { print "FAILED: $phmmer --tblout $msaname.tmp $opts $wrkdir/$msaname.query.fa $fafile\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ssearch-45-
infernal-1.1.3/hmmer/profmark/x-fps-ssearch:46: `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-fps-ssearch-47- if ($?) { print "FAILED: esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ssearch-49- # Extract a list of individual sequence names from the multiple alignment.
infernal-1.1.3/hmmer/profmark/x-fps-ssearch:50: $output = `esl-seqstat -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'`;
infernal-1.1.3/hmmer/profmark/x-fps-ssearch-51- if ($?) { print "FAILED: esl-seqstat -a $wrkdir/$msaname.sto\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-ssearch-58- {
infernal-1.1.3/hmmer/profmark/x-fps-ssearch:59: $output = `esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/profmark/x-fps-ssearch-60- if ($?) { print "FAILED: esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-wublast-45-
infernal-1.1.3/hmmer/profmark/x-fps-wublast:46: `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-fps-wublast-47- if ($?) { print "FAILED: esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-wublast-49- # Extract a list of individual sequence names from the multiple alignment.
infernal-1.1.3/hmmer/profmark/x-fps-wublast:50: $output = `esl-seqstat -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'`;
infernal-1.1.3/hmmer/profmark/x-fps-wublast-51- if ($?) { print "FAILED: esl-seqstat -a $wrkdir/$msaname.sto\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-fps-wublast-59- {
infernal-1.1.3/hmmer/profmark/x-fps-wublast:60: $output = `esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/profmark/x-fps-wublast-61- if ($?) { print "FAILED: esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname\n"; next QUERY; }
##############################################
infernal-1.1.3/hmmer/profmark/x-h2-fs-46-
infernal-1.1.3/hmmer/profmark/x-h2-fs:47: $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-h2-fs-48- if ($?) { print "FAILED: esl-afetch -o $resultdir/$msaname.sto $msafile $msaname\n"; next MSA; }
infernal-1.1.3/hmmer/profmark/x-h2-fs-49-
infernal-1.1.3/hmmer/profmark/x-h2-fs:50: $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-h2-fs-51- if ($?) { print "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto\n"; next MSA; }
infernal-1.1.3/hmmer/profmark/x-h2-fs-52-
infernal-1.1.3/hmmer/profmark/x-h2-fs:53: $output = `$hmmcalibrate $calibrateopts $resultdir/$msaname.hmm`;
infernal-1.1.3/hmmer/profmark/x-h2-fs-54- if ($?) { print "FAILED: $hmmcalibrate\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-h2-ls-46-
infernal-1.1.3/hmmer/profmark/x-h2-ls:47: $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-h2-ls-48- if ($?) { print "FAILED: esl-afetch -o $resultdir/$msaname.sto $msafile $msaname\n"; next MSA; }
infernal-1.1.3/hmmer/profmark/x-h2-ls-49-
infernal-1.1.3/hmmer/profmark/x-h2-ls:50: $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-h2-ls-51- if ($?) { print "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto\n"; next MSA; }
infernal-1.1.3/hmmer/profmark/x-h2-ls-52-
infernal-1.1.3/hmmer/profmark/x-h2-ls:53: $output = `$hmmcalibrate $calibrateopts $resultdir/$msaname.hmm`;
infernal-1.1.3/hmmer/profmark/x-h2-ls-54- if ($?) { print "FAILED: $hmmcalibrate\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-hmmsearch-40-
infernal-1.1.3/hmmer/profmark/x-hmmsearch:41: $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-hmmsearch-42- if ($? != 0) { die "FAILED: esl-afetch -o $resultdir/$msaname.sto $msafile $msaname"; }
infernal-1.1.3/hmmer/profmark/x-hmmsearch-43-
infernal-1.1.3/hmmer/profmark/x-hmmsearch:44: $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-hmmsearch-45- if ($? != 0) { die "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto"; }
infernal-1.1.3/hmmer/profmark/x-hmmsearch-46-
infernal-1.1.3/hmmer/profmark/x-hmmsearch:47: $status = system("$hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > /dev/null");
infernal-1.1.3/hmmer/profmark/x-hmmsearch-48- if ($status != 0) { die "FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max-40-
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max:41: $output = `esl-afetch -o $resultdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max-42- if ($? != 0) { die "FAILED: esl-afetch -o $resultdir/$msaname.sto $msafile $msaname"; }
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max-43-
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max:44: $output = `$hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max-45- if ($? != 0) { die "FAILED: $hmmbuild $buildopts $resultdir/$msaname.hmm $resultdir/$msaname.sto"; }
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max-46-
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max:47: $status = system("$hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile > /dev/null");
infernal-1.1.3/hmmer/profmark/x-hmmsearch-max-48- if ($status != 0) { die "FAILED: $hmmsearch $searchopts --tblout $resultdir/$msaname.tmp $resultdir/$msaname.hmm $fafile"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer-37-
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer:38: $cmd = "esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Fetch the query MSA from the benchmark; tmp .sto file here
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer:39: $cmd = "esl-seqstat --amino -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n", next MSA; } # Extract list of indiv seq names. --amino for robustness, some msa's v. small
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer-40- @qnames = split(/^/,$output);
##############################################
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer-42- $qname = $qnames[0];
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer:43: $cmd = "esl-sfetch -o $wrkdir/$msaname.query $wrkdir/$msaname.sto $qname > /dev/null"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Pick a single seq (first one) to tmp file; tmp .query file here
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer-44-
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer:45: $cmd = "$jackhmmer $iteropts -A $wrkdir/$msaname.jck $wrkdir/$msaname.query $fafile.iter > /dev/null"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Iterate n times on the .iter intermediate database (NR, whatever); alignment to tmp .jck file
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer:46: $cmd = "$hmmbuild --hand $wrkdir/$msaname.hmm $wrkdir/$msaname.jck > /dev/null`"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Build a model from .jck, using the same architecture (--hand)
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer:47: $cmd = "$hmmsearch $searchopts --tblout $wrkdir/$msaname.tmp $wrkdir/$msaname.hmm $fafile > /dev/null"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Search against benchmark .fa file; results to tmp .tmp tbl file
infernal-1.1.3/hmmer/profmark/x-iterate-jackhmmer-48-
##############################################
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast-47-
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast:48: $cmd = "esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Fetch the query MSA from the benchmark; tmp .sto file here
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast:49: $cmd = "esl-seqstat --amino -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n", next MSA; } # Extract list of indiv seq names. --amino for robustness, some msa's v. small
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast-50- @qnames = split(/^/,$output);
##############################################
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast-52- $qname = $qnames[0];
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast:53: $cmd = "esl-sfetch -o $wrkdir/$msaname.query $wrkdir/$msaname.sto $qname > /dev/null"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Pick a single seq (first one) to tmp file; tmp .query file here
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast-54-
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast:55: $cmd = "$blastpgp $blastopts1 -d $fafile.iter -i $wrkdir/$msaname.query -C $wrkdir/$msaname.asnt"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Iterate on the .iter database. tmp .asnt checkpoint file here.
infernal-1.1.3/hmmer/profmark/x-iterate-psiblast-56- $cmd = "$blastpgp $blastopts2 -d $fafile -R $wrkdir/$msaname.asnt 2>/dev/null |"; if (! open(PSIBLAST, "$cmd")) { print "FAILED: $cmd\n"; next MSA; } # Search the benchmark database
##############################################
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus-35- # Fetch the query MSA from the benchmark (.sto file)
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus:36: $output = `$esl_afetch -o $resultdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus-37- if ($? != 0) { die "FAILED: $esl_afetch -o $resultdir/$msaname.sto $msafile $msaname"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus-39- # Create a profile HMM from it (.hmm file; .query.fa file)
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus:40: $output = `$hmmbuild $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus-41- if ($? != 0) { die "FAILED: $hmmbuild $resultdir/$msaname.hmm $resultdir/$msaname.sto"; }
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus-42-
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus:43: $output = `$hmmemit -o $resultdir/$msaname.query.fa $resultdir/$msaname.hmm`;
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus-44- if ($? != 0) { die "FAILED: hmmemit -o $resultdir/$msaname.query.fa $resultdir/$msaname.hmm"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus-46- # PHMMER it against the benchmark
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus:47: $output = `$phmmer $opts --cpu 1 --tblout $resultdir/$msaname.tmp $resultdir/$msaname.query.fa $fafile > /dev/null`;
infernal-1.1.3/hmmer/profmark/x-phmmer-consensus-48- if ($? != 0) { die "FAILED: $phmmer --tblout $resultdir/$msaname.tmp $opts $resultdir/$msaname.query.fa $fafile"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-psiblast-46- # Fetch the query MSA from the benchmark (.sto file)
infernal-1.1.3/hmmer/profmark/x-psiblast:47: $output = `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-psiblast-48- if ($? != 0) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-psiblast-50- # Reformat to psiblast format (.pbl file)
infernal-1.1.3/hmmer/profmark/x-psiblast:51: $output = `esl-reformat -o $wrkdir/$msaname.pbl psiblast $wrkdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-psiblast-52- if ($? != 0) { print "FAILED: esl-reformat psiblast on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-psiblast-54- # Select median length single sequence as the "query" (.query.fa file)
infernal-1.1.3/hmmer/profmark/x-psiblast:55: $output = `esl-seqstat -a $wrkdir/$msaname.sto | grep "^=" | sort -n -k3 | awk '{print \$2}'`;
infernal-1.1.3/hmmer/profmark/x-psiblast-56- if ($?) { print "FAILED: esl-seqstat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-psiblast-59- $qname = $qnames[ int(($#qnames+1) / 2)];
infernal-1.1.3/hmmer/profmark/x-psiblast:60: $output = `esl-sfetch -o $wrkdir/$msaname.query.fa $wrkdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/profmark/x-psiblast-61- if ($?) { print "FAILED: esl-sfetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-psiblast-65- # only the seed seqs)
infernal-1.1.3/hmmer/profmark/x-psiblast:66: $output = `esl-reformat -o $wrkdir/$msaname.fa fasta $wrkdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-psiblast-67- if ($?) { print "FAILED: esl-reformat fasta on $msaname\n"; next MSA; }
infernal-1.1.3/hmmer/profmark/x-psiblast-68-
infernal-1.1.3/hmmer/profmark/x-psiblast:69: $output = `seg $wrkdir/$msaname.fa -x > $wrkdir/$msaname.x.fa`;
infernal-1.1.3/hmmer/profmark/x-psiblast-70- if ($?) { print "FAILED: esl-reformat fasta on $msaname\n"; next MSA; }
infernal-1.1.3/hmmer/profmark/x-psiblast-71-
infernal-1.1.3/hmmer/profmark/x-psiblast:72: $output = `$formatdb -i $wrkdir/$msaname.x.fa`;
infernal-1.1.3/hmmer/profmark/x-psiblast-73- if ($?) { print "FAILED: formatdb on $msaname\n"; next MSA; }
infernal-1.1.3/hmmer/profmark/x-psiblast-74-
infernal-1.1.3/hmmer/profmark/x-psiblast:75: $output = `$blastpgp $blastopts1 -d $wrkdir/$msaname.x.fa -i $wrkdir/$msaname.query.fa -C $wrkdir/$msaname.asnt`;
infernal-1.1.3/hmmer/profmark/x-psiblast-76- if ($?) { print "FAILED: blastpgp checkpoint file on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-psiblast+-44- # Fetch the query MSA from the benchmark (.sto file)
infernal-1.1.3/hmmer/profmark/x-psiblast+:45: $output = `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-psiblast+-46- if ($? != 0) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-psiblast+-48- # Reformat to psiblast format (.pbl file)
infernal-1.1.3/hmmer/profmark/x-psiblast+:49: $output = `esl-reformat -o $wrkdir/$msaname.pbl psiblast $wrkdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-psiblast+-50- if ($? != 0) { print "FAILED: esl-reformat psiblast on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/profmark/x-sam-39- # Fetch query MSA from benchmark's .sto file
infernal-1.1.3/hmmer/profmark/x-sam:40: $output = `esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname`;
infernal-1.1.3/hmmer/profmark/x-sam-41- if ($? != 0) { die "FAILED: esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-sam-43- # Reformat to A2M format (.a2m file)
infernal-1.1.3/hmmer/profmark/x-sam:44: $output = `esl-reformat -o $wrkdir/$msaname.a2m a2m $wrkdir/$msaname.sto`;
infernal-1.1.3/hmmer/profmark/x-sam-45- if ($? != 0) { die "FAILED: esl-reformat"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-sam-47- # Build a model using UCSC's w0.5 script (.mod file)
infernal-1.1.3/hmmer/profmark/x-sam:48: `(cd $wrkdir; $w05 $msaname.a2m $msaname.mod &> /dev/null)`;
infernal-1.1.3/hmmer/profmark/x-sam-49- if ($? != 0) { die "FAILED: $w05"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-sam-51- # Calibrate the model (.mlib file)
infernal-1.1.3/hmmer/profmark/x-sam:52: `(cd $wrkdir; $hmmscore $msaname -i $msaname.mod -calibrate 1 &> /dev/null)`;
infernal-1.1.3/hmmer/profmark/x-sam-53- if ($? != 0) { die "FAILED: $hmmscore -calibrate"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-sam-55- # Run hmmscore, search the benchmark .fa file. The result (a .dist file) drops into the wd.
infernal-1.1.3/hmmer/profmark/x-sam:56: `(cd $wrkdir; $hmmscore $msaname -modellibrary $msaname.mlib -db ../$fafile -sw 2 &> /dev/null)`;
infernal-1.1.3/hmmer/profmark/x-sam-57- if ($? != 0) { die "FAILED: $hmmscore"; }
##############################################
infernal-1.1.3/hmmer/profmark/x-single-ncbiblast-32-
infernal-1.1.3/hmmer/profmark/x-single-ncbiblast:33: $cmd = "esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Fetch the query MSA from the benchmark; tmp .sto file here
infernal-1.1.3/hmmer/profmark/x-single-ncbiblast:34: $cmd = "esl-seqstat --amino -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n", next MSA; } # Extract list of indiv seq names. --amino for robustness, some msa's v. small
infernal-1.1.3/hmmer/profmark/x-single-ncbiblast-35- @qnames = split(/^/,$output);
##############################################
infernal-1.1.3/hmmer/profmark/x-single-ncbiblast-37- $qname = $qnames[0];
infernal-1.1.3/hmmer/profmark/x-single-ncbiblast:38: $cmd = "esl-sfetch -o $wrkdir/$msaname.query $wrkdir/$msaname.sto $qname > /dev/null"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Pick a single seq (first one) to tmp file; tmp .query file here
infernal-1.1.3/hmmer/profmark/x-single-ncbiblast-39-
##############################################
infernal-1.1.3/hmmer/profmark/x-single-phmmer-25-
infernal-1.1.3/hmmer/profmark/x-single-phmmer:26: $cmd = "esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Fetch the query MSA from the benchmark; tmp .sto file here
infernal-1.1.3/hmmer/profmark/x-single-phmmer:27: $cmd = "esl-seqstat --amino -a $wrkdir/$msaname.sto | grep '^=' | awk '{print \$2}'"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n", next MSA; } # Extract list of indiv seq names. --amino for robustness, some msa's v. small
infernal-1.1.3/hmmer/profmark/x-single-phmmer-28- @qnames = split(/^/,$output);
##############################################
infernal-1.1.3/hmmer/profmark/x-single-phmmer-30- $qname = $qnames[0];
infernal-1.1.3/hmmer/profmark/x-single-phmmer:31: $cmd = "esl-sfetch -o $wrkdir/$msaname.query $wrkdir/$msaname.sto $qname > /dev/null"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Pick a single seq (first one) to tmp file; tmp .query file here
infernal-1.1.3/hmmer/profmark/x-single-phmmer-32-
infernal-1.1.3/hmmer/profmark/x-single-phmmer:33: $cmd = "$phmmer $searchopts --tblout $wrkdir/$msaname.tmp $wrkdir/$msaname.query $fafile > /dev/null"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # phmmer against benchmark db; tmp .tmp output file here
infernal-1.1.3/hmmer/profmark/x-single-phmmer-34-
##############################################
infernal-1.1.3/hmmer/profmark/x-single-ssearch-33-
infernal-1.1.3/hmmer/profmark/x-single-ssearch:34: $cmd = "esl-afetch -o $wrkdir/$msaname.sto $msafile $msaname"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Fetch the query MSA from the benchmark; tmp .sto file here
infernal-1.1.3/hmmer/profmark/x-single-ssearch:35: $cmd = "esl-seqstat --amino -a $wrkdir/$msaname.sto | grep "^=" | awk '{print \$2}'"; $output = `$cmd`; if ($?) { print "FAILED: $cmd\n", next MSA; } # Extract list of indiv seq names. --amino for robustness, some msa's v. small
infernal-1.1.3/hmmer/profmark/x-single-ssearch-36- @qnames = split(/^/,$output);
##############################################
infernal-1.1.3/hmmer/profmark/x-single-ssearch-38- $qname = $qnames[0];
infernal-1.1.3/hmmer/profmark/x-single-ssearch:39: $cmd = "esl-sfetch -o $wrkdir/$msaname.query $wrkdir/$msaname.sto $qname > /dev/null"; `$cmd`; if ($?) { print "FAILED: $cmd\n"; next MSA; } # Pick a single seq (first one) to tmp file; tmp .query file here
infernal-1.1.3/hmmer/profmark/x-single-ssearch-40-
##############################################
infernal-1.1.3/hmmer/src/hmmc2.c-273- serv_addr.sin_family = AF_INET;
infernal-1.1.3/hmmer/src/hmmc2.c:274: serv_addr.sin_addr.s_addr = inet_addr(serv_ip);
infernal-1.1.3/hmmer/src/hmmc2.c-275- serv_addr.sin_port = htons(serv_port);
##############################################
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-24-# Make a copy of minifam, so we can whack on it.
infernal-1.1.3/hmmer/src/hmmpress.itest.pl:25:system("cp $minifam $tmppfx.hmm 2>&1");
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-26-if ($? != 0) { die "failed to copy $minifam"; }
##############################################
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-28-# Get the model names from it. We at least need to know how many there are.
infernal-1.1.3/hmmer/src/hmmpress.itest.pl:29:@output = `grep "^NAME " $tmppfx.hmm 2>&1`;
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-30-if ($? != 0) { die "failed to grep $minifam for names"; }
##############################################
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-35-#
infernal-1.1.3/hmmer/src/hmmpress.itest.pl:36:$output = `$hmmpress $tmppfx.hmm 2>&1`;
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-37-if ($? != 0) { die "failed to press $minifam"; }
##############################################
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-42-# This should issue a normal warning that the files already exist.
infernal-1.1.3/hmmer/src/hmmpress.itest.pl:43:$output = `$hmmpress $tmppfx.hmm 2>&1`;
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-44-if ( ($? >> 8) != 1) { die "expected exit code 1 from hmmpress"; }
##############################################
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-48-# Bug #h65 was here.
infernal-1.1.3/hmmer/src/hmmpress.itest.pl:49:$output = `$hmmpress -f $tmppfx.hmm 2>&1`;
infernal-1.1.3/hmmer/src/hmmpress.itest.pl-50-if ($? != 0) { die "hmmpress -f failed to press $minifam"; }
##############################################
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in-110-${UTESTS}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in:111: @BASENAME=`echo $@ | sed -e 's/_utest//'| sed -e 's/^p7_//'` ;\
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in:112: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in-113- DFLAG=p7$${DFLAG}_TESTDRIVE ;\
##############################################
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in-125-${BENCHMARKS}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in:126: @BASENAME=`echo $@ | sed -e 's/_benchmark//' | sed -e 's/^p7_//'`;\
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in:127: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in-128- DFLAG=p7$${DFLAG}_BENCHMARK ;\
##############################################
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in-140-${EXAMPLES}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in:141: @BASENAME=`echo $@ | sed -e 's/_example//'| sed -e 's/^p7_//'` ;\
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in:142: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/impl_sse/Makefile.in-143- DFLAG=p7$${DFLAG}_EXAMPLE ;\
##############################################
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in-109-${UTESTS}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in:110: @BASENAME=`echo $@ | sed -e 's/_utest//'| sed -e 's/^p7_//'` ;\
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in:111: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in-112- DFLAG=p7$${DFLAG}_TESTDRIVE ;\
##############################################
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in-124-${BENCHMARKS}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in:125: @BASENAME=`echo $@ | sed -e 's/_benchmark//' | sed -e 's/^p7_//'`;\
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in:126: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in-127- DFLAG=p7$${DFLAG}_BENCHMARK ;\
##############################################
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in-139-${EXAMPLES}: libhmmer-impl.stamp ../libhmmer.a ${HDRS} ../hmmer.h
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in:140: @BASENAME=`echo $@ | sed -e 's/_example//'| sed -e 's/^p7_//'` ;\
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in:141: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/impl_vmx/Makefile.in-142- DFLAG=p7$${DFLAG}_EXAMPLE ;\
##############################################
infernal-1.1.3/hmmer/src/Makefile.in-283-${UTESTS}: libhmmer.a ${HDRS} p7_config.h
infernal-1.1.3/hmmer/src/Makefile.in:284: @BASENAME=`echo $@ | sed -e 's/_utest//' | sed -e 's/^p7_//'` ;\
infernal-1.1.3/hmmer/src/Makefile.in:285: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/Makefile.in-286- DFLAG=p7$${DFLAG}_TESTDRIVE ;\
##############################################
infernal-1.1.3/hmmer/src/Makefile.in-298-${BENCHMARKS}: libhmmer.a ${HDRS} p7_config.h
infernal-1.1.3/hmmer/src/Makefile.in:299: @BASENAME=`echo $@ | sed -e 's/_benchmark//' | sed -e 's/^p7_//'` ;\
infernal-1.1.3/hmmer/src/Makefile.in:300: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/Makefile.in-301- DFLAG=p7$${DFLAG}_BENCHMARK ;\
##############################################
infernal-1.1.3/hmmer/src/Makefile.in-313-${STATS}: libhmmer.a ${HDRS} p7_config.h
infernal-1.1.3/hmmer/src/Makefile.in:314: @BASENAME=`echo $@ | sed -e 's/_stats//' | sed -e 's/^p7_//'` ;\
infernal-1.1.3/hmmer/src/Makefile.in:315: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/Makefile.in-316- DFLAG=p7$${DFLAG}_STATS ;\
##############################################
infernal-1.1.3/hmmer/src/Makefile.in-328-${EXAMPLES}: libhmmer.a ${HDRS} p7_config.h
infernal-1.1.3/hmmer/src/Makefile.in:329: @BASENAME=`echo $@ | sed -e 's/_example[0-9]*//' | sed -e 's/^p7_//'` ;\
infernal-1.1.3/hmmer/src/Makefile.in:330: DFLAG=p7`echo $@ | sed -e 's/^p7_//' | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/src/Makefile.in-331- if test -e ${srcdir}/p7_$${BASENAME}.c; then \
##############################################
infernal-1.1.3/hmmer/test-speed/component-benchmark.pl-51- {
infernal-1.1.3/hmmer/test-speed/component-benchmark.pl:52: $output = `${top_builddir}/$benchmark ${top_srcdir}/testsuite/$model.hmm`;
infernal-1.1.3/hmmer/test-speed/component-benchmark.pl-53- ($cputime, $M, $Mcs) = &get_results($output);
##############################################
infernal-1.1.3/hmmer/test-speed/speed-master.pl-61-if (-e $resultdir) { die("$resultdir exists");}
infernal-1.1.3/hmmer/test-speed/speed-master.pl:62:system("mkdir $resultdir");
infernal-1.1.3/hmmer/test-speed/speed-master.pl-63-
##############################################
infernal-1.1.3/hmmer/test-speed/speed-master.pl-105-$maxidx = $nproc-1;
infernal-1.1.3/hmmer/test-speed/speed-master.pl:106:system("sbatch --array=0-$maxidx $resultdir.sh");
infernal-1.1.3/hmmer/test-speed/speed-master.pl-107-
##############################################
infernal-1.1.3/hmmer/test-speed/x-fasta-43- # Fetch the query MSA (.sto file)
infernal-1.1.3/hmmer/test-speed/x-fasta:44: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-fasta-45- if ($? != 0) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-fasta-47- # Select median length single sequence as the query (.query.fa file)
infernal-1.1.3/hmmer/test-speed/x-fasta:48: $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
infernal-1.1.3/hmmer/test-speed/x-fasta-49- if ($?) { print "FAILED: esl-seqstat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-fasta-52- $qname = $qnames[ int(($#qnames+1) / 2)];
infernal-1.1.3/hmmer/test-speed/x-fasta:53: $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/test-speed/x-fasta-54- if ($?) { print "FAILED: esl-sfetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-fasta-56- # Warmup. (An untimed run, to encourage filesystem to cache the target database.)
