===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
hisat2-2.2.1/docs/_pages/manual.md-87-where `NCBI_NGS_DIR` and `NCBI_VDB_DIR` will be used in Makefile for `-I` and `-L` compilation options.
hisat2-2.2.1/docs/_pages/manual.md:88:For example, `$(NCBI_NGS_DIR)/include` and `$(NCBI_NGS_DIR)/lib64` will be used.
hisat2-2.2.1/docs/_pages/manual.md-89-
##############################################
hisat2-2.2.1/evaluation/real/calculate_read_cost.py-1513- assert os.path.exists("SJ.out.tab")
hisat2-2.2.1/evaluation/real/calculate_read_cost.py:1514: os.system("awk 'BEGIN {OFS=\"\t\"; strChar[0]=\".\"; strChar[1]=\"+\"; strChar[2]=\"-\";} {if($5>0){print $1,$2,$3,strChar[$4]}}' SJ.out.tab > SJ.out.tab.Pass1.sjdb")
hisat2-2.2.1/evaluation/real/calculate_read_cost.py-1515- for file in os.listdir("."):
##############################################
hisat2-2.2.1/evaluation/simulation/calculate_read_cost.py-2513- assert os.path.exists("SJ.out.tab")
hisat2-2.2.1/evaluation/simulation/calculate_read_cost.py:2514: os.system("awk 'BEGIN {OFS=\"\t\"; strChar[0]=\".\"; strChar[1]=\"+\"; strChar[2]=\"-\";} {if($5>0){print $1,$2,$3,strChar[$4]}}' SJ.out.tab > SJ.out.tab.Pass1.sjdb")
hisat2-2.2.1/evaluation/simulation/calculate_read_cost.py-2515- for file in os.listdir("."):
##############################################
hisat2-2.2.1/evaluation/tests/CODIS/README-19-
hisat2-2.2.1/evaluation/tests/CODIS/README:20: for i in `ls -l ILMN/NA128