infernal-1.1.3/hmmer/test-speed/x-fasta:57: if ($n == 1) { $output = `$fasta $fasta_opts $resultdir/$msaname.query.fa $targetdb 2>&1`; }
infernal-1.1.3/hmmer/test-speed/x-fasta-58-
##############################################
infernal-1.1.3/hmmer/test-speed/x-fasta-60- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-fasta:61: $output = `$fasta $fasta_opts $resultdir/$msaname.query.fa $targetdb 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-fasta-62- if ($? != 0) { print "FAILED: fasta on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmer2-34-
infernal-1.1.3/hmmer/test-speed/x-hmmer2:35:$output = `esl-seqstat $targetdb | grep "^Total"`;
infernal-1.1.3/hmmer/test-speed/x-hmmer2-36-if ($?) { die("esl-seqstat failed"); }
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmer2-48- # Fetch the query MSA (.sto file)
infernal-1.1.3/hmmer/test-speed/x-hmmer2:49: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-hmmer2-50- if ($?) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmer2-52- # Build an HMM in local mode (.hmm file)
infernal-1.1.3/hmmer/test-speed/x-hmmer2:53: $output = `$hmmbuild -F --amino $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/test-speed/x-hmmer2-54- if ($?) { print("FAILED: hmmbuild on $msaname\n"); next MSA;}
infernal-1.1.3/hmmer/test-speed/x-hmmer2-55-
infernal-1.1.3/hmmer/test-speed/x-hmmer2:56: $output = `grep "^LENG" $resultdir/$msaname.hmm`;
infernal-1.1.3/hmmer/test-speed/x-hmmer2-57- if ($?) { print("FAILED: grep on $msaname\n"); next MSA;}
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmer2-60- # Warmup. (An untimed run, to encourage filesystem to cache the target database.)
infernal-1.1.3/hmmer/test-speed/x-hmmer2:61: if ($n == 1) { $output = `$hmmsearch $opts $resultdir/$msaname.hmm $targetdb 2>&1`; }
infernal-1.1.3/hmmer/test-speed/x-hmmer2-62-
infernal-1.1.3/hmmer/test-speed/x-hmmer2-63- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-hmmer2:64: $output = `$hmmsearch $opts $resultdir/$msaname.hmm $targetdb 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-hmmer2-65- if ($?) { print("FAILED: hmmsearch on $msaname\n"); next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-28-
infernal-1.1.3/hmmer/test-speed/x-hmmsearch:29:$output = `esl-seqstat $targetdb | grep "^Total"`;
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-30-if ($?) { die("esl-seqstat failed"); }
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-42- # Fetch the query MSA (.sto file)
infernal-1.1.3/hmmer/test-speed/x-hmmsearch:43: `$esl_afetch -o $resultdir/$msaname.sto $querydb $msaname > /dev/null`;
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-44- if ($? != 0) { print "FAILED: $esl_afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-46- # Build a model (.hmm file)
infernal-1.1.3/hmmer/test-speed/x-hmmsearch:47: $output = `$hmmbuild $resultdir/$msaname.hmm $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-48- if ($?) { print("FAILED: $hmmbuild on $msaname\n"); next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-53- # Warmup. (An untimed run, to encourage filesystem to cache the target database.)
infernal-1.1.3/hmmer/test-speed/x-hmmsearch:54: if ($n==1) { `$hmmsearch --cpu $nthreads $resultdir/$msaname.hmm $targetdb > /dev/null`; }
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-55-
##############################################
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-57- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-hmmsearch:58: `$hmmsearch --cpu $nthreads $resultdir/$msaname.hmm $targetdb > /dev/null`;
infernal-1.1.3/hmmer/test-speed/x-hmmsearch-59- if ($?) { print("FAILED: $hmmsearch on $msaname\n"); next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-42- # Fetch the query MSA (.sto file)
infernal-1.1.3/hmmer/test-speed/x-ncbiblast:43: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-44- if ($? != 0) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-46- # Select median length single sequence as the query (.query.fa file)
infernal-1.1.3/hmmer/test-speed/x-ncbiblast:47: $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-48- if ($?) { print "FAILED: esl-seqstat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-51- $qname = $qnames[ int(($#qnames+1) / 2)];
infernal-1.1.3/hmmer/test-speed/x-ncbiblast:52: $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-53- if ($?) { print "FAILED: esl-sfetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-55- # Warmup. (An untimed run, to encourage filesystem to cache the target database.)
infernal-1.1.3/hmmer/test-speed/x-ncbiblast:56: if ($n==1) { `$blastall $blastopts -d $targetdb -i $resultdir/$msaname.query.fa 2>&1`; }
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-57-
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-59- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast:60: $output = `$blastall $blastopts -d $targetdb -i $resultdir/$msaname.query.fa 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast-61- if ($? != 0) { print "FAILED: ncbi blast on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-42- # Fetch the query MSA (.sto file)
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+:43: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-44- if ($? != 0) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-46- # Select median length single sequence as the query (.query.fa file)
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+:47: $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-48- if ($?) { print "FAILED: esl-seqstat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-51- $qname = $qnames[ int(($#qnames+1) / 2)];
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+:52: $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-53- if ($?) { print "FAILED: esl-sfetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-55- # Warmup. (An untimed run, to encourage filesystem to cache the target database.)
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+:56: if ($n==1) { `$blastp $blastopts -db $targetdb -query $resultdir/$msaname.query.fa 2>&1`; }
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-57-
##############################################
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-59- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+:60: $output = `$blastp $blastopts -db $targetdb -query $resultdir/$msaname.query.fa 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-ncbiblast+-61- if ($? != 0) { print "FAILED: ncbi blastp+ on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast-42- # Fetch the query MSA from the benchmark (.sto file)
infernal-1.1.3/hmmer/test-speed/x-psiblast:43: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-psiblast-44- if ($?) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast-46- # Reformat to psiblast format (.pbl file)
infernal-1.1.3/hmmer/test-speed/x-psiblast:47: $output = `esl-reformat -o $resultdir/$msaname.pbl psiblast $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/test-speed/x-psiblast-48- if ($?) { print "FAILED: esl-reformat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast-50- # Select median length single sequence as the "query" (.query.fa file)
infernal-1.1.3/hmmer/test-speed/x-psiblast:51: $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
infernal-1.1.3/hmmer/test-speed/x-psiblast-52- if ($?) { print "FAILED: esl-seqstat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast-55- $qname = $qnames[ int(($#qnames+1) / 2)];
infernal-1.1.3/hmmer/test-speed/x-psiblast:56: $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/test-speed/x-psiblast-57- if ($?) { print "FAILED: esl-sfetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast-60- if ($n == 1) {
infernal-1.1.3/hmmer/test-speed/x-psiblast:61: $output = `$blastpgp $blastopts -d $targetdb -i $resultdir/$msaname.query.fa -B $resultdir/$msaname.pbl 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-psiblast-62- }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast-65- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-psiblast:66: $output = `$blastpgp $blastopts -d $targetdb -i $resultdir/$msaname.query.fa -B $resultdir/$msaname.pbl 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-psiblast-67- if ($?) { print "FAILED: $blastpgp on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast+-42- # Fetch the query MSA from the benchmark (.sto file)
infernal-1.1.3/hmmer/test-speed/x-psiblast+:43: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-psiblast+-44- if ($?) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast+-46- # Reformat to psiblast format (.pbl file)
infernal-1.1.3/hmmer/test-speed/x-psiblast+:47: $output = `esl-reformat -o $resultdir/$msaname.pbl psiblast $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/test-speed/x-psiblast+-48- if ($?) { print "FAILED: esl-reformat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast+-51- if ($n == 1) {
infernal-1.1.3/hmmer/test-speed/x-psiblast+:52: $output = `$psiblast $blastopts -db $targetdb -in_msa $resultdir/$msaname.pbl 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-psiblast+-53- }
##############################################
infernal-1.1.3/hmmer/test-speed/x-psiblast+-56- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-psiblast+:57: $output = `$psiblast $blastopts -db $targetdb -in_msa $resultdir/$msaname.pbl 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-psiblast+-58- if ($?) { print "FAILED: $psiblast on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-sam-43- # Fetch the query MSA from the benchmark (.sto file)
infernal-1.1.3/hmmer/test-speed/x-sam:44: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-sam-45- if ($?) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-sam-47- # Reformat to A2M format (.a2m file)
infernal-1.1.3/hmmer/test-speed/x-sam:48: $output = `esl-reformat -o $resultdir/$msaname.a2m a2m $resultdir/$msaname.sto`;
infernal-1.1.3/hmmer/test-speed/x-sam-49- if ($?) { print "FAILED: esl-reformat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-sam-51- # Build a model using UCSC's w0.5 script (.mod file)
infernal-1.1.3/hmmer/test-speed/x-sam:52: `(cd $resultdir; $w05 $msaname.a2m $msaname.mod &> /dev/null)`;
infernal-1.1.3/hmmer/test-speed/x-sam-53- if ($? != 0) { print "FAILED: w0.5 on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-sam-56- if ($n == 1) {
infernal-1.1.3/hmmer/test-speed/x-sam:57: $output = `(cd $resultdir; $hmmscore $msaname -i $msaname.mod -db ../$targetdb -sw 2 2>&1)`;
infernal-1.1.3/hmmer/test-speed/x-sam-58- }
##############################################
infernal-1.1.3/hmmer/test-speed/x-sam-61- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-sam:62: $output = `(cd $resultdir; $hmmscore $msaname -i $msaname.mod -db ../$targetdb -sw 2 2>&1)`;
infernal-1.1.3/hmmer/test-speed/x-sam-63- if ($? != 0) { print "FAILED: hmmscore on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ssearch-42- # Fetch the query MSA (.sto file)
infernal-1.1.3/hmmer/test-speed/x-ssearch:43: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-ssearch-44- if ($? != 0) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ssearch-46- # Select median length single sequence as the query (.query.fa file)
infernal-1.1.3/hmmer/test-speed/x-ssearch:47: $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
infernal-1.1.3/hmmer/test-speed/x-ssearch-48- if ($?) { print "FAILED: esl-seqstat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ssearch-51- $qname = $qnames[ int(($#qnames+1) / 2)];
infernal-1.1.3/hmmer/test-speed/x-ssearch:52: $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/test-speed/x-ssearch-53- if ($?) { print "FAILED: esl-sfetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-ssearch-55- # Warmup. (An untimed run, to encourage filesystem to cache the target database.)
infernal-1.1.3/hmmer/test-speed/x-ssearch:56: if ($n == 1) { $output = `$ssearch $ssearch_opts $resultdir/$msaname.query.fa $targetdb 2>&1`; }
infernal-1.1.3/hmmer/test-speed/x-ssearch-57-
##############################################
infernal-1.1.3/hmmer/test-speed/x-ssearch-59- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-ssearch:60: $output = `$ssearch $ssearch_opts $resultdir/$msaname.query.fa $targetdb 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-ssearch-61- if ($? != 0) { print "FAILED: ssearch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-wublast-42- # Fetch the query MSA (.sto file)
infernal-1.1.3/hmmer/test-speed/x-wublast:43: $output = `esl-afetch -o $resultdir/$msaname.sto $querydb $msaname`;
infernal-1.1.3/hmmer/test-speed/x-wublast-44- if ($? != 0) { print "FAILED: esl-afetch on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-wublast-46- # Select median length single sequence as the query (.query.fa file)
infernal-1.1.3/hmmer/test-speed/x-wublast:47: $output = `esl-seqstat -a $resultdir/$msaname.sto | grep "^=" | sort -n -k2 | awk '{print \$2}'`;
infernal-1.1.3/hmmer/test-speed/x-wublast-48- if ($?) { print "FAILED: esl-seqstat on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/test-speed/x-wublast-51- $qname = $qnames[ int(($#qnames+1) / 2)];
infernal-1.1.3/hmmer/test-speed/x-wublast:52: $output = `esl-sfetch -o $resultdir/$msaname.query.fa $resultdir/$msaname.sto $qname`;
infernal-1.1.3/hmmer/test-speed/x-wublast-53- if ($?) { print "FAILED: esl-sfetch on $msaname\n"; next MSA;}
##############################################
infernal-1.1.3/hmmer/test-speed/x-wublast-55- # Warmup. (An untimed run, to encourage filesystem to cache the target database.)
infernal-1.1.3/hmmer/test-speed/x-wublast:56: if ($n==1) { `$blastp $targetdb $resultdir/$msaname.query.fa $blastopts 2>&1`; }
infernal-1.1.3/hmmer/test-speed/x-wublast-57-
##############################################
infernal-1.1.3/hmmer/test-speed/x-wublast-59- $t0 = Benchmark->new;
infernal-1.1.3/hmmer/test-speed/x-wublast:60: $output = `$blastp $targetdb $resultdir/$msaname.query.fa $blastopts 2>&1`;
infernal-1.1.3/hmmer/test-speed/x-wublast-61- if ($? != 0) { print "FAILED: wublast on $msaname\n"; next MSA; }
##############################################
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-64-# Build profiles from the test alignments
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl:65:@output = `$builddir/src/hmmbuild $tmppfx.hmm $tmppfx.sto 2>&1`;
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-66-if ($? != 0) { die "FAIL: hmmbuild failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-68-# You can't hmmpress a file with duplicate HMM names; SSI indexing will reject it.
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl:69:@output = `$builddir/src/hmmpress $tmppfx.hmm 2>&1`;
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-70-if ($? == 0) { die "FAIL: hmmpress should reject indexing an HMM file with duplicate names\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-74-# phmmer should show four results
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl:75:$output = `$builddir/src/phmmer --tblout $tmppfx.tbl $tmppfx.fa $tmppfx.fa 2>&1`;
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-76-if ($? != 0) { die "FAIL: phmmer failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-82-# jackhmmer should show four results
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl:83:$output = `$builddir/src/jackhmmer --tblout $tmppfx.tbl $tmppfx.fa $tmppfx.fa 2>&1`;
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-84-if ($? != 0) { die "FAIL: jackhmmer failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-90-# hmmsearch should show four results
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl:91:$output = `$builddir/src/hmmsearch --tblout $tmppfx.tbl $tmppfx.hmm $tmppfx.fa 2>&1`;
infernal-1.1.3/hmmer/testsuite/i10-duplicate-names.pl-92-if ($? != 0) { die "FAIL: hmmsearch failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl-50-
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl:51:$output = `$builddir/src/hmmbuild -O $tmppfx.sto2 $tmppfx.hmm $tmppfx.sto 2>&1`;
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl-52-if ($? != 0) { die "FAIL: hmmbuild failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl-56-
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl:57:$output = `cat $tmppfx.sto2`;
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl-58-if ($? != 0) { die "FAIL: cat failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl-66-
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl:67:$output = `$builddir/src/hmmalign --mapali $tmppfx.sto $tmppfx.hmm $tmppfx.fa 2>&1`;
infernal-1.1.3/hmmer/testsuite/i11-hmmalign-mapali.pl-68-if ($? != 0) { die "FAIL: hmmalign --mapali failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl-48-
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl:49:@output = `$builddir/src/hmmbuild $tmppfx.hmm $tmppfx.sto 2>&1`;
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl-50-if ($? != 0) { die "FAIL: hmmbuild failed\n"; }
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl-51-
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl:52:$output = `$builddir/src/hmmalign $tmppfx.hmm $tmppfx.fa 2>&1`;
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl-53-if ($? != 0) { die "FAIL: hmmalign failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl-57-
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl:58:#$output = `$builddir/src/hmmalign --allcol $tmppfx.hmm $tmppfx.fa 2>&1`;
infernal-1.1.3/hmmer/testsuite/i12-delete-corruption.pl-59-#if ($? != 0) { die "FAIL: hmmalign failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-31- # homologous sequence fragments: generated from local profile
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:32: `$builddir/src/hmmemit -o $tmppfx.fa -N $n -L 0 -p --unilocal $profile`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-33- if ($? != 0) { die "FAIL: hmmemit"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-38- # random sequences
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:39: `$builddir/easel/miniapps/esl-shuffle -G -N $n -L 50 --amino -o $tmppfx.fa`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-40- if ($? != 0) { die "FAIL: esl-shuffle"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-60-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:61: `$builddir/src/hmmalign -o $tmppfx.sto $hmmfile $fafile > /dev/null 2>&1`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-62- if ($? != 0) { die "FAIL: hmmalign failed"; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-63-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:64: `$builddir/easel/miniapps/esl-reformat -u fasta $tmppfx.sto > $tmppfx.fa1 2>/dev/null`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-65- if ($? != 0) { die "FAIL: first esl-reformat failed"; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-66-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:67: `$builddir/easel/miniapps/esl-reformat -u fasta $fafile > $tmppfx.fa2 2>/dev/null`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-68- if ($? != 0) { die "FAIL: second esl-reformat failed"; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-69-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:70: `diff -b $tmppfx.fa1 $tmppfx.fa2 > /dev/null 2>&1`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-71- if ($? != 0) { die "FAIL: alignment corrupted\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-81- # need report = include threshold to have same hits in .sto, .domtbl
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:82: `$builddir/src/hmmsearch -E 0.01 --domE 0.01 -A $tmppfx.sto --domtbl $tmppfx.dtbl $hmmfile $fafile > /dev/null 2>&1`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-83- if ($? != 0) { die "FAIL: hmmsearch failed"; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-84-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:85: $nlines = `cat $tmppfx.dtbl | grep -v "^#" | wc -l`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-86- if ($nlines == 0) { return 0; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-87-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:88: `$builddir/easel/miniapps/esl-sfetch --index $fafile > /dev/null 2>&1`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-89- if ($? != 0) { die "FAIL: esl-sfetch --index failed"; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-90-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:91: `cat $tmppfx.dtbl | grep -v "^#" | awk '{print \$1, \$18, \$19, \$1}' > $tmppfx.gdf`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-92- if ($? != 0) { die "FAIL: gdf table"; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-93-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:94: `$builddir/easel/miniapps/esl-sfetch -Cf $fafile $tmppfx.gdf > $tmppfx.fa3`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-95- if ($? != 0) { die "FAIL: esl-sfetch failed"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-97- # Grep out name/desc lines because they'll differ: esl-sfetch adds descline.
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:98: `$builddir/easel/miniapps/esl-reformat -u fasta $tmppfx.sto | grep -v "^>" > $tmppfx.fa1 2>/dev/null`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-99- if ($? != 0) { die "FAIL: first esl-reformat failed"; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-100-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:101: `$builddir/easel/miniapps/esl-reformat -u fasta $tmppfx.fa3 | grep -v "^>" > $tmppfx.fa2 2>/dev/null`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-102- if ($? != 0) { die "FAIL: second esl-reformat failed"; }
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-103-
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl:104: `diff -b $tmppfx.fa1 $tmppfx.fa2 > /dev/null 2>&1`;
infernal-1.1.3/hmmer/testsuite/i13-msa-integrity.pl-105- if ($? != 0) { die "FAIL: alignment corrupted"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i14-hmmemit-consensus.pl-66-{
infernal-1.1.3/hmmer/testsuite/i14-hmmemit-consensus.pl:67: @output = `$builddir/src/hmmbuild --wnone --pnone --symfrac $symfrac_choices[$i] $tmppfx.hmm $tmppfx.sto 2>&1`;
infernal-1.1.3/hmmer/testsuite/i14-hmmemit-consensus.pl-68- if ($? != 0) { die "FAIL: hmmbuild failed\n"; }
infernal-1.1.3/hmmer/testsuite/i14-hmmemit-consensus.pl-69-
infernal-1.1.3/hmmer/testsuite/i14-hmmemit-consensus.pl:70: @output = `$builddir/src/hmmemit -C --minl $minl_choices[$i] --minu $minu_choices[$i] $tmppfx.hmm 2>&1`;
infernal-1.1.3/hmmer/testsuite/i14-hmmemit-consensus.pl-71- if ($? != 0) { die "FAIL: hmmemit failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i15-hmmconvert.pl-22-
infernal-1.1.3/hmmer/testsuite/i15-hmmconvert.pl:23:@output = `$builddir/src/hmmconvert $tmppfx.nt.hmm 2>&1`;
infernal-1.1.3/hmmer/testsuite/i15-hmmconvert.pl-24-if ($? != 0) { die "FAIL: hmmconvert of H2 nucleic model failed\n"; }
infernal-1.1.3/hmmer/testsuite/i15-hmmconvert.pl-25-
infernal-1.1.3/hmmer/testsuite/i15-hmmconvert.pl:26:@output = `$builddir/src/hmmconvert $tmppfx.aa.hmm 2>&1`;
infernal-1.1.3/hmmer/testsuite/i15-hmmconvert.pl-27-if ($? != 0) { die "FAIL: hmmconvert of H2 protein model failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i16-build-allins.pl-33-
infernal-1.1.3/hmmer/testsuite/i16-build-allins.pl:34:$output = `$builddir/src/hmmbuild -O $tmppfx.sto2 --hand $tmppfx.hmm $tmppfx.sto`;
infernal-1.1.3/hmmer/testsuite/i16-build-allins.pl-35-if ($? != 0) { die "FAIL: hmmbuild failed unexpectedly\n"; }
infernal-1.1.3/hmmer/testsuite/i16-build-allins.pl-36-
infernal-1.1.3/hmmer/testsuite/i16-build-allins.pl:37:$output = `grep "^seqx" $tmppfx.sto2`;
infernal-1.1.3/hmmer/testsuite/i16-build-allins.pl-38-if ($? != 0) { die "FAIL: grep failed unexpectedly\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-65-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:66:`cat $srcdir/testsuite/$model1.hmm $srcdir/testsuite/$model2.hmm > $tmppfx.hmm`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:67:`cat $srcdir/testsuite/$nmodel1.hmm $srcdir/testsuite/$nmodel2.hmm > $tmppfx.nhmm`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:68:`$builddir/src/hmmpress $tmppfx.hmm`; if ($?) { die "FAIL: hmmpress\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-69-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:70:`cat $srcdir/testsuite/$model1.sto $srcdir/testsuite/$model2.sto > $tmppfx.sto`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-71-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:72:`$builddir/src/hmmemit -c $srcdir/testsuite/$model1.hmm > $tmppfx.fa1`; if ($?) { die "FAIL: hmmemit -c\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:73:`cat $tmppfx.fa1 > $tmppfx.fa2`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:74:`$builddir/src/hmmemit -c $srcdir/testsuite/$model2.hmm >> $tmppfx.fa2`; if ($?) { die "FAIL: hmmemit -c\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-75-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:76:`$builddir/src/hmmemit -N10 $srcdir/testsuite/$model1.hmm > $tmppfx.fa10`; if ($?) { die "FAIL: hmmemit\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-77-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:78:`$builddir/src/hmmemit -p -N10 $srcdir/testsuite/$model1.hmm > $tmppfx.db`; if ($?) { die "FAIL: hmmemit\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:79:`$builddir/src/hmmemit -p -N10 $srcdir/testsuite/$model2.hmm >> $tmppfx.db`; if ($?) { die "FAIL: hmmemit\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:80:`$builddir/easel/miniapps/esl-shuffle -G -N100 -L 400 --amino >> $tmppfx.db`; if ($?) { die "FAIL: esl-shuffle\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-81-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:82:`$builddir/src/hmmemit -p -N2 -L2000 --glocal $srcdir/testsuite/$nmodel1.hmm > $tmppfx.ndb`; if ($?) { die "FAIL: hmmemit\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:83:`$builddir/src/hmmemit -p -N2 -L2000 --glocal $srcdir/testsuite/$nmodel2.hmm >> $tmppfx.ndb`; if ($?) { die "FAIL: hmmemit\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:84:`$builddir/easel/miniapps/esl-shuffle -G -N6 -L 2000 --dna >> $tmppfx.ndb`; if ($?) { die "FAIL: esl-shuffle\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-85-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:86:`echo $model1 > $tmppfx.key`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:87:`echo $model2 >> $tmppfx.key`; if ($?) { die "FAIL: cat\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-88-
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-99-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:100:`$prog $arg1 $arg2 > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:101:`cat $arg1 | $prog - $arg2 > $tmppfx.out2`; if ($?) { die "FAIL: $tag - $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:102:`cat $arg2 | $prog $arg1 - > $tmppfx.out3`; if ($?) { die "FAIL: $tag $tag1 -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-103-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:104:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:105:`diff -b $tmppfx.out1 $tmppfx.out3 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag2 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-106-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:107:$output = `cat $arg1 $arg2 | $prog - - 2>&1`;
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-108-if (!$?) { die "FAIL: $tag should fail on double - -\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-121-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:122:`$prog $tmppfx.hmm.out1 $arg1 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag <hmmfile> $tag1 \n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:123:`cat $arg1 | $prog --informat stockholm $tmppfx.hmm.out2 - | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag <hmmfile> -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:124:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-125-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:126:$output = `$prog - $arg1`;
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-127-if (!$?) { die "FAIL: $tag should reject - for <hmmfile_out>\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-136-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:137:`$prog $arg1 > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:138:`cat $arg1 | $prog - > $tmppfx.out2`; if ($?) { die "FAIL: $tag -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-139-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:140:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`;
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-141-if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-151-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:152:`$prog --seed 42 $arg1 > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:153:`cat $arg1 | $prog --seed 42 - > $tmppfx.out2`; if ($?) { die "FAIL: $tag -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-154-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:155:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`;
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-156-if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-173-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:174:`$prog $arg1 Caudal_act > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:175:`cat $arg1 | $prog - Caudal_act > $tmppfx.out2`; if ($?) { die "FAIL: $tag -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:176:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-177-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:178:`$prog -f $arg1 $arg2 > $tmppfx.out1`; if ($?) { die "FAIL: $tag -f $tag1 $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:179:`cat $arg1 | $prog -f - $arg2 > $tmppfx.out2`; if ($?) { die "FAIL: $tag -f - $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:180:`cat $arg2 | $prog -f $arg1 - > $tmppfx.out3`; if ($?) { die "FAIL: $tag -f $tag1 -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:181:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag -f results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:182:`diff -b $tmppfx.out1 $tmppfx.out3 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag -f results differ if $tag2 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-183-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:184:$output = `cat $arg1 $arg2 | $prog -f - - 2>&1`;
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-185-if (! $?) { die "FAIL: $tag should have failed on double - -\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-187-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:188:`$prog --index $arg1 > $tmppfx.out1`; if ($?) { die "FAIL: $tag --index $tag1\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:189:$output = `cat $arg1 | $prog --index - 2>&1`; if (! $?) { die "FAIL: $tag should reject - for <hmmfile> when using --index\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-190-if ($output !~ /^Can't use - with --index/) { die "FAIL: $tag didn't give expected error message for the - - case.\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-200-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:201:$output = `cat $arg1 | $prog - 2>&1`; if (! $?) { die "FAIL: $tag should reject - for <hmmfile>\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-202-if ($output !~ /^\nError: Can't use - for <hmmfile>/) { die "FAIL: $tag didn't give expected error message.\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-213-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:214:`$prog $arg1 $arg2 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:215:`cat $arg2 | $prog $arg1 - | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag $tag1 -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-216-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:217:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`;
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-218-if ($?) { die "FAIL: $tag results differ if $arg2 comes from stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-219-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:220:$output = `cat $arg1 | $prog - $arg2 2>&1`;
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-221-if (! $?) { die "FAIL: $tag should reject - for $tag1\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-237-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:238:`$prog $arg1 $arg2 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:239:`cat $arg1 | $prog - $arg2 | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag - $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:240:`cat $arg2 | $prog $arg1 - | grep -v "^#" > $tmppfx.out3`; if ($?) { die "FAIL: $tag $tag1 -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-241-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:242:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $prog results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:243:`diff -b $tmppfx.out1 $tmppfx.out3 2>&1 > /dev/null`; if ($?) { die "FAIL: $prog results differ if $tag2 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-244-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:245:$output = `cat $arg1 $arg2 | $prog - - 2>&1`; if (! $?) { die "FAIL: $prog should have failed on double - -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-246-if ($output !~ /^Either <hmmfile> or <seqdb>/) { die "FAIL: $prog didn't give expected error message for the - - case.\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-247-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:248:$output = `cat $arg2 | $prog $arg1b - 2>&1`; if (! $?) { die "FAIL: $prog should fail on multiquery $tag1, stdin $tag2.\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-249-
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-258-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:259:`$prog $arg1 > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:260:`cat $arg1 | $prog - > $tmppfx.out2`; if ($?) { die "FAIL: $tag -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-261-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:262:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $tag results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-263-
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-274-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:275:`$prog $arg1 $arg2 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:276:`cat $arg1 | $prog - $arg2 | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag - $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-277-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:278:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $prog results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-279-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:280:$output = `cat $arg2 | $prog $arg1 - 2>&1`; if (! $?) { die "FAIL: $prog should fail if <seqdb> is -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-281-if ($output !~ /^jackhmmer cannot read <seqdb> from/) { die "FAIL: $prog didn't give expected error message\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-294-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:295:`$prog $arg1 $arg2 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:296:`cat $arg1 | $prog - $arg2 | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag - $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:297:`cat $arg2 | $prog $arg1 - | grep -v "^#" > $tmppfx.out3`; if ($?) { die "FAIL: $tag $tag1 -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-298-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:299:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $prog results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:300:`diff -b $tmppfx.out1 $tmppfx.out3 2>&1 > /dev/null`; if ($?) { die "FAIL: $prog results differ if $tag2 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-301-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:302:$output = `cat $arg1 $arg2 | $prog - - 2>&1`; if (! $?) { die "FAIL: $prog should have failed on double - -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-303-if ($output !~ /^Either <query hmmfile|alignfile> or <seqdb>/) { die "FAIL: $prog didn't give expected error message for the - - case.\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-304-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:305:$output = `cat $arg2 | $prog $arg1b - 2>&1`; if (! $?) { die "FAIL: $prog should fail on multiquery $tag1, stdin $tag2.\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-306-
##############################################
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-316-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:317:`$prog $arg1 $arg2 | grep -v "^#" > $tmppfx.out1`; if ($?) { die "FAIL: $tag $tag1 $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:318:`cat $arg1 | $prog - $arg2 | grep -v "^#" > $tmppfx.out2`; if ($?) { die "FAIL: $tag - $tag2\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:319:`cat $arg2 | $prog $arg1 - | grep -v "^#" > $tmppfx.out3`; if ($?) { die "FAIL: $tag $tag1 -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-320-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:321:`diff -b $tmppfx.out1 $tmppfx.out2 2>&1 > /dev/null`; if ($?) { die "FAIL: $prog results differ if $tag1 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:322:`diff -b $tmppfx.out1 $tmppfx.out3 2>&1 > /dev/null`; if ($?) { die "FAIL: $prog results differ if $tag2 comes through stdin\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-323-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:324:$output = `cat $arg1 $arg2 | $prog - - 2>&1`; if (! $?) { die "FAIL: $prog should have failed on double - -\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-325-if ($output !~ /^Either <seqfile> or <seqdb>/) { die "FAIL: $prog didn't give expected error message for the - - case.\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-326-
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl:327:$output = `cat $arg2 | $prog $arg1b - 2>&1`; if (! $?) { die "FAIL: $prog should fail on multiquery $tag1, stdin $tag2.\n"; }
infernal-1.1.3/hmmer/testsuite/i17-stdin.pl-328-
##############################################
infernal-1.1.3/hmmer/testsuite/i18-nhmmer-generic.pl-127- print "$cmd\n" if $verbose;
infernal-1.1.3/hmmer/testsuite/i18-nhmmer-generic.pl:128: return `$cmd`;
infernal-1.1.3/hmmer/testsuite/i18-nhmmer-generic.pl-129-}
##############################################
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-70-# we don't want the full testsuite to fail.
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl:71:$have_threads = `cat $builddir/src/p7_config.h | grep "^#define HMMER_THREADS"`;
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-72-if($have_threads eq "") {
##############################################
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-92-&create_test_script("$tmppfx.in");
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl:93:`$builddir/src/hmmpress -f $tmppfx.hmm`; if ($?) { die "FAIL: hmmpress"; }
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-94-
##############################################
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-96-# start the hmmpgmd master and 1 worker with 1 core
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl:97:system("$builddir/src/hmmpgmd --master --wport $wport --cport $cport --hmmdb $tmppfx.hmm --pid $tmppfx.pid > /dev/null 2>&1 &");
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-98-if ($?) { die "FAIL: hmmpgmd master failed to start"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-100-sleep 2;
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl:101:system("$builddir/src/hmmpgmd --worker 127.0.0.1 --wport $wport --cpu 1 > /dev/null 2>&1 &");
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-102-if ($?) { die "FAIL: hmmpgmd worker failed to start"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-151- close PID;
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl:152: `kill $pid`;
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-153-
##############################################
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-155- #&create_kill_script("$tmppfx.in");
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl:156: #`cat $tmppfx.in | $builddir/src/hmmc2 -i $host -p $cport -S 2>&1`;
infernal-1.1.3/hmmer/testsuite/i19-hmmpgmd-ga.pl-157- }
##############################################
infernal-1.1.3/hmmer/testsuite/i20-fmindex-core.pl-167- print "$cmd\n" if $verbose;
infernal-1.1.3/hmmer/testsuite/i20-fmindex-core.pl:168: return `$cmd`;
infernal-1.1.3/hmmer/testsuite/i20-fmindex-core.pl-169-}
##############################################
infernal-1.1.3/hmmer/testsuite/i21-rewind.pl-136- print "$cmd\n" if $verbose;
infernal-1.1.3/hmmer/testsuite/i21-rewind.pl:137: return `$cmd`;
infernal-1.1.3/hmmer/testsuite/i21-rewind.pl-138-}
##############################################
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-52-# we don't want the full testsuite to fail.
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl:53:$have_threads = `cat $builddir/src/p7_config.h | grep "^#define HMMER_THREADS"`;
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-54-if($have_threads eq "") {
##############################################
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-74-&create_test_script("$tmppfx.in");
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl:75:`$builddir/src/hmmpress -f $tmppfx.hmm`; if ($?) { die "FAIL: hmmpress"; }
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-76-
##############################################
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-78-# start the hmmpgmd_shard master and 1 worker with 1 core
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl:79:system("$builddir/src/hmmpgmd_shard --master --wport $wport --cport $cport --hmmdb $tmppfx.hmm --pid $tmppfx.pid > /dev/null 2>&1 &");
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-80-if ($?) { die "FAIL: hmmpgmd_shard master failed to start"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-82-sleep 2;
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl:83:system("$builddir/src/hmmpgmd_shard --worker 127.0.0.1 --wport $wport --cpu 1 > /dev/null 2>&1 &");
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-84-if ($?) { die "FAIL: hmmpgmd_shard worker failed to start"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-87-# Run the test script
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl:88:@output = `cat $tmppfx.in | $builddir/src/hmmc2 -i $host -p $cport -S 2>&1`;
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-89-if ($?) { die "FAIL: hmmc2 returned non-zero exit code of $?"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-133- close PID;
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl:134: `kill $pid`;
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-135-
##############################################
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-137- #&create_kill_script("$tmppfx.in");
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl:138: #`cat $tmppfx.in | $builddir/src/hmmc2 -i $host -p $cport -S 2>&1`;
infernal-1.1.3/hmmer/testsuite/i22-hmmpgmd-shard-ga.pl-139- }
##############################################
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-19-
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:20:system("$builddir/src/hmmbuild $tmppfx.hmm $srcdir/testsuite/20aa.sto > /dev/null");
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-21-if ($? != 0) { print "FAIL: hmmbuild failed unexpectedly\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:22:$name = `cat $tmppfx.hmm | grep "^NAME"`;
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-23-if ($name !~ /^NAME \s*test/) { print "FAIL: default naming by MSA name fails\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-24-
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:25:system("$builddir/src/hmmbuild $tmppfx.hmm $srcdir/tutorial/globins4.sto > /dev/null");
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-26-if ($? != 0) { print "FAIL: hmmbuild failed unexpectedly\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:27:$name = `cat $tmppfx.hmm | grep "^NAME"`;
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-28-if ($name !~ /^NAME \s*globins4/) { print "FAIL: naming using file name fails\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-29-
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:30:system("$builddir/src/hmmbuild -n myname $tmppfx.hmm $srcdir/tutorial/fn3.sto > /dev/null");
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-31-if ($? != 0) { print "FAIL: hmmbuild failed unexpectedly\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:32:$name = `cat $tmppfx.hmm | grep "^NAME"`;
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-33-if ($name !~ /^NAME \s*myname/) { print "FAIL: naming using -n fails\n"; exit 1; }
##############################################
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-37-#
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:38:system("cat $srcdir/testsuite/20aa.sto $srcdir/tutorial/fn3.sto > $tmppfx.sto");
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:39:system("$builddir/src/hmmbuild $tmppfx.hmm $tmppfx.sto > /dev/null"); if ($? != 0) { print "FAIL: hmmbuild failed on multi MSA file\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:40:system("$builddir/src/hmmbuild -n myname $tmppfx.hmm $tmppfx.sto > /dev/null 2>&1"); if ($? == 0) { print "FAIL: hmmbuild -n should have failed\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-41-
##############################################
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-44-#
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:45:system("cat $srcdir/testsuite/20aa.sto $srcdir/tutorial/globins4.sto > $tmppfx.sto");
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:46:system("$builddir/src/hmmbuild $tmppfx.hmm $tmppfx.sto > /dev/null 2>&1"); if ($? == 0) { print "FAIL: hmmbuild should have failed\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:47:system("cat $srcdir/tutorial/globins4.sto $srcdir/testsuite/20aa.sto > $tmppfx.sto");
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl:48:system("$builddir/src/hmmbuild $tmppfx.hmm $tmppfx.sto > /dev/null 2>&1"); if ($? == 0) { print "FAIL: hmmbuild should have failed\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i5-hmmbuild-naming.pl-49-
##############################################
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-21-
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl:22:system("$eslreformat -u --rename foo fasta $testsuitedir/Caudal_act.sto > $tmppfx.fa");
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-23-if ($? != 0) { print "FAIL: esl-reformat failed unexpectedly\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-24-
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl:25:system("$hmmalign -o $tmppfx.sto --mapali $testsuitedir/Caudal_act.sto $testsuitedir/Caudal_act.hmm $tmppfx.fa");
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-26-if ($? != 0) { print "FAIL: hmmalign failed unexpectedly\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-27-
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl:28:system("$eslreformat -u fasta $tmppfx.sto > $tmppfx.2.fa");
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-29-if ($? != 0) { print "FAIL: esl-reformat failed unexpectedly\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-30-
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl:31:system("$eslreformat -u fasta $testsuitedir/Caudal_act.sto > $tmppfx.3.fa");
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-32-if ($? != 0) { print "FAIL: esl-reformat failed unexpectedly\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-33-
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl:34:system("cat $tmppfx.fa >> $tmppfx.3.fa");
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-35-if ($? != 0) { print "FAIL: cat failed unexpectedly\n"; exit 1; }
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-36-
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl:37:system("diff $tmppfx.2.fa $tmppfx.3.fa");
infernal-1.1.3/hmmer/testsuite/i6-hmmalign-mapali.pl-38-if ($? != 0) { print "FAIL: --mapali doesn't produce expected sequences\n"; exit 1; }
##############################################
infernal-1.1.3/hmmer/testsuite/i7-hmmbuild-fragments.pl-30-
infernal-1.1.3/hmmer/testsuite/i7-hmmbuild-fragments.pl:31:$output = `$hmmbuild -O $tmppfx.sto2 $tmppfx.hmm $tmppfx.sto 2>&1`;
infernal-1.1.3/hmmer/testsuite/i7-hmmbuild-fragments.pl-32-if ($? != 0) { die "FAIL: hmmbuild failed unexpectedly\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i7-hmmbuild-fragments.pl-37-
infernal-1.1.3/hmmer/testsuite/i7-hmmbuild-fragments.pl:38:$output = `$hmmbuild --fragthresh 0.0 $tmppfx.hmm $tmppfx.sto 2>&1`;
infernal-1.1.3/hmmer/testsuite/i7-hmmbuild-fragments.pl-39-if ($? == 0) { die "FAIL: hmmbuild should have failed but didn't\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i8-nonresidues.pl-45-
infernal-1.1.3/hmmer/testsuite/i8-nonresidues.pl:46:system("$hmmsearch --domtblout $tmppfx.dom $hmm20aa $tmppfx.1 > $tmppfx.out 2>&1");
infernal-1.1.3/hmmer/testsuite/i8-nonresidues.pl-47-if ($? != 0) { die "FAIL: hmmsearch failed on first test sequence\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i8-nonresidues.pl-57-
infernal-1.1.3/hmmer/testsuite/i8-nonresidues.pl:58:system("$hmmsearch --domtblout $tmppfx.dom $hmm20aa $tmppfx.2 > $tmppfx.out 2>&1");
infernal-1.1.3/hmmer/testsuite/i8-nonresidues.pl-59-if ($? != 0) { print "FAIL: hmmsearch failed on second test sequence"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl-63-
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl:64:@output = `$builddir/src/hmmbuild $tmppfx.hmm $tmppfx.sto 2>&1`;
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl-65-if ($? != 0) { die "FAIL: hmmbuild failed\n"; }
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl:66:@output = `$builddir/src/hmmpress $tmppfx.hmm 2>&1`;
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl-67-if ($? != 0) { die "FAIL: hmmpress failed\n"; }
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl-68-
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl:69:@output = `$builddir/src/hmmscan --tblout $tmppfx.tbl1 --domtblout $tmppfx.dtbl1 $tmppfx.hmm $tmppfx.seq 2>&1`;
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl-70-if ($? != 0) { die "FAIL: hmmscan failed\n"; }
##############################################
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl-85-
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl:86:@output = `$builddir/src/hmmsearch --tblout $tmppfx.tbl2 --domtblout $tmppfx.dtbl2 $tmppfx.hmm $tmppfx.seq 2>&1`;
infernal-1.1.3/hmmer/testsuite/i9-optional-annotation.pl-87-if ($? != 0) { die "FAIL: hmmsearch failed\n"; }
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-309-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:310:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-311- + +L +VL GT FL+WL + G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-469-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:470:Query: 55 LVLNLPLQE---AAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-471- + ++ ++L G+ + W+ + G G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-502-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:503:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-504- + + +L +VL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-535-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:536:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-537- + + +L +VL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-663-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:664:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-665- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-696-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:697:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-698- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-729-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:730:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-731- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-761-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:762:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-763- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-794-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:795:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-796- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-826-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:827:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-828- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-859-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:860:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-861- + +L LVL AGT FLIWL D G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-891-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:892:Query: 55 LVLNLPLQE---AAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-893- + ++ +L G+ + W+ + G G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-1180-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:1181:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-1182- + +L +VL AGT FL+WL + + G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-1244-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:1245:Query: 55 LVLNLPL---QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-1246- + + ++ LVL GT FL+WL + + G+G +I+ A +
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-1792-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:1793:Query: 55 LVLNLPLQE----AAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGSIMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-1794- + ++LP + + + L+ GT FL+WL +L G+G I I++ S
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-1825-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:1826:Query: 55 LVLNLPL----QEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGSIMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-1827- + + LP + ++ + L+ T FL+WL +L G+G I I++
##############################################
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-3898-
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out:3899:Query: 58 NL------PLQEAAGVDMTTIMVLDTLVLMAGTYFLIWLTDLNAAMGLGGS-IMIVMASM 110
infernal-1.1.3/hmmer/easel/demotic/examples/example.psiblast.out-3900- L GV I L + L G ++++ ++ + G+G + ++A +
##############################################
infernal-1.1.3/hmmer/easel/devkit/autodoc-64-
infernal-1.1.3/hmmer/easel/devkit/autodoc:65:$text = `cat $cfile`;
infernal-1.1.3/hmmer/easel/devkit/autodoc-66-$nfuncs = &parse_function_documentation($text);
##############################################
infernal-1.1.3/hmmer/easel/devkit/autodoc.md-143-3. An unindented closing brace followed by a blank line.
infernal-1.1.3/hmmer/easel/devkit/autodoc.md:144: The regex fragment for this is `^\}\s*$^\s*$`.
infernal-1.1.3/hmmer/easel/devkit/autodoc.md-145-
##############################################
infernal-1.1.3/hmmer/easel/devkit/sedition-53-
infernal-1.1.3/hmmer/easel/devkit/sedition:54:system("cp $filename $filename.sed.tmp");
infernal-1.1.3/hmmer/easel/devkit/sedition-55-if ($? != 0) {die "failed to make tmp copy"; }
infernal-1.1.3/hmmer/easel/devkit/sedition-56-if (! $writable) {
infernal-1.1.3/hmmer/easel/devkit/sedition:57: system("chmod +w $filename");
infernal-1.1.3/hmmer/easel/devkit/sedition-58- if ($? != 0) { choke "failed to make $filename temporarily writable"; }
infernal-1.1.3/hmmer/easel/devkit/sedition-59-}
infernal-1.1.3/hmmer/easel/devkit/sedition:60:system("sed $sedargs $filename.sed.tmp > $filename");
infernal-1.1.3/hmmer/easel/devkit/sedition-61-if ($? != 0) {choke "sed failed"; }
infernal-1.1.3/hmmer/easel/devkit/sedition-62-if (! $writable) {
infernal-1.1.3/hmmer/easel/devkit/sedition:63: system("chmod -w $filename");
infernal-1.1.3/hmmer/easel/devkit/sedition-64- if ($? != 0) { choke "failed to make $filename temporarily writable"; }
##############################################
infernal-1.1.3/hmmer/easel/devkit/sedition-pp-87-unlink $sourcefile;
infernal-1.1.3/hmmer/easel/devkit/sedition-pp:88:system("mv /tmp/tmp.pp.sedition $sourcefile");
infernal-1.1.3/hmmer/easel/devkit/sedition-pp-89-chmod $mode, $sourcefile;
##############################################
infernal-1.1.3/hmmer/easel/devkit/sqc-414- #
infernal-1.1.3/hmmer/easel/devkit/sqc:415: # The `(true; $cmd)` stuff is because a segfault gets reported by shell,
infernal-1.1.3/hmmer/easel/devkit/sqc-416- # not the process itself; we want to redirect that output too.
##############################################
infernal-1.1.3/hmmer/easel/devkit/sqc-419- print "sqc: running cmd: $cmd\n" if $verbose;
infernal-1.1.3/hmmer/easel/devkit/sqc:420: `(true; $cmd) 2> /dev/null > /dev/null`;
infernal-1.1.3/hmmer/easel/devkit/sqc-421- $status1 = $?;
##############################################
infernal-1.1.3/hmmer/easel/devkit/sqc-423- if ($testtype eq "regression") {
infernal-1.1.3/hmmer/easel/devkit/sqc:424: `(true; $cmd2) 2> /dev/null > /dev/null`;
infernal-1.1.3/hmmer/easel/devkit/sqc-425- $status2 = $?;
##############################################
infernal-1.1.3/hmmer/easel/devkit/sqc-467- {
infernal-1.1.3/hmmer/easel/devkit/sqc:468: system("diff $tmp.REGRESSION.old.$i $tmp.REGRESSION.new.$i > /dev/null");
infernal-1.1.3/hmmer/easel/devkit/sqc-469- if ($? != 0) { $nregress_failed++; }
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6172-%+8tC>YJ,J=T>1<`(U*i7Z\RRc#YTPI6[:*Wna,tE+8s+Khi0QZn<qVN)HT,4I^U<<qbR7_<VuX9nac'c?b^@9c'uItp#=Nf2a;Za
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6173:%`J`ILp#Gdrp$1XC?N5fNig]K3H)n[R^H_YTq3U-d:Ohp"7K</W?b`]rT!sbfq;&))lcY>"p\V//qWc&kdJs5,m*C0prqTXA?]8@*
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6174:%HMqE'qbTI\Xr#QZYM8m92t`+!Z\Rl0a4Gh>ZG$%EO5FuEU]:0`hLBU[Zi0^rjnIg&>6^,r$_Hd1s7I0M&'rQCQKu:-s7(<nMs#$8
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6175-%^92CH^O#^RTD6g+s16u]qYTe_]t_D"3"GueQo?+93G/6d`S::?4FHo<5JI*<_u8`skpp+dF+(*.U@@s@ra328\%dFOl+`hps8V%f
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6195-%qc3LQZ]Bk<DOj"W04Od=(]2VWanMH40<WVUZ-OKYr5gsk^@UdalR^XiV2+ql/d)(-:OVdh\+.b=K^1&3_R"IV#7cq^50VKBnJ#ft
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6196:%PN.(qaq#:u[.sX.>fZPa0)+tH:C[03,:<![\$'`Kl#K86p>$7P_W/rqIgFlEj2;#LV`p(<4hENDoVn&0kN-T2q8n@Rh>Ni10-;b2
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6197-%l.*g>q04:UDtW?"#5R)%k^3GjcS'KhK%iB0acAslj:1JAh6VllO67H@H/44$q/-QN&*r7;s69JE4T++X]q>?!YM@%oAK=QFoPf#7
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6212-%'Do'&@H=ku3Li5SrQ)=Q^@#c1q)ClLQae&]:GJ[[O&F.]C//99A_ZBob[iHtkktd&BI/A/T1@eJ<(lI[9ZLghhtDJOI`>LT^94m2
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6213:%AKT[jq(*i\j&efE.3'f)ZYZluHRa<l1rjosQH"3'(s`idfIJ$pSR\bEZH'8+@pbRtT$)C#HTm`?nB9U1/i\nDbZO"4(/?sVZHXB;
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6214-%a@BS.&[uq:[-$u"JOWl/1/hH/hFk%8p)(<QI9Y=*V4A.Cg1E<:3bCq+aT/HFbo'$3r@%JH(n-'je2*o1DYY[h_6!=bo=!5cn8<NN
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6220-%!C*N1POC&TfniAJV1l%D[ka<<M]I:<UB_!Dh>$+mc9*;K>j'M>a>ladla`V>_iY^hX8s#N8IX6+AnV,4SoAK`>8Z<Yb?0fMa!MQY
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6221:%k'C`d_N&gDbboEa*k7A2(-DdX86B-c>f+<qI<$)"`%:DY&9/)tL.d@"b0VnbX^aZU9GNp4l]sR6LP=:Ge89sg*X>G_N,9$ehY0-R
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6222-%!M7jop*Cg8EpeSUghmsOY5o=E^`=9!E;@W9jP1sAL+2+m#6<CC%=R3SN[JEY,G,nb'^!gV".6O%e;C#]UPE-E8fNDiCtq/B1<[8h
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6223-%/IV/H;EEQ=q*G)Pg8n_59arUiI"(.H]e*!T,IVtTjZ#d5_e/7;glBo=Nb<"9f!]X)k6=Gq%d1XlFc;@(L3;/b*L'F;8.(P8n<#<0
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6224:%Yh$PU5[V[d?,EB3(!#MuT'*t(Q?@/h'AtF8m0gtldTSTlX!ZsdHhP.(`(^aCkmEf!0"($r,JTJe]lsJSLiH3@@s'W4\#(r$`u7=t
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6225-%.e>cApbnN'jd6_U4!VWIhJH]i@G*ro1@mi&#n0iqkIOZ"j7"Lq*m\]Zc9\+jS^ZZ,0>KI(@kIka?b)mgloX^!8!oqMG')YsH10oA
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6235-%Qgh)<e3Tnl%oI/Y["]D+c%JrK]RY#I_8Yr?_/OR1>rm3]^c!aQ1U(jF+O>'1-pcuQ']O?=WM)?T/+.PBX?a:lhWGa"$=WCVhk1Ul
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6236:%"q7`=`sG+,J9$26Uj[au0VSU^Ws=$&J;V*N-k`e:h*XM1`X,%lF5>e)K6c+o0NlRJ<<md,jfRO9=<1?kj1S)K'6Ag]_A)K_#+oi.
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6237-%J>mP>!=so8oQ1jg(42#<Mbc]A3h3s;054"SaTlTcQt?$t6\^PU\!)AsHE9rK^<\jL%XR,^nA6D.VQ(1B6l]UGFP4A/E]m#+`"ttf
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6241-%8cG9#[4hoEEsFWHdKMQrJT,\SjB9d_&eU4>O5T)XCFTFL4LclJ!$Z*s_/\][SAMEJL2ui/1'#?IONYkm_%.)$-S?E*^S;bf;&?sd
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6242:%NV>#s3NSl)KGA@3-]G_`D6o6eq.Aaf$'2#,W'BJ(L@GbNo?cb6LdX`I*VpCILXmV@O;,2gUBi%mM9C^JW'D3kM*bZ>&9gUp99-lT
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6243-%,<39-/Q^jPMM*LsQK7'&:%#Ji/dRDn_Cp:lOTP#Kcc"SX2`%]QlAL`Sg]>!MqsK,JPh*-W"=<-uh?'-%mYVPl%+GFgIM*7bga9,>
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6266-%Ck7ETEq+Om$=1L#+LSWbV/Jnq'"][:5hY:7$Ff3`"QR^J%icXiHS1!/'D_^G6)FZ?G[6&%5b-2\-NoO;SHH?U4:nA#:^"bMY:*A)
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6267:%bVd7_i;'PG+I*7tLeNI&?UAe,"$n72L%%g`4J==QF"W0.0KOZl@sbLS#Y<V>H#6mIXW=llp$@@fEEUgL1YD,T5lk!Ao/iC&@t_`/
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6268-%G`rE*gr;OFD4mkJ!/*%p[6\N"4>;BLJnf>b"Y..uX<V_;l,6QK,C&k>o#q<[+acZA3f;\Z/]8<cA=XH`LDN5]K6/#1KtO1>i@"^`
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6270-%\6j$%DVPep"MCPU<;2L5Ru.=#e.EGI":ds0PDSp?oIrInqgr<&B`i*gYDVHO7#b#G6K3U)JL4%t2q;nn(K;!`/tHCA-YrkI8"@L)
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6273-%Xget\7(?)/LhEjm?MiQ38OOuEdYm/6@*3G%2\q0)S(>KV\.K#R?Q%&(nd0jY+QOmQ&@htXm"e)hduAHO'8Uol[muBY*R!/?Ooo4t
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##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6280-%esAP%phq93Y1\Ne0_ak@2#KYY$iH]IK>[t7C1[P`cPV_&],n@::`:>c2AdU86(&b8GTS))ZB4G8!Peuk,t`;93"Dg>."DO(_bdRV
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6282-%P5^"bc[m]s$aWr^GG09!k8VPVJO3Ur72*:G38JrBPm509%N7Xm-B<d^N.>#8i@rN16%Vh*5M&[&$`d7s'TPP9KcT8Eb_7@Z+X>]Q
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6283:%WF3lgd(<\1+p_gk`oM<uD$_Q%<-RaTYX$uGY5L,W<k?1r`M0Ko$:Nb\lS:H:SKmZ"IWf7H&e5*6ir9BRcnHTL$%BVK%i_*mJ/WHS
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6284-%'YjOq0tP]V5rAq&5@QZ-oU;<:"q,X_GeMTN[X2b_,/*O&-.*^+QmX$o$\8WN%Iq;Ji=<C?d"u_rh9RDL7X.'k^:HGQCc@P9b'#AM
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6294-%irULX"\'!&*k*.5N1Wj?WbU;8:g8)*ESDc<=O/nqIH];$%UIt/-Hm%gH,#V[h$lHY6id<!&aQ_Se7hEXS_,E&Y+$^"VGZ3RI)Xo9
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6299:%4)kGM0o!O+\G-46bj?#B\.A]j=%*[\`8W?a]Qu#L\l,'F<riGGqZI]$ipE#`L<2btYuF*o,j`U]ba?:O[\Yc&!(Q-PM-56q"$j\A
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6301-%WFc:UmXi4dM\aRV@/MG/:0c+_5OQ<SG/&q/Vh;\G/t`:J89&k`3miZ%;T!LTbLQu;].;<fF>eb9':HDlb4QH-ZBj8MLOc.-,M9X:
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps:6302:%?+M@9mX.,,1NSQZM]n`Q%7XWT"5GGH_7d?qCZ<:Xr%PKO-C+\e4HR!"$>^#W$+&d;&Z?R$=mcZOSBNdCEoG3Z`?=7=l894Hg]:dR
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-ecoli.eps-6303-%&YN1-&2Sjm,QOXmM&E)c;]!?fJ[6<u@c'e"h8FHBFtFutP;h8;:N>>!C5!oXr:U8+;JU6PB(a;ZbV$$#B#A-JLTOQ4)\9.S.I?>A
##############################################
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11298-%,>)Y"65B%EcuON1g:o1aB^U,$)"%,ec/VanfQ+5QDOTN"-+t543IX#^=^N,i(D1EBUZ8)VEPgXUofQM,fS"W2KPEHe#2D#U9Nbi[
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11303-%OcKUqE2$tFoBN>!-eWY8>o_S49q7rTQr6+BCSQ=g9uO9ai@!5h7Y*2TobD(uO<>Y'mJ_rb9$^CY(o.6-%^K7C5P-'?AWNr6%!dHg
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11305-%oRhAo+1FqMd\l+g"n(D6S$Ua'5;_glI1)NH]T6P:OhZ*rk!p?LPEfOF_mZ5>^qG@oiCB%Scf"Cfm+rZcWPH3"S<:D*g:r3p^ns\W
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11314-%=BZC1T"K"0m?u.=3/qY8^aGpAmrOHspDJu:9LQtVj@/mtF!IG4]-G"sGVouWiCm?sG*SJVFOs"%3l#$Z7t@1D63Fn`*t5N3<Fu-M
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps:11315:%7c=HhMo#KR2W0`ZD3Y)]3^X2Z;M=Z+L4O/H$LE(ll*b2f>Bgea31-QNQu;iVOnEbU(@5?ZnQ88VBJu5[#4hSXVDQ'tLrZ.T?FB`&
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11316-%>j7NQ#psT+!s"+Yr8Y^<*m;FDD(mU&4KiU'GR8.X-[#OL1;aV'f5Y&da%%Oq>lo)`.@.#XAR/=A5]1E%Xd3dhec;e!k]-5frf7QA
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11320-%>$<dUNoW,t`fK<4p8d:FZ5I^<mjdYdM8r=TSL2a(%Q<8;4QhP4?[g/(BFaj+jpL*o_UF^Eo&SsHDMd0o_<m:]4gJ')7'Z)m/or#k
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps:11321:%M&Rc_$`.\c9Pq\c1Oldl.I_WaCc[M9c[?d`]O.cA=4I9XkQMLnI7FUaZCp0TL4D2sf)rgL?._mhRs[`la/$aM/"_Z`7\OS,;ko2l
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##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11324-%I8b:<5%/%\NU`n;\qPEGX+d\>8`u3/3\QOeXHFd>g<-4]`AF\pi$a.c1A$Wd<q0jr?),26*-cSF4^if_<g6X=el5%+Y"Ic;@So74
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##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11330-%!`M%X8TFD*:eL-YL@nE+_@C+RVecf3%hbWP$$X9P7TG#k$_U)r_afQNWd+Te86:=W1;qOJU.Jpr'$K?KYsS4L;\E99##cPQ=CC,+
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##############################################
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps:11356:%8Ofa0Kd-;'[>0t+Na.7I62DZ+0;R.n@,5K#K6#ai^A+H#It-A4`3\ecB,I3Q3U[o'()$e3ZBZ[7CgrpI$"pEBrW]nu`I`*Fqd6Im
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11357-%4.BN!I8^K8%]Nb>.rqB^;HkWj@SC?][LO$m_3cuaX]RM'BkfB>*I_mjTdq3KS%WeLa)-<jq&`1:F5!*^ogIKmlf/56fpdNP..tL<
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11359-%iA<V-n)/0)B"DTfRSmhK6B39/4KZ-f9(N]t6Rn\c61f8Q"d0';kjth&r.GKB^-0*gpMnfa&!/\hKPPXKrFXr,X\'E?19sV/4d37G
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11361-%FTl))JG$1NH'27FquDp^_,c)7%SQIIe-F+b0ENW8Di$e$Jote*#VAPL"4H:*m745G"Er>)Sg5P@YUhR'\O;JPj,ABQqOt!F*?K>?
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11378-%Ol;g%kTbi4Rn0Gg7Q`]bVC`lpr<W^8<^2VTaaOV>5;e/FRiY@^=>YlpcQ+k+YSr.?lAbci*"a^8r`m:%PXkG/64Vdq[;e(VmKo6&
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11380-%VKm1b+<i('ld4+tF+kULr3YB9QrmeIr-Uj/Y<s3Z$R)l!nP^ZF*V*06g'RJ^IiA#Wr[a(H*[1EC8b\;_g#qOh9FFkBL<!L]q?ebd
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11382-%9?[ZT3e4r&#i$ZrqZf.QGQdn6>CH-[2fRV+*4XT+ef\*6.o<B]s*iS@o[pH]H?(!NaZ$oT?BN_3G)i3UfZh$65[2P7!MhEI&Qh-c
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11384-%*00mJDOjuc*Iu]?e=R`/%<=E)/mc!g?$CTVK7i1cfQG\qF8u6q+e20%'@ACAZqg$Y<hSR/;Lhm8),fhH5ec;gU"T^5X,:nOp>1Zq
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11393-%^XAn_eumLP)1c'`]sQ/k@S<aqXos3X]VSW:Zd)nD*hVkOm:dVi9;Dgd*OYkeMkNgIb4Y!k(Ia[i5]#U/m2S>j\eE^O_ZroJhZLKN
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps:11394:%f&$cmHJ[fY`F48kVcQqYQZ#+`m-a$6G(Y^h3GcjBCs`SSYW+O!Ro`rqBr(9nF>PsZqspf^htutSJg7m"pn.S5R`nVe2Ic<?%i2'+
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11395-%HgX"`N22P<4XR>t#N<[j%Qn'a^\lD*gYtY`ZJDYAC%C88!+TY48a,"<YXQ$L:.gsBe-0F_R^,OR31!dKR&UFk0O,X!G?;1m%oi43
##############################################
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11398-%\Ad5P&p"l/,j$^2K"4Iu`D4XjpiJ\.7iu^FI?kM3Mu48;<#0"..luh"qC:"s6,jDPVPRo?]/7nMVhSM=%)%Vo((+AZqkSa7r]s@B
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infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps:11403:%c<JYc\+Uru`KV'ine<%c#B$!Hcn:`DYbXE&56XY,7<"O-UZm@j>XTSlI9U5GBHPdH1^:EB/aIS,&f,ok),U7_bNnUL+0I6A2m?\I
infernal-1.1.3/hmmer/easel/documentation/figures/rnaseP-bsu-alignment.eps-11404-%;0:r^^Z,E?k5:HE<"F'b2Qo:nSPH$)o$<VOYPun>ErXOOD>*\^5E?1YcKuXSII@gIZ"O?^[S8Y#hHhmEhZ\QIIk2!'fXC=#$=+Lu
##############################################
infernal-1.1.3/hmmer/easel/esl_gumbel.tex-476-We start with the same likelihood equation that arises in censored
infernal-1.1.3/hmmer/easel/esl_gumbel.tex:477:data for a \emph{known} total number of samples $N$ (where $N=n+z$),
infernal-1.1.3/hmmer/easel/esl_gumbel.tex-478-but since $N$ is unknown, we need to integrate over all possible $N$
##############################################
infernal-1.1.3/hmmer/easel/esl_scorematrix.c-352- *
infernal-1.1.3/hmmer/easel/esl_scorematrix.c:353: * $P(b \mid a) = P(ab) / P(a)$, where $P(a) = \sum_b P(ab)$.
infernal-1.1.3/hmmer/easel/esl_scorematrix.c-354- *
##############################################
infernal-1.1.3/hmmer/easel/install-sh-97- case $1 in
infernal-1.1.3/hmmer/easel/install-sh:98: -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
infernal-1.1.3/hmmer/easel/install-sh-99- shift
##############################################
infernal-1.1.3/hmmer/easel/install-sh-130-
infernal-1.1.3/hmmer/easel/install-sh:131: -t=*) transformarg=`echo $1 | sed 's/-t=//'`
infernal-1.1.3/hmmer/easel/install-sh-132- shift
##############################################
infernal-1.1.3/hmmer/easel/install-sh-190- if test -d "$dst"; then
infernal-1.1.3/hmmer/easel/install-sh:191: dst=$dst/`basename "$src"`
infernal-1.1.3/hmmer/easel/install-sh-192- fi
##############################################
infernal-1.1.3/hmmer/easel/install-sh-195-# This sed command emulates the dirname command.
infernal-1.1.3/hmmer/easel/install-sh:196:dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
infernal-1.1.3/hmmer/easel/install-sh-197-
##############################################
infernal-1.1.3/hmmer/easel/install-sh-208- IFS='%'
infernal-1.1.3/hmmer/easel/install-sh:209: set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
infernal-1.1.3/hmmer/easel/install-sh-210- IFS=$oIFS
##############################################
infernal-1.1.3/hmmer/easel/install-sh-231- if test -z "$transformarg"; then
infernal-1.1.3/hmmer/easel/install-sh:232: dstfile=`basename "$dst"`
infernal-1.1.3/hmmer/easel/install-sh-233- else
##############################################
infernal-1.1.3/hmmer/easel/install-sh-238- # don't allow the sed command to completely eliminate the filename.
infernal-1.1.3/hmmer/easel/install-sh:239: test -z "$dstfile" && dstfile=`basename "$dst"`
infernal-1.1.3/hmmer/easel/install-sh-240-
##############################################
infernal-1.1.3/hmmer/easel/m4/ax_compiler_vendor.m4-76- *:) vendor=$ventest; continue ;;
infernal-1.1.3/hmmer/easel/m4/ax_compiler_vendor.m4:77: *) vencpp="defined("`echo $ventest | sed 's/,/) || defined(/g'`")" ;;
infernal-1.1.3/hmmer/easel/m4/ax_compiler_vendor.m4-78- esac
##############################################
infernal-1.1.3/hmmer/easel/m4/ax_compiler_vendor.m4-84- done
infernal-1.1.3/hmmer/easel/m4/ax_compiler_vendor.m4:85: ax_cv_[]_AC_LANG_ABBREV[]_compiler_vendor=`echo $vendor | cut -d: -f1`
infernal-1.1.3/hmmer/easel/m4/ax_compiler_vendor.m4-86- ])
##############################################
infernal-1.1.3/hmmer/easel/m4/ax_pthread.m4-296- ax_pthread_sed='s/conftest\.\$ac_ext/conftest.$ac_objext/g'
infernal-1.1.3/hmmer/easel/m4/ax_pthread.m4:297: ax_pthread_link_step=`$as_echo "$ac_link" | sed "$ax_pthread_sed"`
infernal-1.1.3/hmmer/easel/m4/ax_pthread.m4-298- ax_pthread_2step_ac_link="($ac_compile) && (echo ==== >&5) && ($ax_pthread_link_step)"
##############################################
infernal-1.1.3/hmmer/easel/m4/esl_pic_flags.m4-96- linux*|k*bsd*-gnu)
infernal-1.1.3/hmmer/easel/m4/esl_pic_flags.m4:97: case `basename "$CC"` in
infernal-1.1.3/hmmer/easel/m4/esl_pic_flags.m4-98- icc*|ecc*|ifort*)
##############################################
infernal-1.1.3/hmmer/easel/m4/esl_pic_flags.m4-113- *)
infernal-1.1.3/hmmer/easel/m4/esl_pic_flags.m4:114: case `$CC -V 2>&1 | sed 5q` in
infernal-1.1.3/hmmer/easel/m4/esl_pic_flags.m4-115- *Sun\ C*|*Sun\ F*)
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-58-#
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:59:@output = `$esl_afetch $tmppfx.sto baz`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-60-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-64-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:65:@output = `$esl_afetch $tmppfx.sto XX00003.3`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-66-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-71-# Without SSI, when fetching from a list, MSAs are in order of .sto file, not .list file
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:72:@output = `$esl_afetch -f $tmppfx.sto $tmppfx.list`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-73-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-77-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:78:@output = `$esl_afetch -O $tmppfx.sto $tmppfx.name`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:79:@output = `$esl_afetch $tmppfx.sto $tmppfx.name > $tmppfx.tmp`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-80-system "diff $tmppfx.name $tmppfx.tmp > /dev/null 2>&1"; if ($? != 0) { die "FAIL: esl-afetch bad diff"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-81-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:82:@output = `$esl_afetch -f -o $tmppfx.tmp $tmppfx.sto $tmppfx.list`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:83:@output = `$esl_afetch -f $tmppfx.sto $tmppfx.list > $tmppfx.tmp2`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-84-system "diff $tmppfx.tmp $tmppfx.tmp2 > /dev/null 2>&1"; if ($? != 0) { die "FAIL: esl-afetch bad diff"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-85-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:86:@output = `$esl_afetch --informat stockholm $tmppfx.sto baz`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-87-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-88-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:89:@output = `$esl_afetch --outformat clustal $tmppfx.sto XX00003.3`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-90-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-95-#
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:96:@output = `$esl_afetch --index $tmppfx.sto`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-97-if ($? != 0) { die "FAIL: esl-afetch indexing failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-103-# so the test alignments are fetched with no blank line between #=GF AC line and first seq.
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:104:@output = `$esl_afetch $tmppfx.sto baz`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-105-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-109-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:110:@output = `$esl_afetch $tmppfx.sto XX00003.3`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-111-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-116-# With SSI, when fetching from a list, MSAs are in order of .list file, not .sto file
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:117:@output = `$esl_afetch -f $tmppfx.sto $tmppfx.list`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-118-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-122-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:123:@output = `$esl_afetch -O $tmppfx.sto $tmppfx.name`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:124:@output = `$esl_afetch $tmppfx.sto $tmppfx.name > $tmppfx.tmp`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-125-system "diff $tmppfx.name $tmppfx.tmp > /dev/null 2>&1"; if ($? != 0) { die "FAIL: esl-afetch bad diff"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-126-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:127:@output = `$esl_afetch -f -o $tmppfx.tmp $tmppfx.sto $tmppfx.list`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:128:@output = `$esl_afetch -f $tmppfx.sto $tmppfx.list > $tmppfx.tmp2`; if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-129-system "diff $tmppfx.tmp $tmppfx.tmp2 > /dev/null 2>&1"; if ($? != 0) { die "FAIL: esl-afetch bad diff"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-130-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:131:@output = `$esl_afetch --informat stockholm $tmppfx.sto baz`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-132-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-133-
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl:134:@output = `$esl_afetch --outformat clustal $tmppfx.sto XX00003.3`;
infernal-1.1.3/hmmer/easel/miniapps/esl-afetch.itest.pl-135-if ($? != 0) { die "FAIL: esl-afetch failed, returned nonzero"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-118-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:119:$output = `$eslalimanip -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-120-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-122-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:123:$output = `$eslalimanip --devhelp`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-124-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-127-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:128:$output = `$eslalimanip --rna $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-129-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-131-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:132:system("$eslalimanip -o $tmppfx.o.stk --rna $tmppfx.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-133-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:134:$output = `cat $tmppfx.o.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-135-if ($output !~ /\#=GR seq1 PP 5789\*\*..\*\*88...\*9.9\*\*\*\*88.7..776543210/) { die "FAIL: alignment manipulated incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-136-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:137:$output = `$eslalimanip --dna $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-138-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-140-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:141:$output = `$eslalimanip --amino $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-142-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-144-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:145:$output = `$eslalimanip --rna --informat stockholm $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-146-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-148-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:149:$output = `$eslalimanip --rna --informat pfam $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-150-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-152-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:153:$output = `$eslalimanip --rna --informat afa $tmppfx.afa 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-154-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-156-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:157:$output = `$eslalimanip --rna --outformat afa $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-158-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-160-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:161:$output = `$eslalimanip --rna --outformat psiblast $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-162-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-164-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:165:$output = `$eslalimanip --rna --outformat a2m $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-166-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-168-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:169:$output = `$eslalimanip --rna --lnfract 0.9 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-170-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-172-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:173:$output = `$eslalimanip --rna --lnfract 0.9 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-174-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-179-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:180:$output = `$eslalimanip --rna --lxfract 1.02 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-181-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-186-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:187:$output = `$eslalimanip --rna --lmin 30 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-188-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-193-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:194:$output = `$eslalimanip --rna --lmax 29 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-195-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-200-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:201:$output = `$eslalimanip --rna --rffract 0.953 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-202-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-207-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:208:$output = `$eslalimanip --rna --detrunc 1 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-209-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-214-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:215:$output = `$eslalimanip --rna --xambig 0 $tmppfx.stk2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-216-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-221-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:222:$output = `$eslalimanip --rna --seq-k $tmppfx.list $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-223-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-228-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:229:$output = `$eslalimanip --rna --seq-k $tmppfx.list --informat pfam --small $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-230-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-235-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:236:$output = `$eslalimanip --rna --k-reorder --seq-k $tmppfx.list $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-237-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-242-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:243:$output = `$eslalimanip --rna --seq-r $tmppfx.list $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-244-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-249-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:250:$output = `$eslalimanip --rna --seq-r $tmppfx.list --informat pfam --small $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-251-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-256-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:257:$output = `$eslalimanip --rna --seq-ins 9 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-258-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-263-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:264:$output = `$eslalimanip --rna --seq-ins 9 --seq-ni 3 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-265-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-270-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:271:$output = `$eslalimanip --rna --seq-ins 9 --seq-xi 2 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-272-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-277-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:278:$output = `$eslalimanip --rna --trim $tmppfx.trim.fa $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-279-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-282-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:283:$output = `$eslalimanip --rna --minpp 0.9 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-284-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-287-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:288:$output = `$eslalimanip --rna --reorder $tmppfx.list2 $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-289-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-294-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:295:$output = `$eslalimanip --rna --mask2rf $tmppfx.rfmask $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-296-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-298-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:299:$output = `$eslalimanip --rna --m-keeprf --mask2rf $tmppfx.rfmask $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-300-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-302-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:303:$output = `$eslalimanip --rna --mask2rf $tmppfx.amask $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-304-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-306-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:307:$output = `$eslalimanip --rna --m-keeprf --mask2rf $tmppfx.amask $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-308-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-310-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:311:$output = `$eslalimanip --rna --num-all $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-312-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-315-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:316:$output = `$eslalimanip --rna --num-rf $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-317-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-320-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:321:$output = `$eslalimanip --rna --rm-gc RF $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-322-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-324-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:325:$output = `$eslalimanip --rna --rm-gc SS_cons $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-326-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-328-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:329:$output = `$eslalimanip --rna --rm-gc PP_cons $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-330-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-332-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:333:$output = `$eslalimanip --rna --sindi $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-334-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-337-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl:338:$output = `$eslalimanip --rna --post2pp $tmppfx.post.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimanip.itest.pl-339-if ($? != 0) { die "FAIL: esl-alimanip failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-92-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:93:$output = `$eslalimap -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-94-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-96-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:97:$output = `$eslalimap $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-98-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-101-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:102:$output = `$eslalimap --dna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-103-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-106-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:107:$output = `$eslalimap $tmppfx.1 $tmppfx.3 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-108-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-111-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:112:system("$eslalimap --mask-a2a $tmppfx.a2a --mask-a2rf $tmppfx.a2rf --mask-rf2a $tmppfx.rf2a --mask-rf2rf $tmppfx.rf2rf $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-113-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:114:$output = `cat $tmppfx.a2a`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-115-if ($output !~ /111111111111111111011111111/) { die "FAIL: alignments mapped incorrectly."; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-116-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:117:$output = `cat $tmppfx.a2rf`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-118-if ($output !~ /001111111111111111011111111/) { die "FAIL: alignments mapped incorrectly."; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-119-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:120:$output = `cat $tmppfx.rf2a`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-121-if ($output !~ /111111111111111101111111/) { die "FAIL: alignments mapped incorrectly."; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-122-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:123:$output = `cat $tmppfx.rf2rf`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-124-if ($output !~ /111111111111111101111111/) { die "FAIL: alignments mapped incorrectly."; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-125-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:126:system("$eslalimap --rna --submap $tmppfx.submask $tmppfx.4 $tmppfx.5 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-127-if ($? != 0) { die "FAIL: esl-alimap failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl:128:$output = `cat $tmppfx.submask`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimap.itest.pl-129-if ($output !~ /0011001100111/) { die "FAIL: alignments mapped incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-84-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:85:$output = `$eslalimask -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-86-if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-91-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:92: $output = `$eslalimask $smallA[$pass] --rna $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-93- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-100- if($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:101: $output = `$eslalimask $smallA[$pass] --dna $afileA[$pass] $tmppfx.rfmask 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-102- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-106- }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:107: system("$eslalimask $smallA[$pass] --amino -o $tmppfx.out $afileA[$pass] $tmppfx.fullmask > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:108: $output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-109- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-115-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:116: system("$eslalimask $smallA[$pass] --rna -q -o $tmppfx.out $afileA[$pass] $tmppfx.fullmask > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:117: $output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-118- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-124-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:125: $output = `$eslalimask $smallA[$pass] --amino --informat pfam $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-126- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-132-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:133: $output = `$eslalimask $smallA[$pass] --rna --outformat pfam $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-134- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-141- if($smallA[$pass] eq "") {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:142: $output = `$eslalimask $smallA[$pass] --rna --outformat a2m $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-143- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-150-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:151: $output = `$eslalimask $smallA[$pass] --rna --outformat psiblast $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-152- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-159-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:160: $output = `$eslalimask $smallA[$pass] --rna --outformat afa $afileA[$pass] $tmppfx.fullmask 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-161- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-164-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:165: $output = `$eslalimask $smallA[$pass] --rna -t $afileA[$pass] 12-23 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-166- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-173- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:174: $output = `$eslalimask $smallA[$pass] --rna -t --t-rf $afileA[$pass] 18: 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-175- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-181- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:182: $output = `$eslalimask $smallA[$pass] --rna -t --t-rmins --t-rf $afileA[$pass] 18: 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-183- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-189- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:190: $output = `$eslalimask $smallA[$pass] --rna -t --t-rmins --t-rf $afileA[$pass] 18: 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-191- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-196-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:197: $output = `$eslalimask $smallA[$pass] --rna -g $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-198- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-209- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:210: $output = `$eslalimask $smallA[$pass] --rna -g --keepins $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-211- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-217- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:218: $output = `$eslalimask $smallA[$pass] --rna -g --keepins --gapthresh 0.3 $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-219- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-225- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:226: $output = `$eslalimask $smallA[$pass] --rna -g --keepins --gapthresh 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-227- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-233- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:234: $output = `$eslalimask $smallA[$pass] --rna -g --keepins --gapthresh 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-235- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-240-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:241: $output = `$eslalimask $smallA[$pass] --gmask-all $tmppfx.gmaskall --rna -g --gapthresh 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-242- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:243: $output = `cat $tmppfx.gmaskall`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-244- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-245- if ($output !~ /00111100111100010001111110100111110000/) { die "FAIL: alignment masked incorrectly on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:246: $output = `$eslalimask $smallA[$pass] --gmask-rf $tmppfx.gmaskrf --rna -g --gapthresh 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-247- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:248: $output = `cat $tmppfx.gmaskrf`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-249- if ($output !~ /111111111111111111111/) { die "FAIL: alignment masked incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-254-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:255: $output = `$eslalimask $smallA[$pass] -p --rna $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-256- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-266-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:267: $output = `$eslalimask $smallA[$pass] --pavg 0.73 -p --rna $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-268- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-279- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:280: $output = `$eslalimask $smallA[$pass] --ppcons 0.85 -p --rna $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-281- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-285-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:286: $output = `$eslalimask $smallA[$pass] --pthresh 0.85 --pfract 0.5 --rna -p $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-287- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-296-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:297: $output = `$eslalimask $smallA[$pass] --pmask-all $tmppfx.pmaskall --rna -p --pthresh 0.75 --pfract 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-298- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:299: $output = `cat $tmppfx.pmaskall`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-300- if ($have_rfA[$pass]) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-301- if ($output !~ /00000000010000000001111110000000000000/) { die "FAIL: alignment masked incorrectly on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:302: $output = `$eslalimask $smallA[$pass] --pmask-rf $tmppfx.pmaskrf --rna -p --pthresh 0.75 --pfract 0.7 $afileA[$pass] 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-303- if ($? != 0) { die "FAIL: esl-alimask failed unexpectedly on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl:304: $output = `cat $tmppfx.pmaskrf`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimask.itest.pl-305- if ($output !~ /000001000111111000000/) { die "FAIL: alignment masked incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-73-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:74:$output = `$eslalimerge -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-75-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-77-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:78:$output = `$eslalimerge --rna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-79-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-83-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:84:$output = `$eslalimerge --dna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-85-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-89-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:90:$output = `$eslalimerge --amino $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-91-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-95-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:96:$output = `$eslalimerge --rna --list $tmppfx.list 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-97-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-100-if ($output !~ /\.\.AAAA\.AaaAAAaccccC\.\.\.\-CccCCCCccc\.cccgGggGGggGGg\.\.\./) { die "FAIL: alignments merged incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:101:system("$eslalimerge --rna -o $tmppfx.out $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-102-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:103:$output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-104-if ($output !~ /sequence 3 is the best/) { die "FAIL: alignments merged incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-107-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:108:system("$eslalimerge --rna -v -o $tmppfx.out $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-109-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-110-# don't worry about checking verbose output printed to stdout
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:111:$output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-112-if ($output !~ /sequence 3 is the best/) { die "FAIL: alignments merged incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-114-if ($output !~ /\.\.AAAA\.AaaAAAaccccC\.\.\.\-CccCCCCccccccgGggGGggGGg\.\.\./) { die "FAIL: alignments merged incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:115:$output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-116-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:117:$output = `$eslalimerge --rna --outformat pfam $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-118-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-122-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:123:$output = `$eslalimerge --rna --outformat a2m $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-124-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-127-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:128:$output = `$eslalimerge --rna --outformat psiblast $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-129-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-132-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:133:$output = `$eslalimerge --rna --outformat afa $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-134-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-137-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:138:$output = `$eslalimerge --rna --rfonly $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-139-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-144-# test that hmmer3 fragment annotation is correctly handled (this WILL NOT WORK currently with --small!)
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:145:$output = `$eslalimerge --rna $tmppfx.4 $tmppfx.5 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-146-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-149-# repeat all the same tests (except a2m and psiblast output) but now in small memory mode
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:150:$output = `$eslalimerge --small --rna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-151-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-155-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:156:$output = `$eslalimerge --small --dna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-157-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-161-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:162:$output = `$eslalimerge --small --amino $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-163-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-167-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:168:$output = `$eslalimerge --small --rna --list $tmppfx.list 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-169-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-173-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:174:system("$eslalimerge --small --rna -o $tmppfx.out $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-175-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:176:$output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-177-if ($output !~ /sequence 3 is the best/) { die "FAIL: alignments merged incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-180-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:181:system("$eslalimerge --small --rna -v -o $tmppfx.out $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-182-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-183-# don't worry about checking verbose output printed to stdout
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:184:$output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-185-if ($output !~ /sequence 3 is the best/) { die "FAIL: alignments merged incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-187-if ($output !~ /\.\.AAAA\.AaaAAAaccccC\.\.\.\-CccCCCCccccccgGggGGggGGg\.\.\./) { die "FAIL: alignments merged incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:188:$output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-189-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:190:$output = `$eslalimerge --small --rna --outformat pfam $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-191-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-195-
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl:196:$output = `$eslalimerge --small --rna --rfonly $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alimerge.itest.pl-197-if ($? != 0) { die "FAIL: esl-alimerge failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-68-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:69:$output = `$eslalistat -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-70-if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-79-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:80: $output = `$eslalistat $smallA[$pass] --rna $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-81- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-91-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:92: $output = `$eslalistat $smallA[$pass] --dna $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-93- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-103-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:104: $output = `$eslalistat $smallA[$pass] --amino $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-105- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-116- if($pass == 0) {
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:117: $output = `$eslalistat $smallA[$pass] --informat afa --rna $tmppfx.afa 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-118- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-124-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:125: $output = `$eslalistat $smallA[$pass] -1 --rna $tmppfx.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-126- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-134- # test a file with 2 alignments
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:135: $output = `$eslalistat $smallA[$pass] --rna $tmppfx.dbl.stk 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-136- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-149- # test output file options
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:150: system("$eslalistat --icinfo $tmppfx.ic $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-151- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:152: $output = `cat $tmppfx.ic`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-153- if($output !~ /5 9 1.0\d+ 2.0\d+/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-155-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:156: system("$eslalistat --rinfo $tmppfx.r $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-157- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:158: $output = `cat $tmppfx.r`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-159- if($output !~ /21 34 2.0 0.66\d+ 1.0 0.33\d+/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-161-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:162: system("$eslalistat --pcinfo $tmppfx.pc $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-163- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:164: $output = `cat $tmppfx.pc`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-165- if($output !~ /31\s+18\s+3.0\s+0.0\s+0.0\s+0.0\s+0.0\s+0.0\s+0.0\s+0.0\s+1.0\s+1.0\s+0.0\s+1.0\s+0.0\s+0.82\d+/) {
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-169-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:170: system("$eslalistat --list $tmppfx.list $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-171- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:172: $output = `cat $tmppfx.list`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-173- if($output !~ /seq2.+seq2/s) { die "FAIL: alignment lists created incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-176- if($pass == 0) { # these are incompatible with --small
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:177: system("$eslalistat --psinfo $tmppfx.ps $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-178- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:179: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-180- if($output !~ /seq3 20 0 0 0 1 3 4 0 0 9 2 1 0.67\d+/) {
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-186-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:187: system("$eslalistat --iinfo $tmppfx.i $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-188- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:189: $output = `cat $tmppfx.i`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-190- if($output !~ /16\s+1.0\s+0.33\d+\s+2.0/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-192-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:193: system("$eslalistat --cinfo $tmppfx.c --noambig $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-194- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:195: $output = `cat $tmppfx.c`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-196- if($output !~ /3\s+3\.\d+\s+0\.\d+\s+0\.\d+\s+0/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-198-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:199: system("$eslalistat --bpinfo $tmppfx.bp $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-200- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:201: $output = `cat $tmppfx.bp`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-202- if($output !~ /16\s+34\s+0\s+0\s+0\s+0\s+0\s+0\s+2\s+0\s+0\s+0\s+0\s+0\s+0\s+0\s+0\s+0\s+/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-204-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:205: system("$eslalistat --weight --cinfo $tmppfx.c $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-206- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:207: $output = `cat $tmppfx.c`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-208- if($output !~ /2\s+1\.5\s+0\.\d+\s+0\.\d+\s+0/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-211-
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:212: system("$eslalistat --cinfo $tmppfx.c $smallA[$pass] --rna $tmppfx.dbl.stk > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-213- if ($? != 0) { die "FAIL: esl-alistat failed unexpectedly";}
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl:214: $output = `cat $tmppfx.c`;
infernal-1.1.3/hmmer/easel/miniapps/esl-alistat.itest.pl-215- if($output !~ /3\s+3\.\d+\s+0\.\d+\s+0\.\d+\s+0/) { die "FAIL: alignment statistics calculated incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-71-
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl:72:$output = `$eslcompalign -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-73-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-75-
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl:76:$output = `$eslcompalign --rna $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-77-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-80-
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl:81:$output = `$eslcompalign -c $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-82-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-84-
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl:85:$output = `$eslcompalign -p $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-86-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-88-
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl:89:$output = `$eslcompalign --p-mask $tmppfx.mask -p $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-90-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-92-
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl:93:system("$eslcompalign -c --c2dfile $tmppfx.dfile $tmppfx.1 $tmppfx.2 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-94-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl:95:$output = `cat $tmppfx.dfile`;
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-96-if ($output !~ /^0.000 0.33\d+ 0.000 0.000/) { die "FAIL: alignments compared incorrectly."; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-98-#Test that esl-compalign can handle '~' characters annotating fragments, a la hmmbuild -O in hmmer3.
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl:99:$output = `$eslcompalign --rna $tmppfx.1 $tmppfx.3 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-compalign.itest.pl-100-if ($? != 0) { die "FAIL: esl-compalign failed unexpectedly";}
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-60-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:61:$output = `$eslconstruct -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-62-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-64-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:65:$output = `$eslconstruct $tmppfx.1 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-66-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-70-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:71:$output = `$eslconstruct $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-72-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-74-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:75:$output = `$eslconstruct $tmppfx.3 3>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-76-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-79-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:80:$output = `$eslconstruct -a $tmppfx.1 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-81-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-86-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:87:$output = `$eslconstruct -v $tmppfx.1 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-88-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-94-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:95:system("$eslconstruct -o $tmppfx.stk -x $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-96-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:97:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-98-if ($output !~ /\#=GC SS_cons ::::::::::::::::<<_______>>/) { die "FAIL: consensus structure calculated incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-99-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:100:system("$eslconstruct -o $tmppfx.stk -r $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-101-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:102:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-103-if ($output !~ /\#=GC SS_cons :::::<_______>::<<_______>>/) { die "FAIL: consensus structure calculated incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-104-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:105:system("$eslconstruct -o $tmppfx.stk -c $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-106-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:107:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-108-if ($output !~ /#=GC SS_cons ::::<<<____>->>:<<-<____>>>/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-109-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:110:system("$eslconstruct -o $tmppfx.stk -c --rfc $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-111-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:112:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-113-if ($output !~ /#=GC SS_cons ::::<<<____>->>:<<-<____>>>/) { die "FAIL: consensus stucture calculated incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-115-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:116:system("$eslconstruct -o $tmppfx.stk --indi simpex-2 $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-117-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:118:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-119-if ($output !~ /\#=GC SS_cons ::::<<<____>->>::<--<___>>:/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-120-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:121:system("$eslconstruct -o $tmppfx.stk --indi simpex-2 --rfindi $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-122-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:123:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-124-if ($output !~ /\#=GC SS_cons ::::<<<____>->>::<--<___>>:/) { die "FAIL: consensus stucture calculated incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-126-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:127:system("$eslconstruct -o $tmppfx.stk --ffreq 0.6 $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-128-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:129:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-130-if ($output !~ /#=GC SS_cons ::::<<<____>->>:<<-<____>>>/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-131-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:132:system("$eslconstruct -o $tmppfx.stk --ffreq 0.7 $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-133-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:134:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-135-if ($output !~ /#=GC SS_cons :::::::::::::::::<_______>:/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-136-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:137:system("$eslconstruct -o $tmppfx.stk --fmin $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-138-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:139:$output = `cat $tmppfx.stk`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-140-if ($output !~ /#=GC SS_cons ::::<<<____>->>:<<-<____>>>/) { die "FAIL: consensus stucture calculated incorrectly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-141-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:142:system("$eslconstruct -l $tmppfx.list -o $tmppfx.stk --fmin $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-143-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:144:$output = `cat $tmppfx.list`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-145-if ($output !~ /simpex-1/) { die "FAIL: consensus stucture calculated incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-147-
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:148:system("$eslconstruct --lmax 1 -l $tmppfx.list -o $tmppfx.stk --fmin $tmppfx.1 > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-149-if ($? != 0) { die "FAIL: esl-construct failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl:150:$output = `cat $tmppfx.list`;
infernal-1.1.3/hmmer/easel/miniapps/esl-construct.itest.pl-151-if ($output !~ /simpex-1/) { die "FAIL: consensus stucture calculated incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-32-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:33:$output = `$eslmask -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-34-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-36-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:37:$output = `$eslmask $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-38-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-41-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:42:$output = `$eslmask -r $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-43-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-46-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:47:system("$eslmask -o $tmppfx.out $tmppfx.1 $tmppfx.2 2>&1");
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-48-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:49:$output = `cat $tmppfx.out`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-50-if ($output !~ /aaAAAAAAAAXXXXXXXXXXCCCCCCCCcc/) { die "FAIL: seq masked incorrectly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-52-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:53:$output = `$eslmask -l $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-54-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-57-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:58:$output = `$eslmask -lr $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-59-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-62-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:63:$output = `$eslmask -m N $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-64-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-67-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:68:$output = `$eslmask -x 2 $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-69-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-72-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:73:$output = `$eslmask -x 7 $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-74-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-77-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:78:$output = `$eslmask -rx 2 $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-79-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-82-
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl:83:$output = `$eslmask -rx 7 $tmppfx.1 $tmppfx.2 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-mask.itest.pl-84-if ($? != 0) { die "FAIL: esl-mask failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-83-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:84:$output = `$eslseqrange -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-85-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-89-if(-e "$tmppfx.fa.ssi") { unlink "$tmppfx.fa.ssi"; } # erase the index if it exists
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:90:$output = `$eslsfetch --index $tmppfx.fa 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-91-if ($? != 0) { die "FAIL: esl-sfetch --index failed unexpectedly"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-92-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:93:$output = `$eslseqrange $tmppfx.fa 1 31 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-94-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-97-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:98:$output = `$eslseqrange $tmppfx.fa 1 31 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-99-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-101-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:102:$output = `$eslseqrange $tmppfx.fa 17 31 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-103-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-105-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:106:$output = `$eslseqrange $tmppfx.fa 1 13 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-107-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-109-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:110:$output = `$eslseqrange $tmppfx.fa 1 3 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-111-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-113-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:114:$output = `$eslseqrange $tmppfx.fa 2 3 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-115-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-117-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:118:$output = `$eslseqrange $tmppfx.fa 3 3 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-119-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-122-# test --informat
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:123:$output = `$eslseqrange --informat fasta $tmppfx.fa 3 3 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-124-if ($? != 0) { die "FAIL: esl-seqrange failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-127-# test cases we expect to fail
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:128:$output = `$eslseqrange $tmppfx.fa 1 32 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-129-if ($? == 0) { die "FAIL: esl-seqrange did not fail when expected"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-130-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:131:$output = `$eslseqrange $tmppfx.fa 31 1 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-132-if ($? == 0) { die "FAIL: esl-seqrange did not fail when expected"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-133-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:134:$output = `$eslseqrange $tmppfx.fa -1 1 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-135-if ($? == 0) { die "FAIL: esl-seqrange did not fail when expected"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-136-
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl:137:$output = `$eslseqrange $tmppfx.fa 1 -1 2>&1`;
infernal-1.1.3/hmmer/easel/miniapps/esl-seqrange.itest.pl-138-if ($? == 0) { die "FAIL: esl-seqrange did not fail when expected"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-344-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:345:$output = `$eslssdraw -h`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-346-if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-360-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:361: system("$eslssdraw $smallA[$pass] $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-362- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:363: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-364- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-368-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:369: system("$eslssdraw $smallA[$pass] -d $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-370- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:371: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-372- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-376-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:377: system("$eslssdraw $smallA[$pass] --prob $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-378- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:379: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-380- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-383-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:384: system("$eslssdraw $smallA[$pass] --ifreq $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-385- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:386: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-387- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-390-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:391: system("$eslssdraw $smallA[$pass] --iavglen $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-392- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:393: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-394- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-398-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:399: system("$eslssdraw $smallA[$pass] --dall $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-400- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:401: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-402- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-405-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:406: system("$eslssdraw $smallA[$pass] --dint $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-407- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:408: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-409- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-412-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:413: system("$eslssdraw $smallA[$pass] --mutinfo $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-414- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:415: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-416- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-419-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:420: system("$eslssdraw $smallA[$pass] --span $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-421- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:422: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-423- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-426-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:427: system("$eslssdraw $smallA[$pass] --span $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-428- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:429: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-430- if($output !~ /\(tRNA 71 21\)/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-433-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:434: system("$eslssdraw $smallA[$pass] --info --prob --ifreq --dall --dint --mutinfo --span --tabfile $tmppfx.tab $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-435- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:436: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-437- if($output !~ /setcmykcolor \(g\).+moveto show/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:438: $output = `cat $tmppfx.tab`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-439- if($output !~ /Information content data/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-453-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:454: system("$eslssdraw $smallA[$pass] --rf $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-455- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:456: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-457- if($output !~ /\(\*REFERENCE\* \(\"#=GC RF\"\)\) 212.49 418.24 moveto show/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-460- if($pass == 0) {
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:461: system("$eslssdraw $smallA[$pass] --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-462- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:463: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-464- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-474-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:475: system("$eslssdraw $smallA[$pass] --mask-col --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-476- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:477: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-478- if($output !~ /\%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.00\d* 1.00\d* 0.00\d* 0.00\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-479-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:480: system("$eslssdraw $smallA[$pass] --mask-diff $tmppfx.mask2 --mask-col --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-481- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:482: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-483- if($output !~ /\%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.00\d* 0.00\d* 0.00\d* 0.20\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-484-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:485: system("$eslssdraw $smallA[$pass] --mask-diff $tmppfx.mask2 --mask-col --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-486- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:487: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-488- if($output !~ /\%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.00\d* 0.00\d* 0.00\d* 0.20\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-489-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:490: system("$eslssdraw $smallA[$pass] --no-leg $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-491- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:492: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-493- if($output =~ /\(LEGEND\) 134.00 216.00 moveto show/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-494-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:495: system("$eslssdraw $smallA[$pass] --no-head $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-496- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:497: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-498- if($output =~ /\(tRNA 71 21\) 96.98 418.24 moveto show/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-499-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:500: system("$eslssdraw $smallA[$pass] --no-foot $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-501- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:502: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-503- if($output =~ /\(Created by 'esl-ssdraw'. Copyright \(C\) 2010 Howard Hughes Medical Institute.\) 12.00 12.00 moveto show/) { die "FAIL: postscript diagram drawn incorrectly on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-506- if($pass == 0) {
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:507: system("$eslssdraw $smallA[$pass] --no-pp --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-508- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:509: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-510- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-521-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:522: system("$eslssdraw $smallA[$pass] --no-bp --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-523- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:524: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-525- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-536-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:537: system("$eslssdraw $smallA[$pass] --no-ol --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-538- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:539: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-540- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-552- # NOTE: for --no-ntpp we don't actually check that residues are not drawn on PP diagrams
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:553: system("$eslssdraw $smallA[$pass] --no-ntpp --indi $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-554- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:555: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-556- # should include tRNA2, tRNA3, and tRNA5 only
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-568-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:569: system("$eslssdraw $smallA[$pass] --no-cnt --info $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-570- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:571: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-572- if($output =~ /setcmykcolor (g)\s+168\.\d+\s+392\.\d+\s+moveto show/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-573-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:574: system("$eslssdraw $smallA[$pass] --cthresh 0.4 --info $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-575- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:576: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-577- if($output =~ /setcmykcolor (G)\s+168\.\d+\s+392\.\d+\s+moveto show/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-578-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:579: system("$eslssdraw $smallA[$pass] --cambig --info $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-580- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:581: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-582- if($output =~ /setcmykcolor (K)\s+168\.\d+\s+392\.\d+\s+moveto show/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-583-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:584: system("$eslssdraw $smallA[$pass] --cambig --cthresh 0.4 --info $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-585- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:586: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-587- if($output =~ /setcmykcolor (C)\s+168\.\d+\s+376\.\d+\s+moveto show/) { die "FAIL: tab file incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-588-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:589: system("$eslssdraw $smallA[$pass] --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-590- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:591: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-592- if($output !~ /\%nucleotide 3\nnewpath\n 171.00 379.00 3.0 0 360 arc closepath\n 0.0\d*0 0.63\d* 1.0\d*0 0.0\d*0 setcmykcolor\n stroke/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-593-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:594: system("$eslssdraw $smallA[$pass] --mask-x --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-595- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:596: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-597- if($output !~ /stroke\n 175.00 375.00 moveto -8.0 8.0 rlineto closepath/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-598-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:599: system("$eslssdraw $smallA[$pass] --mask-u --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-600- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:601: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-602- if($output !~ /\%nucleotide 3\nnewpath\n 168.00 376.00 moveto 0 6.0 rlineto 6.0 0 rlineto 0 -6.0 rlineto closepath\n 0.00\d* 0.63\d* 1.00\d* 0.00\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-603-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:604: system("$eslssdraw $smallA[$pass] --mask-a --mask-x --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-605- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:606: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-607- if($output !~ /%nucleotide 3\nnewpath\n 0.00\d* 0.63\d* 1.00\d* 0.00\d* setcmykcolor\n 167.00 375.00 moveto 8.0 8.0 rlineto closepath\n stroke/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-608-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:609: system("$eslssdraw $smallA[$pass] --mask-a --mask-u --mask $tmppfx.mask1 $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-610- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:611: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-612- if($output !~ /\%nucleotide 3\nnewpath\n 168.50 376.50 moveto 0 5.0 rlineto 5.0 0 rlineto 0 -5.0 rlineto closepath\n 0.00\d* 0.63\d* 1.00\d* 0.00\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-613-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:614: system("$eslssdraw $smallA[$pass] --dfile $tmppfx.dfile $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:615: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-616- if($output !~ /%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.92\d* 0.84\d* 0.00\d* 0.08\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-617-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:618: system("$eslssdraw $smallA[$pass] --mask $tmppfx.mask1 --dfile $tmppfx.dfile $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:619: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-620- if($output !~ /%nucleotide 3\nnewpath\n 171.00 379.00 3.0 0 360 arc closepath\n 0.9200 0.8400 0.00\d* 0.0800 setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-621-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:622: system("$eslssdraw $smallA[$pass] --efile $tmppfx.efile $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:623: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-624- if($output !~ /\%nucleotide 3\nnewpath\n 166.40 374.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.03 0.17 0.20 0.14 setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-625-
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:626: system("$eslssdraw $smallA[$pass] --ifreq --ifile $tmppfx.ifile $alifile $templatefile $tmppfx.ps > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-627- if ($? != 0) { die "FAIL: esl-ssdraw failed unexpectedly on pass $pass2write";}
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl:628: $output = `cat $tmppfx.ps`;
infernal-1.1.3/hmmer/easel/miniapps/esl-ssdraw.itest.pl-629- if($output !~ /\%nucleotide 45\nnewpath\n 198.40 312.40 moveto 0 8 rlineto 8 0 rlineto 0 -8 rlineto closepath\n 0.00\d* 0.94\d* 1.00\d* 0.00\d* setcmykcolor/) { die "FAIL: postscript diagram drawn incorrectly written on pass $pass2write"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-28-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:29:$output = `$builddir/miniapps/esl-translate -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-30-if ($output !~ / coords=1\.\.192\s+length=64\s+frame=1/) { die "FAIL: standard genetic code mistranslated? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-32-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:33:$output = `$builddir/miniapps/esl-translate -c 3 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-34-if ($output !~ / coords=1\.\.195\s+length=65\s+frame=1/) { die "FAIL: yeast mito genetic code mistranslated? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-36-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:37:$output = `$builddir/miniapps/esl-translate -c 14 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-38-if ($output !~ / coords=1\.\.198\s+length=66\s+frame=1/) { die "FAIL: alt flatworm genetic code mistranslated? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-43-# Initiator is always M.
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:44:$output = `$builddir/miniapps/esl-translate -M -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-45-if ($output !~ / coords=1\.\.192\s+length=64\s+frame=1/) { die "FAIL: standard genetic code initiators mishandled w/ -M? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-47-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:48:$output = `$builddir/miniapps/esl-translate -M -c 3 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-49-if ($output !~ / coords=4\.\.195\s+length=64\s+frame=1/) { die "FAIL: yeast mito genetic code initiators mishandled w/ -M? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-51-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:52:$output = `$builddir/miniapps/esl-translate -M -c 14 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-53-if ($output !~ / coords=7\.\.198\s+length=64\s+frame=1/) { die "FAIL: alt flatworm genetic code initiators mishandled w/ -M? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-56-# Use only AUG initiator, -m option.
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:57:$output = `$builddir/miniapps/esl-translate -m -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-58-if ($output !~ / coords=7\.\.192\s+length=62\s+frame=1/) { die "FAIL: standard genetic code AUG starts mishandled w/ -m? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-60-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:61:$output = `$builddir/miniapps/esl-translate -m -c 3 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-62-if ($output !~ / coords=7\.\.195\s+length=63\s+frame=1/) { die "FAIL: yeast mito genetic code AUG starts mishandled w/ -m? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-64-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:65:$output = `$builddir/miniapps/esl-translate -m -c 14 -l 60 $tmppfx.fa | $builddir/miniapps/esl-reformat pfam -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-66-if ($output !~ / coords=7\.\.198\s+length=64\s+frame=1/) { die "FAIL: alt flatworm genetic code AUG starts mishandled w/ -m? unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-86-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:87:$output = `$builddir/miniapps/esl-translate -l 25 --watson $tmppfx.fa`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-88-if ($output !~ / coords=4\.\.81\s+length=26\s+frame=1/) { die "FAIL: ambiguity codes mishandled by translation - unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-90-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:91:$output = `$builddir/miniapps/esl-translate -M -l 25 --watson $tmppfx.fa`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-92-if ($output !~ / coords=4\.\.81\s+length=26\s+frame=1/) { die "FAIL: ambiguity codes mishandled by translation - unexpected desc line"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-99-#
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:100:system("$builddir/miniapps/esl-shuffle -G --dna -N 2 -L 10000 > $tmppfx.fa");
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:101:$out1 = `$builddir/miniapps/esl-translate $tmppfx.fa`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:102:$out2 = `$builddir/miniapps/esl-translate -W $tmppfx.fa`;;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-103-if ($out1 ne $out2) { die "FAIL: default vs. windowed (-W) give different results"; }
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-108-#
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:109:system("$builddir/miniapps/esl-sfetch --index $tmppfx.fa > /dev/null");
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:110:@output = `$builddir/miniapps/esl-translate -l 100 $tmppfx.fa`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-111-foreach $line (@output)
##############################################
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-136-
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl:137: $out2 = `$builddir/miniapps/esl-sfetch -c $start..$end $tmppfx.fa $source | $builddir/miniapps/esl-translate -l $aalen -`;
infernal-1.1.3/hmmer/easel/miniapps/esl-translate.itest.pl-138- if ($has_leading_stop) { $expected_start = 4; } else { $expected_start = 1; }
##############################################
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl-73- # one way to fail: there isn't a test driver at all
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl:74: `grep $flag $module`;
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl-75- if ($? != 0) { printf("%40s[NO DRIVER]\n", ""); push @nodriverlist, $module; next; }
##############################################
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl-81-
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl:82: `$top_builddir/$progname > /dev/null 2>&1`;
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl-83- if ($? != 0) { printf("%40s[UTEST FAILED ]\n", ""); next; };
##############################################
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl-85-
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl:86: $output = `(cd $top_builddir; gcov $basecfile)`;
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl-87- if ($output =~ /File.*$basecfile.*\nLines executed:\s*(\d+\.\d+)% of\s+(\d+)/) {
##############################################
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl-100- foreach $badmodule (@nodriverlist) {
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl:101: $output = `sloccount $badmodule`;
infernal-1.1.3/hmmer/easel/testsuite/coverage_report.pl-102- if ($output =~ /ansic:\s+(\d+)/) { $nlines_nodrivers += $1; }
##############################################
infernal-1.1.3/hmmer/easel/testsuite/e2.sh-13-
infernal-1.1.3/hmmer/easel/testsuite/e2.sh:14:output=`cat $alifile | $prog - 2>&1 | head -n 1 | grep -c "^Format of seqfile - unrecognized."`
infernal-1.1.3/hmmer/easel/testsuite/e2.sh-15-if test "$output" = 0
##############################################
infernal-1.1.3/hmmer/easel/testsuite/e2.sh-20-
infernal-1.1.3/hmmer/easel/testsuite/e2.sh:21:output=`cat $alifile | $prog --informat stockholm - 2>&1`
infernal-1.1.3/hmmer/easel/testsuite/e2.sh-22-if test $? -gt 0
##############################################
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-45-# esl-reformat tests
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:46:system("$reformat fasta $tmppfx.dna > $tmppfx.out 2>&1"); if ($? != 0) { print "FAIL: reformat failed on .dna test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:47:system("diff $tmppfx.dna $tmppfx.out > /dev/null 2>&1"); if ($? != 0) { print "FAIL: reformat changed .dna test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-48-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:49:system("$reformat fasta $tmppfx.aa > $tmppfx.out 2>&1"); if ($? != 0) { print "FAIL: reformat failed on .aa test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:50:system("diff $tmppfx.aa $tmppfx.out > /dev/null 2>&1"); if ($? != 0) { print "FAIL: reformat changed .aa test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-51-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:52:$output = `$reformat fasta $tmppfx.bad 2>&1`; if ($? == 0) { print "FAIL: reformat should have failed on .bad test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-53-if (! $output =~ /Illegal character %/) { print "FAIL: reformat should have found illegal % in .bad test\n"; exit 1; }
##############################################
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-55-# esl-seqstat tests
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:56:$output = `$seqstat --dna $tmppfx.dna 2>&1`; if ($? != 0) { print "FAIL: seqstat failed on .dna test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-57-($n) = $output =~ /Total # residues:\s+(\d+)/; if ($n != 32) { print "FAIL: seqstat sees wrong residue count ($n) in .dna test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-58-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:59:$output = `$seqstat $tmppfx.aa 2>&1`; if ($? != 0) { print "FAIL: seqstat failed on .aa test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-60-($n) = $output =~ /Total # residues:\s+(\d+)/; if ($n != 53) { print "FAIL: seqstat sees wrong residue count ($n) in .aa test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-61-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:62:$output = `$seqstat $tmppfx.bad 2>&1`; if ($? == 0) { print "FAIL: seqstat should have failed on .bad test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-63-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-64-# esl-shuffle tests
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:65:system("$shuffle $tmppfx.dna > $tmppfx.out 2>&1"); if ($? != 0) { print "FAIL: shuffle failed on .dna test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:66:system("$seqstat --dna -c $tmppfx.out > $tmppfx.out2 2>&1"); if ($? != 0) { print "FAIL: seqstat -c failed on shuffled .dna\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:67:system("$seqstat --dna -c $tmppfx.dna > $tmppfx.out3 2>&1"); if ($? != 0) { print "FAIL: seqstat -c failed on .dna test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:68:system("diff $tmppfx.out2 $tmppfx.out3 > /dev/null 2>&1"); if ($? != 0) { print "FAIL: shuffle changed .dna composition\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-69-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:70:system("$shuffle $tmppfx.aa > $tmppfx.out 2>&1"); if ($? != 0) { print "FAIL: shuffle failed on .aa test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:71:system("$seqstat -c $tmppfx.out > $tmppfx.out2 2>&1"); if ($? != 0) { print "FAIL: seqstat -c failed on shuffled .aa\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:72:system("$seqstat -c $tmppfx.aa > $tmppfx.out3 2>&1"); if ($? != 0) { print "FAIL: seqstat -c failed on .aa test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:73:system("diff $tmppfx.out2 $tmppfx.out3 > /dev/null 2>&1"); if ($? != 0) { print "FAIL: shuffle changed .aa composition\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-74-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:75:$output = `$shuffle $tmppfx.bad 2>&1`; if ($? == 0) { print "FAIL: shuffle should have failed on .bad test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-76-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-77-# esl-sfetch tests
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:78:system("$sfetch --index $tmppfx.aa >/dev/null 2>&1"); if ($? != 0) { print "FAIL: sfetch --index failed on .aa test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:79:$output = `$sfetch -c 27..27 $tmppfx.aa test 2>&1 | grep -v "^>"`; if ($? != 0) { print "FAIL: sfetch failed on .aa test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-80-if (! $output =~ /^\*/) { print "FAIL: sfetch didn't retrieve * on .aa test ($output)\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-81-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:82:system("$sfetch --index $tmppfx.dna >/dev/null 2>&1"); if ($? != 0) { print "FAIL: sfetch --index failed on .dna test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:83:$output = `$sfetch -c 16..16 $tmppfx.aa test 2>&1 | grep -v "^>"`; if ($? != 0) { print "FAIL: sfetch failed on .dna test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-84-if (! $output =~ /^\*/) { print "FAIL: sfetch didn't retrieve * on .dna test ($output)\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-85-
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl:86:$output = `$sfetch --index $tmppfx.bad 2>&1`; if ($? == 0) { print "FAIL: sfetch --index should have failed on .bad test\n"; exit 1; }
infernal-1.1.3/hmmer/easel/testsuite/i1-degen-residues.pl-87-
##############################################
infernal-1.1.3/hmmer/easel/testsuite/i2-ncbi-indices.pl-35-#
infernal-1.1.3/hmmer/easel/testsuite/i2-ncbi-indices.pl:36:$output = `$top_builddir/miniapps/esl-seqstat -a $tmppfx.fa 2>&1`;
infernal-1.1.3/hmmer/easel/testsuite/i2-ncbi-indices.pl-37-if ($? != 0) { die "FAIL: esl-seqstat fails to read BLAST-formatted FASTA file\n"; }
##############################################
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl-76-
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl:77:$output = `$builddir/miniapps/esl-reformat stockholm $tmppfx.sto1 2>&1`;
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl-78-if ($? == 0) { die "FAIL: blank AC,DE lines should be invalid Stockholm format (bug #e5) (1)\n"; }
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl-79-
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl:80:$output = `$builddir/miniapps/esl-reformat stockholm $tmppfx.sto2 2>&1`;
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl-81-if ($? == 0) { die "FAIL: blank AC,DE lines should be invalid Stockholm format (bug #e5) (2)\n"; }
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl-82-
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl:83:$output = `$builddir/miniapps/esl-reformat stockholm $tmppfx.sto3`;
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl-84-if ($? != 0) { die "FAIL: blank CC line should be valid Stockholm format (1)\n"; }
##############################################
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl-86-
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl:87:$output = `$builddir/miniapps/esl-reformat stockholm $tmppfx.sto4`;
infernal-1.1.3/hmmer/easel/testsuite/i3-blank-gf.pl-88-if ($? != 0) { die "FAIL: blank CC line should be valid Stockholm format (2)\n"; }
##############################################
infernal-1.1.3/hmmer/easel/testsuite/valgrind_report.pl-55- # one way to fail: there isn't a test driver at all
infernal-1.1.3/hmmer/easel/testsuite/valgrind_report.pl:56: `grep $flag $module`;
infernal-1.1.3/hmmer/easel/testsuite/valgrind_report.pl-57- if ($? != 0) { printf(" [NO DRIVER]\n"); next; }
##############################################
infernal-1.1.3/hmmer/easel/testsuite/valgrind_report.pl-64-
infernal-1.1.3/hmmer/easel/testsuite/valgrind_report.pl:65: $output = `valgrind $top_builddir/$progname 2>&1`;
infernal-1.1.3/hmmer/easel/testsuite/valgrind_report.pl-66- if ($? != 0) { printf(" [VALGRIND FAILED]\n"); next; };
##############################################
infernal-1.1.3/hmmer/easel/config.guess-34-
infernal-1.1.3/hmmer/easel/config.guess:35:me=`echo "$0" | sed -e 's,.*/,,'`
infernal-1.1.3/hmmer/easel/config.guess-36-
##############################################
infernal-1.1.3/hmmer/easel/config.guess-102-: ${TMPDIR=/tmp} ;
infernal-1.1.3/hmmer/easel/config.guess:103: { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
infernal-1.1.3/hmmer/easel/config.guess-104- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
##############################################
infernal-1.1.3/hmmer/easel/config.guess-151- EOF
infernal-1.1.3/hmmer/easel/config.guess:152: eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`"
infernal-1.1.3/hmmer/easel/config.guess-153-
##############################################
infernal-1.1.3/hmmer/easel/config.guess-188- earmv*)
infernal-1.1.3/hmmer/easel/config.guess:189: arch=`echo "$UNAME_MACHINE_ARCH" | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
infernal-1.1.3/hmmer/easel/config.guess:190: endian=`echo "$UNAME_MACHINE_ARCH" | sed -ne 's,^.*\(eb\)$,\1,p'`
infernal-1.1.3/hmmer/easel/config.guess-191- machine="${arch}${endian}"-unknown
##############################################
infernal-1.1.3/hmmer/easel/config.guess-220- expr='s/^earmv[0-9]/-eabi/;s/eb$//'
infernal-1.1.3/hmmer/easel/config.guess:221: abi=`echo "$UNAME_MACHINE_ARCH" | sed -e "$expr"`
infernal-1.1.3/hmmer/easel/config.guess-222- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-233- *)
infernal-1.1.3/hmmer/easel/config.guess:234: release=`echo "$UNAME_RELEASE" | sed -e 's/[-_].*//' | cut -d. -f1,2`
infernal-1.1.3/hmmer/easel/config.guess-235- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-280- *4.0)
infernal-1.1.3/hmmer/easel/config.guess:281: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
infernal-1.1.3/hmmer/easel/config.guess-282- ;;
infernal-1.1.3/hmmer/easel/config.guess-283- *5.*)
infernal-1.1.3/hmmer/easel/config.guess:284: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
infernal-1.1.3/hmmer/easel/config.guess-285- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-290- # types through head -n 1, so we only detect the type of CPU 0.
infernal-1.1.3/hmmer/easel/config.guess:291: ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
infernal-1.1.3/hmmer/easel/config.guess-292- case "$ALPHA_CPU_TYPE" in
##############################################
infernal-1.1.3/hmmer/easel/config.guess-328- # 1.2 uses "1.2" for uname -r.
infernal-1.1.3/hmmer/easel/config.guess:329: echo "$UNAME_MACHINE"-dec-osf"`echo "$UNAME_RELEASE" | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`"
infernal-1.1.3/hmmer/easel/config.guess-330- # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
##############################################
infernal-1.1.3/hmmer/easel/config.guess-379- s390x:SunOS:*:*)
infernal-1.1.3/hmmer/easel/config.guess:380: echo "$UNAME_MACHINE"-ibm-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/easel/config.guess-381- exit ;;
infernal-1.1.3/hmmer/easel/config.guess-382- sun4H:SunOS:5.*:*)
infernal-1.1.3/hmmer/easel/config.guess:383: echo sparc-hal-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/easel/config.guess-384- exit ;;
infernal-1.1.3/hmmer/easel/config.guess-385- sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
infernal-1.1.3/hmmer/easel/config.guess:386: echo sparc-sun-solaris2"`echo "$UNAME_RELEASE" | sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/easel/config.guess-387- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-404- fi
infernal-1.1.3/hmmer/easel/config.guess:405: echo "$SUN_ARCH"-pc-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/easel/config.guess-406- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-410- # it's likely to be more like Solaris than SunOS4.
infernal-1.1.3/hmmer/easel/config.guess:411: echo sparc-sun-solaris3"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/easel/config.guess-412- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-419- # Japanese Language versions have a version number like `4.1.3-JL'.
infernal-1.1.3/hmmer/easel/config.guess:420: echo sparc-sun-sunos"`echo "$UNAME_RELEASE"|sed -e 's/-/_/'`"
infernal-1.1.3/hmmer/easel/config.guess-421- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-425- sun*:*:4.2BSD:*)
infernal-1.1.3/hmmer/easel/config.guess:426: UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
infernal-1.1.3/hmmer/easel/config.guess-427- test "x$UNAME_RELEASE" = x && UNAME_RELEASE=3
##############################################
infernal-1.1.3/hmmer/easel/config.guess-507- $CC_FOR_BUILD -o "$dummy" "$dummy.c" &&
infernal-1.1.3/hmmer/easel/config.guess:508: dummyarg=`echo "$UNAME_RELEASE" | sed -n 's/\([0-9]*\).*/\1/p'` &&
infernal-1.1.3/hmmer/easel/config.guess:509: SYSTEM_NAME=`"$dummy" "$dummyarg"` &&
infernal-1.1.3/hmmer/easel/config.guess-510- { echo "$SYSTEM_NAME"; exit; }
##############################################
infernal-1.1.3/hmmer/easel/config.guess-563- *:IRIX*:*:*)
infernal-1.1.3/hmmer/easel/config.guess:564: echo mips-sgi-irix"`echo "$UNAME_RELEASE"|sed -e 's/-/_/g'`"
infernal-1.1.3/hmmer/easel/config.guess-565- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-593-EOF
infernal-1.1.3/hmmer/easel/config.guess:594: if $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"`
infernal-1.1.3/hmmer/easel/config.guess-595- then
##############################################
infernal-1.1.3/hmmer/easel/config.guess-606- *:AIX:*:[4567])
infernal-1.1.3/hmmer/easel/config.guess:607: IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
infernal-1.1.3/hmmer/easel/config.guess-608- if /usr/sbin/lsattr -El "$IBM_CPU_ID" | grep ' POWER' >/dev/null 2>&1; then
##############################################
infernal-1.1.3/hmmer/easel/config.guess-642- 9000/[34678]??:HP-UX:*:*)
infernal-1.1.3/hmmer/easel/config.guess:643: HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
infernal-1.1.3/hmmer/easel/config.guess-644- case "$UNAME_MACHINE" in
##############################################
infernal-1.1.3/hmmer/easel/config.guess-696-EOF
infernal-1.1.3/hmmer/easel/config.guess:697: (CCOPTS="" $CC_FOR_BUILD -o "$dummy" "$dummy.c" 2>/dev/null) && HP_ARCH=`"$dummy"`
infernal-1.1.3/hmmer/easel/config.guess-698- test -z "$HP_ARCH" && HP_ARCH=hppa
##############################################
infernal-1.1.3/hmmer/easel/config.guess-724- ia64:HP-UX:*:*)
infernal-1.1.3/hmmer/easel/config.guess:725: HPUX_REV=`echo "$UNAME_RELEASE"|sed -e 's/[^.]*.[0B]*//'`
infernal-1.1.3/hmmer/easel/config.guess-726- echo ia64-hp-hpux"$HPUX_REV"
##############################################
infernal-1.1.3/hmmer/easel/config.guess-754-EOF
infernal-1.1.3/hmmer/easel/config.guess:755: $CC_FOR_BUILD -o "$dummy" "$dummy.c" && SYSTEM_NAME=`"$dummy"` &&
infernal-1.1.3/hmmer/easel/config.guess-756- { echo "$SYSTEM_NAME"; exit; }
##############################################
infernal-1.1.3/hmmer/easel/config.guess-825- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
infernal-1.1.3/hmmer/easel/config.guess:826: FUJITSU_REL=`echo "$UNAME_RELEASE" | sed -e 's/ /_/'`
infernal-1.1.3/hmmer/easel/config.guess-827- echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
infernal-1.1.3/hmmer/easel/config.guess-830- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
infernal-1.1.3/hmmer/easel/config.guess:831: FUJITSU_REL=`echo "$UNAME_RELEASE" | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
infernal-1.1.3/hmmer/easel/config.guess-832- echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
infernal-1.1.3/hmmer/easel/config.guess-850- esac
infernal-1.1.3/hmmer/easel/config.guess:851: echo "$UNAME_PROCESSOR"-unknown-freebsd"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
infernal-1.1.3/hmmer/easel/config.guess-852- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-886- prep*:SunOS:5.*:*)
infernal-1.1.3/hmmer/easel/config.guess:887: echo powerpcle-unknown-solaris2"`echo "$UNAME_RELEASE"|sed -e 's/[^.]*//'`"
infernal-1.1.3/hmmer/easel/config.guess-888- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-890- # the GNU system
infernal-1.1.3/hmmer/easel/config.guess:891: echo "`echo "$UNAME_MACHINE"|sed -e 's,[-/].*$,,'`-unknown-$LIBC`echo "$UNAME_RELEASE"|sed -e 's,/.*$,,'`"
infernal-1.1.3/hmmer/easel/config.guess-892- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-894- # other systems with GNU libc and userland
infernal-1.1.3/hmmer/easel/config.guess:895: echo "$UNAME_MACHINE-unknown-`echo "$UNAME_SYSTEM" | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"``echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`-$LIBC"
infernal-1.1.3/hmmer/easel/config.guess-896- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-988-EOF
infernal-1.1.3/hmmer/easel/config.guess:989: eval "`$CC_FOR_BUILD -E "$dummy.c" 2>/dev/null | grep '^CPU'`"
infernal-1.1.3/hmmer/easel/config.guess-990- test "x$CPU" != x && { echo "$CPU-unknown-linux-$LIBC"; exit; }
##############################################
infernal-1.1.3/hmmer/easel/config.guess-1088- i*86:*:4.*:*)
infernal-1.1.3/hmmer/easel/config.guess:1089: UNAME_REL=`echo "$UNAME_RELEASE" | sed 's/\/MP$//'`
infernal-1.1.3/hmmer/easel/config.guess-1090- if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
##############################################
infernal-1.1.3/hmmer/easel/config.guess-1291- fi
infernal-1.1.3/hmmer/easel/config.guess:1292: if test "`echo "$UNAME_RELEASE" | sed -e 's/\..*//'`" -le 10 ; then
infernal-1.1.3/hmmer/easel/config.guess-1293- if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
##############################################
infernal-1.1.3/hmmer/easel/config.guess-1389- *:DragonFly:*:*)
infernal-1.1.3/hmmer/easel/config.guess:1390: echo "$UNAME_MACHINE"-unknown-dragonfly"`echo "$UNAME_RELEASE"|sed -e 's/[-(].*//'`"
infernal-1.1.3/hmmer/easel/config.guess-1391- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.guess-1402- i*86:skyos:*:*)
infernal-1.1.3/hmmer/easel/config.guess:1403: echo "$UNAME_MACHINE"-pc-skyos"`echo "$UNAME_RELEASE" | sed -e 's/ .*$//'`"
infernal-1.1.3/hmmer/easel/config.guess-1404- exit ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-52-
infernal-1.1.3/hmmer/easel/config.sub:53:me=`echo "$0" | sed -e 's,.*/,,'`
infernal-1.1.3/hmmer/easel/config.sub-54-
##############################################
infernal-1.1.3/hmmer/easel/config.sub-114-# Here we must recognize all the valid KERNEL-OS combinations.
infernal-1.1.3/hmmer/easel/config.sub:115:maybe_os=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
infernal-1.1.3/hmmer/easel/config.sub-116-case $maybe_os in
##############################################
infernal-1.1.3/hmmer/easel/config.sub-122- os=-$maybe_os
infernal-1.1.3/hmmer/easel/config.sub:123: basic_machine=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
infernal-1.1.3/hmmer/easel/config.sub-124- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-126- os=-linux-android
infernal-1.1.3/hmmer/easel/config.sub:127: basic_machine=`echo "$1" | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`-unknown
infernal-1.1.3/hmmer/easel/config.sub-128- ;;
infernal-1.1.3/hmmer/easel/config.sub-129- *)
infernal-1.1.3/hmmer/easel/config.sub:130: basic_machine=`echo "$1" | sed 's/-[^-]*$//'`
infernal-1.1.3/hmmer/easel/config.sub-131- if [ "$basic_machine" != "$1" ]
infernal-1.1.3/hmmer/easel/config.sub:132: then os=`echo "$1" | sed 's/.*-/-/'`
infernal-1.1.3/hmmer/easel/config.sub-133- else os=; fi
##############################################
infernal-1.1.3/hmmer/easel/config.sub-180- os=-sco5v6
infernal-1.1.3/hmmer/easel/config.sub:181: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-182- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-184- os=-sco3.2v5
infernal-1.1.3/hmmer/easel/config.sub:185: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-186- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-188- os=-sco3.2v4
infernal-1.1.3/hmmer/easel/config.sub:189: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-190- ;;
infernal-1.1.3/hmmer/easel/config.sub-191- -sco3.2.[4-9]*)
infernal-1.1.3/hmmer/easel/config.sub:192: os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
infernal-1.1.3/hmmer/easel/config.sub:193: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-194- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-196- # Don't forget version if it is 3.2v4 or newer.
infernal-1.1.3/hmmer/easel/config.sub:197: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-198- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-200- # Don't forget version if it is 3.2v4 or newer.
infernal-1.1.3/hmmer/easel/config.sub:201: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-202- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-204- os=-sco3.2v2
infernal-1.1.3/hmmer/easel/config.sub:205: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-206- ;;
infernal-1.1.3/hmmer/easel/config.sub-207- -udk*)
infernal-1.1.3/hmmer/easel/config.sub:208: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-209- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-211- os=-isc2.2
infernal-1.1.3/hmmer/easel/config.sub:212: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-213- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-217- -isc*)
infernal-1.1.3/hmmer/easel/config.sub:218: basic_machine=`echo "$1" | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-219- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-229- -ptx*)
infernal-1.1.3/hmmer/easel/config.sub:230: basic_machine=`echo "$1" | sed -e 's/86-.*/86-sequent/'`
infernal-1.1.3/hmmer/easel/config.sub-231- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-364- *-*-*)
infernal-1.1.3/hmmer/easel/config.sub:365: echo Invalid configuration \`"$1"\': machine \`"$basic_machine"\' not recognized 1>&2
infernal-1.1.3/hmmer/easel/config.sub-366- exit 1
##############################################
infernal-1.1.3/hmmer/easel/config.sub-493- amd64-*)
infernal-1.1.3/hmmer/easel/config.sub:494: basic_machine=x86_64-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-495- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-538- blackfin-*)
infernal-1.1.3/hmmer/easel/config.sub:539: basic_machine=bfin-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-540- os=-linux
##############################################
infernal-1.1.3/hmmer/easel/config.sub-546- c54x-*)
infernal-1.1.3/hmmer/easel/config.sub:547: basic_machine=tic54x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-548- ;;
infernal-1.1.3/hmmer/easel/config.sub-549- c55x-*)
infernal-1.1.3/hmmer/easel/config.sub:550: basic_machine=tic55x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-551- ;;
infernal-1.1.3/hmmer/easel/config.sub-552- c6x-*)
infernal-1.1.3/hmmer/easel/config.sub:553: basic_machine=tic6x-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-554- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-650- e500v[12]-*)
infernal-1.1.3/hmmer/easel/config.sub:651: basic_machine=powerpc-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-652- os=$os"spe"
##############################################
infernal-1.1.3/hmmer/easel/config.sub-754- i*86v32)
infernal-1.1.3/hmmer/easel/config.sub:755: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-756- os=-sysv32
##############################################
infernal-1.1.3/hmmer/easel/config.sub-758- i*86v4*)
infernal-1.1.3/hmmer/easel/config.sub:759: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-760- os=-sysv4
##############################################
infernal-1.1.3/hmmer/easel/config.sub-762- i*86v)
infernal-1.1.3/hmmer/easel/config.sub:763: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-764- os=-sysv
##############################################
infernal-1.1.3/hmmer/easel/config.sub-766- i*86sol2)
infernal-1.1.3/hmmer/easel/config.sub:767: basic_machine=`echo "$1" | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/hmmer/easel/config.sub-768- os=-solaris2
##############################################
infernal-1.1.3/hmmer/easel/config.sub-792- leon-*|leon[3-9]-*)
infernal-1.1.3/hmmer/easel/config.sub:793: basic_machine=sparc-`echo "$basic_machine" | sed 's/-.*//'`
infernal-1.1.3/hmmer/easel/config.sub-794- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-799- m68knommu-*)
infernal-1.1.3/hmmer/easel/config.sub:800: basic_machine=m68k-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-801- os=-linux
##############################################
infernal-1.1.3/hmmer/easel/config.sub-833- mips3*-*)
infernal-1.1.3/hmmer/easel/config.sub:834: basic_machine=`echo "$basic_machine" | sed -e 's/mips3/mips64/'`
infernal-1.1.3/hmmer/easel/config.sub-835- ;;
infernal-1.1.3/hmmer/easel/config.sub-836- mips3*)
infernal-1.1.3/hmmer/easel/config.sub:837: basic_machine=`echo "$basic_machine" | sed -e 's/mips3/mips64/'`-unknown
infernal-1.1.3/hmmer/easel/config.sub-838- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-855- ms1-*)
infernal-1.1.3/hmmer/easel/config.sub:856: basic_machine=`echo "$basic_machine" | sed -e 's/ms1-/mt-/'`
infernal-1.1.3/hmmer/easel/config.sub-857- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-980- parisc-*)
infernal-1.1.3/hmmer/easel/config.sub:981: basic_machine=hppa-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-982- os=-linux
##############################################
infernal-1.1.3/hmmer/easel/config.sub-996- pc98-*)
infernal-1.1.3/hmmer/easel/config.sub:997: basic_machine=i386-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-998- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1011- pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
infernal-1.1.3/hmmer/easel/config.sub:1012: basic_machine=i586-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1013- ;;
infernal-1.1.3/hmmer/easel/config.sub-1014- pentiumpro-* | p6-* | 6x86-* | athlon-*)
infernal-1.1.3/hmmer/easel/config.sub:1015: basic_machine=i686-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1016- ;;
infernal-1.1.3/hmmer/easel/config.sub-1017- pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
infernal-1.1.3/hmmer/easel/config.sub:1018: basic_machine=i686-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1019- ;;
infernal-1.1.3/hmmer/easel/config.sub-1020- pentium4-*)
infernal-1.1.3/hmmer/easel/config.sub:1021: basic_machine=i786-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1022- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1030- ppc-* | ppcbe-*)
infernal-1.1.3/hmmer/easel/config.sub:1031: basic_machine=powerpc-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1032- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1036- ppcle-* | powerpclittle-*)
infernal-1.1.3/hmmer/easel/config.sub:1037: basic_machine=powerpcle-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1038- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1040- ;;
infernal-1.1.3/hmmer/easel/config.sub:1041: ppc64-*) basic_machine=powerpc64-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1042- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1046- ppc64le-* | powerpc64little-*)
infernal-1.1.3/hmmer/easel/config.sub:1047: basic_machine=powerpc64le-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1048- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1122- strongarm-* | thumb-*)
infernal-1.1.3/hmmer/easel/config.sub:1123: basic_machine=arm-`echo "$basic_machine" | sed 's/^[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub-1124- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1255- xscale-* | xscalee[bl]-*)
infernal-1.1.3/hmmer/easel/config.sub:1256: basic_machine=`echo "$basic_machine" | sed 's/^xscale/arm/'`
infernal-1.1.3/hmmer/easel/config.sub-1257- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1317- *)
infernal-1.1.3/hmmer/easel/config.sub:1318: echo Invalid configuration \`"$1"\': machine \`"$basic_machine"\' not recognized 1>&2
infernal-1.1.3/hmmer/easel/config.sub-1319- exit 1
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1325- *-digital*)
infernal-1.1.3/hmmer/easel/config.sub:1326: basic_machine=`echo "$basic_machine" | sed 's/digital.*/dec/'`
infernal-1.1.3/hmmer/easel/config.sub-1327- ;;
infernal-1.1.3/hmmer/easel/config.sub-1328- *-commodore*)
infernal-1.1.3/hmmer/easel/config.sub:1329: basic_machine=`echo "$basic_machine" | sed 's/commodore.*/cbm/'`
infernal-1.1.3/hmmer/easel/config.sub-1330- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1346- -solaris1 | -solaris1.*)
infernal-1.1.3/hmmer/easel/config.sub:1347: os=`echo $os | sed -e 's|solaris1|sunos4|'`
infernal-1.1.3/hmmer/easel/config.sub-1348- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1355- -gnu/linux*)
infernal-1.1.3/hmmer/easel/config.sub:1356: os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
infernal-1.1.3/hmmer/easel/config.sub-1357- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1407- -nto*)
infernal-1.1.3/hmmer/easel/config.sub:1408: os=`echo $os | sed -e 's|nto|nto-qnx|'`
infernal-1.1.3/hmmer/easel/config.sub-1409- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1414- -mac*)
infernal-1.1.3/hmmer/easel/config.sub:1415: os=`echo "$os" | sed -e 's|mac|macos|'`
infernal-1.1.3/hmmer/easel/config.sub-1416- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1420- -linux*)
infernal-1.1.3/hmmer/easel/config.sub:1421: os=`echo $os | sed -e 's|linux|linux-gnu|'`
infernal-1.1.3/hmmer/easel/config.sub-1422- ;;
infernal-1.1.3/hmmer/easel/config.sub-1423- -sunos5*)
infernal-1.1.3/hmmer/easel/config.sub:1424: os=`echo "$os" | sed -e 's|sunos5|solaris2|'`
infernal-1.1.3/hmmer/easel/config.sub-1425- ;;
infernal-1.1.3/hmmer/easel/config.sub-1426- -sunos6*)
infernal-1.1.3/hmmer/easel/config.sub:1427: os=`echo "$os" | sed -e 's|sunos6|solaris3|'`
infernal-1.1.3/hmmer/easel/config.sub-1428- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1469- -sinix5.*)
infernal-1.1.3/hmmer/easel/config.sub:1470: os=`echo $os | sed -e 's|sinix|sysv|'`
infernal-1.1.3/hmmer/easel/config.sub-1471- ;;
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1528- # Get rid of the `-' at the beginning of $os.
infernal-1.1.3/hmmer/easel/config.sub:1529: os=`echo $os | sed 's/[^-]*-//'`
infernal-1.1.3/hmmer/easel/config.sub:1530: echo Invalid configuration \`"$1"\': system \`"$os"\' not recognized 1>&2
infernal-1.1.3/hmmer/easel/config.sub-1531- exit 1
##############################################
infernal-1.1.3/hmmer/easel/config.sub-1788- esac
infernal-1.1.3/hmmer/easel/config.sub:1789: basic_machine=`echo "$basic_machine" | sed "s/unknown/$vendor/"`
infernal-1.1.3/hmmer/easel/config.sub-1790- ;;
##############################################
infernal-1.1.3/hmmer/easel/Makefile.in-567-${ALL_UTESTS}: libeasel.a
infernal-1.1.3/hmmer/easel/Makefile.in:568: @BASENAME=`echo $@ | sed -e 's/_utest//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/hmmer/easel/Makefile.in:569: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/easel/Makefile.in-570- DFLAG=esl$${DFLAG}_TESTDRIVE ;\
##############################################
infernal-1.1.3/hmmer/easel/Makefile.in-581-${ALL_BENCHMARKS}: libeasel.a
infernal-1.1.3/hmmer/easel/Makefile.in:582: @BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/hmmer/easel/Makefile.in:583: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/easel/Makefile.in-584- DFLAG=esl$${DFLAG}_BENCHMARK ;\
##############################################
infernal-1.1.3/hmmer/easel/Makefile.in-595-${ALL_EXPERIMENTS}: libeasel.a
infernal-1.1.3/hmmer/easel/Makefile.in:596: @BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/hmmer/easel/Makefile.in:597: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/easel/Makefile.in-598- DFLAG=esl$${DFLAG}_EXPERIMENT ;\
##############################################
infernal-1.1.3/hmmer/easel/Makefile.in-609-${ALL_EXAMPLES}: libeasel.a
infernal-1.1.3/hmmer/easel/Makefile.in:610: @BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/hmmer/easel/Makefile.in:611: DFLAG=esl`echo $@ | sed -e 's/^esl_//' | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/hmmer/easel/Makefile.in-612- if test $@ = "easel_example"; \
##############################################
infernal-1.1.3/config.sub-56-
infernal-1.1.3/config.sub:57:me=`echo "$0" | sed -e 's,.*/,,'`
infernal-1.1.3/config.sub-58-
##############################################
infernal-1.1.3/config.sub-120-# Here we must recognize all the valid KERNEL-OS combinations.
infernal-1.1.3/config.sub:121:maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'`
infernal-1.1.3/config.sub-122-case $maybe_os in
##############################################
infernal-1.1.3/config.sub-126- os=-$maybe_os
infernal-1.1.3/config.sub:127: basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'`
infernal-1.1.3/config.sub-128- ;;
infernal-1.1.3/config.sub-129- *)
infernal-1.1.3/config.sub:130: basic_machine=`echo $1 | sed 's/-[^-]*$//'`
infernal-1.1.3/config.sub-131- if [ $basic_machine != $1 ]
infernal-1.1.3/config.sub:132: then os=`echo $1 | sed 's/.*-/-/'`
infernal-1.1.3/config.sub-133- else os=; fi
##############################################
infernal-1.1.3/config.sub-177- os=-sco5v6
infernal-1.1.3/config.sub:178: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-179- ;;
##############################################
infernal-1.1.3/config.sub-181- os=-sco3.2v5
infernal-1.1.3/config.sub:182: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-183- ;;
##############################################
infernal-1.1.3/config.sub-185- os=-sco3.2v4
infernal-1.1.3/config.sub:186: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-187- ;;
infernal-1.1.3/config.sub-188- -sco3.2.[4-9]*)
infernal-1.1.3/config.sub:189: os=`echo $os | sed -e 's/sco3.2./sco3.2v/'`
infernal-1.1.3/config.sub:190: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-191- ;;
##############################################
infernal-1.1.3/config.sub-193- # Don't forget version if it is 3.2v4 or newer.
infernal-1.1.3/config.sub:194: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-195- ;;
##############################################
infernal-1.1.3/config.sub-197- # Don't forget version if it is 3.2v4 or newer.
infernal-1.1.3/config.sub:198: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-199- ;;
##############################################
infernal-1.1.3/config.sub-201- os=-sco3.2v2
infernal-1.1.3/config.sub:202: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-203- ;;
infernal-1.1.3/config.sub-204- -udk*)
infernal-1.1.3/config.sub:205: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-206- ;;
##############################################
infernal-1.1.3/config.sub-208- os=-isc2.2
infernal-1.1.3/config.sub:209: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-210- ;;
##############################################
infernal-1.1.3/config.sub-214- -isc*)
infernal-1.1.3/config.sub:215: basic_machine=`echo $1 | sed -e 's/86-.*/86-pc/'`
infernal-1.1.3/config.sub-216- ;;
##############################################
infernal-1.1.3/config.sub-220- -ptx*)
infernal-1.1.3/config.sub:221: basic_machine=`echo $1 | sed -e 's/86-.*/86-sequent/'`
infernal-1.1.3/config.sub-222- ;;
infernal-1.1.3/config.sub-223- -windowsnt*)
infernal-1.1.3/config.sub:224: os=`echo $os | sed -e 's/windowsnt/winnt/'`
infernal-1.1.3/config.sub-225- ;;
##############################################
infernal-1.1.3/config.sub-312- *-*-*)
infernal-1.1.3/config.sub:313: echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
infernal-1.1.3/config.sub-314- exit 1
##############################################
infernal-1.1.3/config.sub-420- amd64-*)
infernal-1.1.3/config.sub:421: basic_machine=x86_64-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-422- ;;
##############################################
infernal-1.1.3/config.sub-458- blackfin-*)
infernal-1.1.3/config.sub:459: basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-460- os=-linux
##############################################
infernal-1.1.3/config.sub-657- i*86v32)
infernal-1.1.3/config.sub:658: basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/config.sub-659- os=-sysv32
##############################################
infernal-1.1.3/config.sub-661- i*86v4*)
infernal-1.1.3/config.sub:662: basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/config.sub-663- os=-sysv4
##############################################
infernal-1.1.3/config.sub-665- i*86v)
infernal-1.1.3/config.sub:666: basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/config.sub-667- os=-sysv
##############################################
infernal-1.1.3/config.sub-669- i*86sol2)
infernal-1.1.3/config.sub:670: basic_machine=`echo $1 | sed -e 's/86.*/86-pc/'`
infernal-1.1.3/config.sub-671- os=-solaris2
##############################################
infernal-1.1.3/config.sub-699- m68knommu-*)
infernal-1.1.3/config.sub:700: basic_machine=m68k-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-701- os=-linux
##############################################
infernal-1.1.3/config.sub-729- mips3*-*)
infernal-1.1.3/config.sub:730: basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`
infernal-1.1.3/config.sub-731- ;;
infernal-1.1.3/config.sub-732- mips3*)
infernal-1.1.3/config.sub:733: basic_machine=`echo $basic_machine | sed -e 's/mips3/mips64/'`-unknown
infernal-1.1.3/config.sub-734- ;;
##############################################
infernal-1.1.3/config.sub-747- ms1-*)
infernal-1.1.3/config.sub:748: basic_machine=`echo $basic_machine | sed -e 's/ms1-/mt-/'`
infernal-1.1.3/config.sub-749- ;;
##############################################
infernal-1.1.3/config.sub-852- parisc-*)
infernal-1.1.3/config.sub:853: basic_machine=hppa-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-854- os=-linux
##############################################
infernal-1.1.3/config.sub-868- pc98-*)
infernal-1.1.3/config.sub:869: basic_machine=i386-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-870- ;;
##############################################
infernal-1.1.3/config.sub-883- pentium-* | p5-* | k5-* | k6-* | nexgen-* | viac3-*)
infernal-1.1.3/config.sub:884: basic_machine=i586-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-885- ;;
infernal-1.1.3/config.sub-886- pentiumpro-* | p6-* | 6x86-* | athlon-*)
infernal-1.1.3/config.sub:887: basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-888- ;;
infernal-1.1.3/config.sub-889- pentiumii-* | pentium2-* | pentiumiii-* | pentium3-*)
infernal-1.1.3/config.sub:890: basic_machine=i686-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-891- ;;
infernal-1.1.3/config.sub-892- pentium4-*)
infernal-1.1.3/config.sub:893: basic_machine=i786-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-894- ;;
##############################################
infernal-1.1.3/config.sub-901- ;;
infernal-1.1.3/config.sub:902: ppc-*) basic_machine=powerpc-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-903- ;;
##############################################
infernal-1.1.3/config.sub-907- ppcle-* | powerpclittle-*)
infernal-1.1.3/config.sub:908: basic_machine=powerpcle-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-909- ;;
##############################################
infernal-1.1.3/config.sub-911- ;;
infernal-1.1.3/config.sub:912: ppc64-*) basic_machine=powerpc64-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-913- ;;
##############################################
infernal-1.1.3/config.sub-917- ppc64le-* | powerpc64little-*)
infernal-1.1.3/config.sub:918: basic_machine=powerpc64le-`echo $basic_machine | sed 's/^[^-]*-//'`
infernal-1.1.3/config.sub-919- ;;
##############################################
infernal-1.1.3/config.sub-1209- *)
infernal-1.1.3/config.sub:1210: echo Invalid configuration \`$1\': machine \`$basic_machine\' not recognized 1>&2
infernal-1.1.3/config.sub-1211- exit 1
##############################################
infernal-1.1.3/config.sub-1217- *-digital*)
infernal-1.1.3/config.sub:1218: basic_machine=`echo $basic_machine | sed 's/digital.*/dec/'`
infernal-1.1.3/config.sub-1219- ;;
infernal-1.1.3/config.sub-1220- *-commodore*)
infernal-1.1.3/config.sub:1221: basic_machine=`echo $basic_machine | sed 's/commodore.*/cbm/'`
infernal-1.1.3/config.sub-1222- ;;
##############################################
infernal-1.1.3/config.sub-1235- -solaris1 | -solaris1.*)
infernal-1.1.3/config.sub:1236: os=`echo $os | sed -e 's|solaris1|sunos4|'`
infernal-1.1.3/config.sub-1237- ;;
##############################################
infernal-1.1.3/config.sub-1247- -gnu/linux*)
infernal-1.1.3/config.sub:1248: os=`echo $os | sed -e 's|gnu/linux|linux-gnu|'`
infernal-1.1.3/config.sub-1249- ;;
##############################################
infernal-1.1.3/config.sub-1291- -nto*)
infernal-1.1.3/config.sub:1292: os=`echo $os | sed -e 's|nto|nto-qnx|'`
infernal-1.1.3/config.sub-1293- ;;
##############################################
infernal-1.1.3/config.sub-1298- -mac*)
infernal-1.1.3/config.sub:1299: os=`echo $os | sed -e 's|mac|macos|'`
infernal-1.1.3/config.sub-1300- ;;
##############################################
infernal-1.1.3/config.sub-1304- -linux*)
infernal-1.1.3/config.sub:1305: os=`echo $os | sed -e 's|linux|linux-gnu|'`
infernal-1.1.3/config.sub-1306- ;;
infernal-1.1.3/config.sub-1307- -sunos5*)
infernal-1.1.3/config.sub:1308: os=`echo $os | sed -e 's|sunos5|solaris2|'`
infernal-1.1.3/config.sub-1309- ;;
infernal-1.1.3/config.sub-1310- -sunos6*)
infernal-1.1.3/config.sub:1311: os=`echo $os | sed -e 's|sunos6|solaris3|'`
infernal-1.1.3/config.sub-1312- ;;
##############################################
infernal-1.1.3/config.sub-1359- -sinix5.*)
infernal-1.1.3/config.sub:1360: os=`echo $os | sed -e 's|sinix|sysv|'`
infernal-1.1.3/config.sub-1361- ;;
##############################################
infernal-1.1.3/config.sub-1413- # Get rid of the `-' at the beginning of $os.
infernal-1.1.3/config.sub:1414: os=`echo $os | sed 's/[^-]*-//'`
infernal-1.1.3/config.sub:1415: echo Invalid configuration \`$1\': system \`$os\' not recognized 1>&2
infernal-1.1.3/config.sub-1416- exit 1
##############################################
infernal-1.1.3/config.sub-1664- esac
infernal-1.1.3/config.sub:1665: basic_machine=`echo $basic_machine | sed "s/unknown/$vendor/"`
infernal-1.1.3/config.sub-1666- ;;
##############################################
infernal-1.1.3/configure-45-if test -z "$BASH_VERSION$ZSH_VERSION" \
infernal-1.1.3/configure:46: && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
infernal-1.1.3/configure-47- as_echo='print -r --'
infernal-1.1.3/configure-48- as_echo_n='print -rn --'
infernal-1.1.3/configure:49:elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
infernal-1.1.3/configure-50- as_echo='printf %s\n'
##############################################
infernal-1.1.3/configure-52-else
infernal-1.1.3/configure:53: if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
infernal-1.1.3/configure-54- as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
##############################################
infernal-1.1.3/configure-62- expr "X$arg" : "X\\(.*\\)$as_nl";
infernal-1.1.3/configure:63: arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
infernal-1.1.3/configure-64- esac;
##############################################
infernal-1.1.3/configure-199- eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
infernal-1.1.3/configure:200: test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
infernal-1.1.3/configure-201-test \$(( 1 + 1 )) = 2 || exit 1"
##############################################
infernal-1.1.3/configure-327- case $as_dir in #(
infernal-1.1.3/configure:328: *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
infernal-1.1.3/configure-329- *) as_qdir=$as_dir;;
##############################################
infernal-1.1.3/configure-400- {
infernal-1.1.3/configure:401: as_val=`expr "$@" || test $? -eq 1`
infernal-1.1.3/configure-402- }
##############################################
infernal-1.1.3/configure-407-# ----------------------------------------
infernal-1.1.3/configure:408:# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
infernal-1.1.3/configure-409-# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
##############################################
infernal-1.1.3/configure-470- eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
infernal-1.1.3/configure:471: test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
infernal-1.1.3/configure-472- # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
##############################################
infernal-1.1.3/configure-817- case $ac_option in
infernal-1.1.3/configure:818: *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;;
infernal-1.1.3/configure-819- *=) ac_optarg= ;;
##############################################
infernal-1.1.3/configure-861- -disable-* | --disable-*)
infernal-1.1.3/configure:862: ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'`
infernal-1.1.3/configure-863- # Reject names that are not valid shell variable names.
##############################################
infernal-1.1.3/configure-866- ac_useropt_orig=$ac_useropt
infernal-1.1.3/configure:867: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
infernal-1.1.3/configure-868- case $ac_user_opts in
##############################################
infernal-1.1.3/configure-887- -enable-* | --enable-*)
infernal-1.1.3/configure:888: ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'`
infernal-1.1.3/configure-889- # Reject names that are not valid shell variable names.
##############################################
infernal-1.1.3/configure-892- ac_useropt_orig=$ac_useropt
infernal-1.1.3/configure:893: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
infernal-1.1.3/configure-894- case $ac_user_opts in
##############################################
infernal-1.1.3/configure-1091- -with-* | --with-*)
infernal-1.1.3/configure:1092: ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'`
infernal-1.1.3/configure-1093- # Reject names that are not valid shell variable names.
##############################################
infernal-1.1.3/configure-1096- ac_useropt_orig=$ac_useropt
infernal-1.1.3/configure:1097: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
infernal-1.1.3/configure-1098- case $ac_user_opts in
##############################################
infernal-1.1.3/configure-1107- -without-* | --without-*)
infernal-1.1.3/configure:1108: ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'`
infernal-1.1.3/configure-1109- # Reject names that are not valid shell variable names.
##############################################
infernal-1.1.3/configure-1112- ac_useropt_orig=$ac_useropt
infernal-1.1.3/configure:1113: ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'`
infernal-1.1.3/configure-1114- case $ac_user_opts in
##############################################
infernal-1.1.3/configure-1145- *=*)
infernal-1.1.3/configure:1146: ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='`
infernal-1.1.3/configure-1147- # Reject names that are not valid shell variable names.
##############################################
infernal-1.1.3/configure-1166-if test -n "$ac_prev"; then
infernal-1.1.3/configure:1167: ac_option=--`echo $ac_prev | sed 's/_/-/g'`
infernal-1.1.3/configure-1168- as_fn_error $? "missing argument to $ac_option"
##############################################
infernal-1.1.3/configure-1188- */ )
infernal-1.1.3/configure:1189: ac_val=`expr "X$ac_val" : 'X\(.*[^/]\)' \| "X$ac_val" : 'X\(.*\)'`
infernal-1.1.3/configure-1190- eval $ac_var=\$ac_val;;
##############################################
infernal-1.1.3/configure-1223-ac_ls_di=`ls -di .` &&
infernal-1.1.3/configure:1224:ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` ||
infernal-1.1.3/configure-1225- as_fn_error $? "working directory cannot be determined"
##############################################
infernal-1.1.3/configure-1279-case $srcdir in
infernal-1.1.3/configure:1280:*/) srcdir=`expr "X$srcdir" : 'X\(.*[^/]\)' \| "X$srcdir" : 'X\(.*\)'`;;
infernal-1.1.3/configure-1281-esac
##############################################
infernal-1.1.3/configure-1322-By default, \`make install' will install all the files in
infernal-1.1.3/configure:1323:\`$ac_default_prefix/bin', \`$ac_default_prefix/lib' etc. You can specify
infernal-1.1.3/configure:1324:an installation prefix other than \`$ac_default_prefix' using \`--prefix',
infernal-1.1.3/configure-1325-for instance \`--prefix=\$HOME'.
##############################################
infernal-1.1.3/configure-1419-*)
infernal-1.1.3/configure:1420: ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
infernal-1.1.3/configure-1421- # A ".." for each directory in $ac_dir_suffix.
infernal-1.1.3/configure:1422: ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
infernal-1.1.3/configure-1423- case $ac_top_builddir_sub in
##############################################
infernal-1.1.3/configure-2015- *\'*)
infernal-1.1.3/configure:2016: ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;;
infernal-1.1.3/configure-2017- esac
##############################################
infernal-1.1.3/configure-2098- case $ac_val in
infernal-1.1.3/configure:2099: *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
infernal-1.1.3/configure-2100- esac
##############################################
infernal-1.1.3/configure-2113- case $ac_val in
infernal-1.1.3/configure:2114: *\'\''*) ac_val=`$as_echo "$ac_val" | sed "s/'\''/'\''\\\\\\\\'\'''\''/g"`;;
infernal-1.1.3/configure-2115- esac
##############################################
infernal-1.1.3/configure-2233- set,)
infernal-1.1.3/configure:2234: { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5
infernal-1.1.3/configure:2235:$as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;}
infernal-1.1.3/configure-2236- ac_cache_corrupted=: ;;
##############################################
infernal-1.1.3/configure-2244- # differences in whitespace do not lead to failure.
infernal-1.1.3/configure:2245: ac_old_val_w=`echo x $ac_old_val`
infernal-1.1.3/configure:2246: ac_new_val_w=`echo x $ac_new_val`
infernal-1.1.3/configure-2247- if test "$ac_old_val_w" != "$ac_new_val_w"; then
##############################################
infernal-1.1.3/configure-2264- case $ac_new_val in
infernal-1.1.3/configure:2265: *\'*) ac_arg=$ac_var=`$as_echo "$ac_new_val" | sed "s/'/'\\\\\\\\''/g"` ;;
infernal-1.1.3/configure-2266- *) ac_arg=$ac_var=$ac_new_val ;;
##############################################
infernal-1.1.3/configure-2497-test "x$ac_build_alias" = x &&
infernal-1.1.3/configure:2498: ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"`
infernal-1.1.3/configure-2499-test "x$ac_build_alias" = x &&
infernal-1.1.3/configure-2500- as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5
infernal-1.1.3/configure:2501:ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` ||
infernal-1.1.3/configure-2502- as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5
##############################################
infernal-1.1.3/configure-2521-IFS=$ac_save_IFS
infernal-1.1.3/configure:2522:case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac
infernal-1.1.3/configure-2523-
##############################################
infernal-1.1.3/configure-2532-else
infernal-1.1.3/configure:2533: ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` ||
infernal-1.1.3/configure-2534- as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5
##############################################
infernal-1.1.3/configure-2554-IFS=$ac_save_IFS
infernal-1.1.3/configure:2555:case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac
infernal-1.1.3/configure-2556-
##############################################
infernal-1.1.3/configure-3027-$as_echo_n "checking whether the C compiler works... " >&6; }
infernal-1.1.3/configure:3028:ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'`
infernal-1.1.3/configure-3029-
##############################################
infernal-1.1.3/configure-3071- then :; else
infernal-1.1.3/configure:3072: ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
infernal-1.1.3/configure-3073- fi
##############################################
infernal-1.1.3/configure-3131- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;;
infernal-1.1.3/configure:3132: *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'`
infernal-1.1.3/configure-3133- break;;
##############################################
infernal-1.1.3/configure-3240- *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM ) ;;
infernal-1.1.3/configure:3241: *) ac_cv_objext=`expr "$ac_file" : '.*\.\(.*\)'`
infernal-1.1.3/configure-3242- break;;
##############################################
infernal-1.1.3/configure-4440- linux*|k*bsd*-gnu)
infernal-1.1.3/configure:4441: case `basename "$CC"` in
infernal-1.1.3/configure-4442- icc*|ecc*|ifort*)
##############################################
infernal-1.1.3/configure-4457- *)
infernal-1.1.3/configure:4458: case `$CC -V 2>&1 | sed 5q` in
infernal-1.1.3/configure-4459- *Sun\ C*|*Sun\ F*)
##############################################
infernal-1.1.3/configure-4509- # Check for GNU $ac_path_SED
infernal-1.1.3/configure:4510:case `"$ac_path_SED" --version 2>&1` in
infernal-1.1.3/configure-4511-*GNU*)
##############################################
infernal-1.1.3/configure-4573- # Check for GNU $ac_path_GREP
infernal-1.1.3/configure:4574:case `"$ac_path_GREP" --version 2>&1` in
infernal-1.1.3/configure-4575-*GNU*)
##############################################
infernal-1.1.3/configure-4639- # Check for GNU $ac_path_EGREP
infernal-1.1.3/configure:4640:case `"$ac_path_EGREP" --version 2>&1` in
infernal-1.1.3/configure-4641-*GNU*)
##############################################
infernal-1.1.3/configure-4951- ax_pthread_sed='s/conftest\.\$ac_ext/conftest.$ac_objext/g'
infernal-1.1.3/configure:4952: ax_pthread_link_step=`$as_echo "$ac_link" | sed "$ax_pthread_sed"`
infernal-1.1.3/configure-4953- ax_pthread_2step_ac_link="($ac_compile) && (echo ==== >&5) && ($ax_pthread_link_step)"
##############################################
infernal-1.1.3/configure-5926-do :
infernal-1.1.3/configure:5927: as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
infernal-1.1.3/configure-5928-ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
##############################################
infernal-1.1.3/configure-5931- cat >>confdefs.h <<_ACEOF
infernal-1.1.3/configure:5932:#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
infernal-1.1.3/configure-5933-_ACEOF
##############################################
infernal-1.1.3/configure-5948-do :
infernal-1.1.3/configure:5949: as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
infernal-1.1.3/configure-5950-ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
##############################################
infernal-1.1.3/configure-5952- cat >>confdefs.h <<_ACEOF
infernal-1.1.3/configure:5953:#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
infernal-1.1.3/configure-5954-_ACEOF
##############################################
infernal-1.1.3/configure-7398- ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
infernal-1.1.3/configure:7399: ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
infernal-1.1.3/configure-7400- # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
##############################################
infernal-1.1.3/configure-7466-if test -z "$BASH_VERSION$ZSH_VERSION" \
infernal-1.1.3/configure:7467: && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
infernal-1.1.3/configure-7468- as_echo='print -r --'
infernal-1.1.3/configure-7469- as_echo_n='print -rn --'
infernal-1.1.3/configure:7470:elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
infernal-1.1.3/configure-7471- as_echo='printf %s\n'
##############################################
infernal-1.1.3/configure-7473-else
infernal-1.1.3/configure:7474: if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
infernal-1.1.3/configure-7475- as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
##############################################
infernal-1.1.3/configure-7483- expr "X$arg" : "X\\(.*\\)$as_nl";
infernal-1.1.3/configure:7484: arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
infernal-1.1.3/configure-7485- esac;
##############################################
infernal-1.1.3/configure-7560-# ----------------------------------------
infernal-1.1.3/configure:7561:# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
infernal-1.1.3/configure-7562-# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
##############################################
infernal-1.1.3/configure-7632- {
infernal-1.1.3/configure:7633: as_val=`expr "$@" || test $? -eq 1`
infernal-1.1.3/configure-7634- }
##############################################
infernal-1.1.3/configure-7736- case $as_dir in #(
infernal-1.1.3/configure:7737: *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
infernal-1.1.3/configure-7738- *) as_qdir=$as_dir;;
##############################################
infernal-1.1.3/configure-7867-cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
infernal-1.1.3/configure:7868:ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
infernal-1.1.3/configure-7869-ac_cs_version="\\
##############################################
infernal-1.1.3/configure-7890- --*=?*)
infernal-1.1.3/configure:7891: ac_option=`expr "X$1" : 'X\([^=]*\)='`
infernal-1.1.3/configure:7892: ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'`
infernal-1.1.3/configure-7893- ac_shift=:
##############################################
infernal-1.1.3/configure-7895- --*=)
infernal-1.1.3/configure:7896: ac_option=`expr "X$1" : 'X\([^=]*\)='`
infernal-1.1.3/configure-7897- ac_optarg=
##############################################
infernal-1.1.3/configure-7919- case $ac_optarg in
infernal-1.1.3/configure:7920: *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
infernal-1.1.3/configure-7921- '') as_fn_error $? "missing file argument" ;;
##############################################
infernal-1.1.3/configure-7927- case $ac_optarg in
infernal-1.1.3/configure:7928: *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;;
infernal-1.1.3/configure-7929- esac
##############################################
infernal-1.1.3/configure-8121-fi
infernal-1.1.3/configure:8122:ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' </dev/null 2>/dev/null`
infernal-1.1.3/configure-8123-if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then
##############################################
infernal-1.1.3/configure-8138- as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5
infernal-1.1.3/configure:8139:ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'`
infernal-1.1.3/configure-8140-ac_delim='%!_!# '
##############################################
infernal-1.1.3/configure-8144-
infernal-1.1.3/configure:8145: ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X`
infernal-1.1.3/configure-8146- if test $ac_delim_n = $ac_delim_num; then
##############################################
infernal-1.1.3/configure-8282-for ac_last_try in false false :; do
infernal-1.1.3/configure:8283: ac_tt=`sed -n "/$ac_delim/p" confdefs.h`
infernal-1.1.3/configure-8284- if test -z "$ac_tt"; then
##############################################
infernal-1.1.3/configure-8414- esac
infernal-1.1.3/configure:8415: case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac
infernal-1.1.3/configure-8416- as_fn_append ac_file_inputs " '$ac_f'"
##############################################
infernal-1.1.3/configure-8473-*)
infernal-1.1.3/configure:8474: ac_dir_suffix=/`$as_echo "$ac_dir" | sed 's|^\.[\\/]||'`
infernal-1.1.3/configure-8475- # A ".." for each directory in $ac_dir_suffix.
infernal-1.1.3/configure:8476: ac_top_builddir_sub=`$as_echo "$ac_dir_suffix" | sed 's|/[^\\/]*|/..|g;s|/||'`
infernal-1.1.3/configure-8477- case $ac_top_builddir_sub in
##############################################
infernal-1.1.3/configure-8529-/@mandir@/p'
infernal-1.1.3/configure:8530:case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in
infernal-1.1.3/configure-8531-*datarootdir*) ac_datarootdir_seen=yes;;
##############################################
infernal-1.1.3/configure-8546-
infernal-1.1.3/configure:8547:# Neutralize VPATH when `$srcdir' = `.'.
infernal-1.1.3/configure-8548-# Shell code in configure.ac might set extrasub.
##############################################
infernal-1.1.3/configure-8573-test -z "$ac_datarootdir_hack$ac_datarootdir_seen" &&
infernal-1.1.3/configure:8574: { ac_out=`sed -n '/\${datarootdir}/p' "$ac_tmp/out"`; test -n "$ac_out"; } &&
infernal-1.1.3/configure-8575- { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' \
##############################################
infernal-1.1.3/install-sh-97- case $1 in
infernal-1.1.3/install-sh:98: -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
infernal-1.1.3/install-sh-99- shift
##############################################
infernal-1.1.3/install-sh-130-
infernal-1.1.3/install-sh:131: -t=*) transformarg=`echo $1 | sed 's/-t=//'`
infernal-1.1.3/install-sh-132- shift
##############################################
infernal-1.1.3/install-sh-190- if test -d "$dst"; then
infernal-1.1.3/install-sh:191: dst=$dst/`basename "$src"`
infernal-1.1.3/install-sh-192- fi
##############################################
infernal-1.1.3/install-sh-195-# This sed command emulates the dirname command.
infernal-1.1.3/install-sh:196:dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
infernal-1.1.3/install-sh-197-
##############################################
infernal-1.1.3/install-sh-208- IFS='%'
infernal-1.1.3/install-sh:209: set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
infernal-1.1.3/install-sh-210- IFS=$oIFS
##############################################
infernal-1.1.3/install-sh-231- if test -z "$transformarg"; then
infernal-1.1.3/install-sh:232: dstfile=`basename "$dst"`
infernal-1.1.3/install-sh-233- else
##############################################
infernal-1.1.3/install-sh-238- # don't allow the sed command to completely eliminate the filename.
infernal-1.1.3/install-sh:239: test -z "$dstfile" && dstfile=`basename "$dst"`
infernal-1.1.3/install-sh-240-
##############################################
infernal-1.1.3/config.guess-34-
infernal-1.1.3/config.guess:35:me=`echo "$0" | sed -e 's,.*/,,'`
infernal-1.1.3/config.guess-36-
##############################################
infernal-1.1.3/config.guess-102-: ${TMPDIR=/tmp} ;
infernal-1.1.3/config.guess:103: { tmp=`(umask 077 && mktemp -d "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
infernal-1.1.3/config.guess-104- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
##############################################
infernal-1.1.3/config.guess-151- EOF
infernal-1.1.3/config.guess:152: eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC' | sed 's, ,,g'`
infernal-1.1.3/config.guess-153- ;;
##############################################
infernal-1.1.3/config.guess-181- earmv*)
infernal-1.1.3/config.guess:182: arch=`echo ${UNAME_MACHINE_ARCH} | sed -e 's,^e\(armv[0-9]\).*$,\1,'`
infernal-1.1.3/config.guess:183: endian=`echo ${UNAME_MACHINE_ARCH} | sed -ne 's,^.*\(eb\)$,\1,p'`
infernal-1.1.3/config.guess-184- machine=${arch}${endian}-unknown
##############################################
infernal-1.1.3/config.guess-213- expr='s/^earmv[0-9]/-eabi/;s/eb$//'
infernal-1.1.3/config.guess:214: abi=`echo ${UNAME_MACHINE_ARCH} | sed -e "$expr"`
infernal-1.1.3/config.guess-215- ;;
##############################################
infernal-1.1.3/config.guess-226- *)
infernal-1.1.3/config.guess:227: release=`echo ${UNAME_RELEASE} | sed -e 's/[-_].*//' | cut -d. -f1,2`
infernal-1.1.3/config.guess-228- ;;
##############################################
infernal-1.1.3/config.guess-264- *4.0)
infernal-1.1.3/config.guess:265: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
infernal-1.1.3/config.guess-266- ;;
infernal-1.1.3/config.guess-267- *5.*)
infernal-1.1.3/config.guess:268: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $4}'`
infernal-1.1.3/config.guess-269- ;;
##############################################
infernal-1.1.3/config.guess-274- # types through head -n 1, so we only detect the type of CPU 0.
infernal-1.1.3/config.guess:275: ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
infernal-1.1.3/config.guess-276- case "$ALPHA_CPU_TYPE" in
##############################################
infernal-1.1.3/config.guess-312- # 1.2 uses "1.2" for uname -r.
infernal-1.1.3/config.guess:313: echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[PVTX]//' | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz`
infernal-1.1.3/config.guess-314- # Reset EXIT trap before exiting to avoid spurious non-zero exit code.
##############################################
infernal-1.1.3/config.guess-372- s390x:SunOS:*:*)
infernal-1.1.3/config.guess:373: echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
infernal-1.1.3/config.guess-374- exit ;;
infernal-1.1.3/config.guess-375- sun4H:SunOS:5.*:*)
infernal-1.1.3/config.guess:376: echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
infernal-1.1.3/config.guess-377- exit ;;
infernal-1.1.3/config.guess-378- sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
infernal-1.1.3/config.guess:379: echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
infernal-1.1.3/config.guess-380- exit ;;
##############################################
infernal-1.1.3/config.guess-397- fi
infernal-1.1.3/config.guess:398: echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
infernal-1.1.3/config.guess-399- exit ;;
##############################################
infernal-1.1.3/config.guess-403- # it's likely to be more like Solaris than SunOS4.
infernal-1.1.3/config.guess:404: echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
infernal-1.1.3/config.guess-405- exit ;;
##############################################
infernal-1.1.3/config.guess-412- # Japanese Language versions have a version number like `4.1.3-JL'.
infernal-1.1.3/config.guess:413: echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
infernal-1.1.3/config.guess-414- exit ;;
##############################################
infernal-1.1.3/config.guess-418- sun*:*:4.2BSD:*)
infernal-1.1.3/config.guess:419: UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
infernal-1.1.3/config.guess-420- test "x${UNAME_RELEASE}" = x && UNAME_RELEASE=3
##############################################
infernal-1.1.3/config.guess-500- $CC_FOR_BUILD -o $dummy $dummy.c &&
infernal-1.1.3/config.guess:501: dummyarg=`echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` &&
infernal-1.1.3/config.guess:502: SYSTEM_NAME=`$dummy $dummyarg` &&
infernal-1.1.3/config.guess-503- { echo "$SYSTEM_NAME"; exit; }
##############################################
infernal-1.1.3/config.guess-556- *:IRIX*:*:*)
infernal-1.1.3/config.guess:557: echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
infernal-1.1.3/config.guess-558- exit ;;
##############################################
infernal-1.1.3/config.guess-586-EOF
infernal-1.1.3/config.guess:587: if $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy`
infernal-1.1.3/config.guess-588- then
##############################################
infernal-1.1.3/config.guess-599- *:AIX:*:[4567])
infernal-1.1.3/config.guess:600: IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
infernal-1.1.3/config.guess-601- if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
##############################################
infernal-1.1.3/config.guess-635- 9000/[34678]??:HP-UX:*:*)
infernal-1.1.3/config.guess:636: HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
infernal-1.1.3/config.guess-637- case "${UNAME_MACHINE}" in
##############################################
infernal-1.1.3/config.guess-689-EOF
infernal-1.1.3/config.guess:690: (CCOPTS="" $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
infernal-1.1.3/config.guess-691- test -z "$HP_ARCH" && HP_ARCH=hppa
##############################################
infernal-1.1.3/config.guess-717- ia64:HP-UX:*:*)
infernal-1.1.3/config.guess:718: HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
infernal-1.1.3/config.guess-719- echo ia64-hp-hpux${HPUX_REV}
##############################################
infernal-1.1.3/config.guess-747-EOF
infernal-1.1.3/config.guess:748: $CC_FOR_BUILD -o $dummy $dummy.c && SYSTEM_NAME=`$dummy` &&
infernal-1.1.3/config.guess-749- { echo "$SYSTEM_NAME"; exit; }
##############################################
infernal-1.1.3/config.guess-818- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
infernal-1.1.3/config.guess:819: FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
infernal-1.1.3/config.guess-820- echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
infernal-1.1.3/config.guess-823- FUJITSU_SYS=`uname -p | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/\///'`
infernal-1.1.3/config.guess:824: FUJITSU_REL=`echo ${UNAME_RELEASE} | tr ABCDEFGHIJKLMNOPQRSTUVWXYZ abcdefghijklmnopqrstuvwxyz | sed -e 's/ /_/'`
infernal-1.1.3/config.guess-825- echo "sparc-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
infernal-1.1.3/config.guess-839- amd64)
infernal-1.1.3/config.guess:840: echo x86_64-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
infernal-1.1.3/config.guess-841- *)
infernal-1.1.3/config.guess:842: echo ${UNAME_PROCESSOR}-unknown-freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'` ;;
infernal-1.1.3/config.guess-843- esac
##############################################
infernal-1.1.3/config.guess-897- prep*:SunOS:5.*:*)
infernal-1.1.3/config.guess:898: echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
infernal-1.1.3/config.guess-899- exit ;;
##############################################
infernal-1.1.3/config.guess-901- # the GNU system
infernal-1.1.3/config.guess:902: echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-${LIBC}`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
infernal-1.1.3/config.guess-903- exit ;;
##############################################
infernal-1.1.3/config.guess-905- # other systems with GNU libc and userland
infernal-1.1.3/config.guess:906: echo ${UNAME_MACHINE}-unknown-`echo ${UNAME_SYSTEM} | sed 's,^[^/]*/,,' | tr "[:upper:]" "[:lower:]"``echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`-${LIBC}
infernal-1.1.3/config.guess-907- exit ;;
##############################################
infernal-1.1.3/config.guess-999-EOF
infernal-1.1.3/config.guess:1000: eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'`
infernal-1.1.3/config.guess-1001- test x"${CPU}" != x && { echo "${CPU}-unknown-linux-${LIBC}"; exit; }
##############################################
infernal-1.1.3/config.guess-1099- i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
infernal-1.1.3/config.guess:1100: UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
infernal-1.1.3/config.guess-1101- if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
##############################################
infernal-1.1.3/config.guess-1302- fi
infernal-1.1.3/config.guess:1303: if test `echo "$UNAME_RELEASE" | sed -e 's/\..*//'` -le 10 ; then
infernal-1.1.3/config.guess-1304- if [ "$CC_FOR_BUILD" != no_compiler_found ]; then
##############################################
infernal-1.1.3/config.guess-1387- *:DragonFly:*:*)
infernal-1.1.3/config.guess:1388: echo ${UNAME_MACHINE}-unknown-dragonfly`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`
infernal-1.1.3/config.guess-1389- exit ;;
##############################################
infernal-1.1.3/config.guess-1400- i*86:skyos:*:*)
infernal-1.1.3/config.guess:1401: echo ${UNAME_MACHINE}-pc-skyos`echo ${UNAME_RELEASE} | sed -e 's/ .*$//'`
infernal-1.1.3/config.guess-1402- exit ;;
##############################################
infernal-1.1.3/debian/bin/cmalign-1-#!/bin/sh
infernal-1.1.3/debian/bin/cmalign:2:BINNAME=`basename $0`
infernal-1.1.3/debian/bin/cmalign-3-
##############################################
infernal-1.1.3/debian/patches/hardening-25- ${ALL_BENCHMARKS}: libeasel.a
infernal-1.1.3/debian/patches/hardening:26: @BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/debian/patches/hardening-27-@@ -587,10 +587,10 @@
##############################################
infernal-1.1.3/debian/patches/hardening-38- ${ALL_EXPERIMENTS}: libeasel.a
infernal-1.1.3/debian/patches/hardening:39: @BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/debian/patches/hardening-40-@@ -601,10 +601,10 @@
##############################################
infernal-1.1.3/debian/patches/hardening-51- ${ALL_EXAMPLES}: libeasel.a
infernal-1.1.3/debian/patches/hardening:52: @BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/debian/patches/hardening-53-@@ -614,10 +614,10 @@
##############################################
infernal-1.1.3/debian/rules-32- dh_install
infernal-1.1.3/debian/rules:33: for bin in `ls $(CURDIR)/debian/infernal/usr/lib/infernal` ; do \
infernal-1.1.3/debian/rules-34- if [ $$bin != cmalign ] ; then \
##############################################
infernal-1.1.3/debian/tests/run-unit-test-6-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
infernal-1.1.3/debian/tests/run-unit-test:7: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
infernal-1.1.3/debian/tests/run-unit-test-8-fi
##############################################
infernal-1.1.3/.pc/hardening/easel/Makefile.in-567-${ALL_UTESTS}: libeasel.a
infernal-1.1.3/.pc/hardening/easel/Makefile.in:568: @BASENAME=`echo $@ | sed -e 's/_utest//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/.pc/hardening/easel/Makefile.in:569: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/.pc/hardening/easel/Makefile.in-570- DFLAG=esl$${DFLAG}_TESTDRIVE ;\
##############################################
infernal-1.1.3/.pc/hardening/easel/Makefile.in-581-${ALL_BENCHMARKS}: libeasel.a
infernal-1.1.3/.pc/hardening/easel/Makefile.in:582: @BASENAME=`echo $@ | sed -e 's/_benchmark//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/.pc/hardening/easel/Makefile.in:583: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/.pc/hardening/easel/Makefile.in-584- DFLAG=esl$${DFLAG}_BENCHMARK ;\
##############################################
infernal-1.1.3/.pc/hardening/easel/Makefile.in-595-${ALL_EXPERIMENTS}: libeasel.a
infernal-1.1.3/.pc/hardening/easel/Makefile.in:596: @BASENAME=`echo $@ | sed -e 's/_experiment//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/.pc/hardening/easel/Makefile.in:597: DFLAG=`echo $${BASENAME} | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/.pc/hardening/easel/Makefile.in-598- DFLAG=esl$${DFLAG}_EXPERIMENT ;\
##############################################
infernal-1.1.3/.pc/hardening/easel/Makefile.in-609-${ALL_EXAMPLES}: libeasel.a
infernal-1.1.3/.pc/hardening/easel/Makefile.in:610: @BASENAME=`echo $@ | sed -e 's/_example[0-9]*//'| sed -e 's/^esl_//'` ;\
infernal-1.1.3/.pc/hardening/easel/Makefile.in:611: DFLAG=esl`echo $@ | sed -e 's/^esl_//' | sed -e 'y/abcdefghijklmnopqrstuvwxyz/ABCDEFGHIJKLMNOPQRSTUVWXYZ/'`;\
infernal-1.1.3/.pc/hardening/easel/Makefile.in-612- if test $@ = "easel_example"; \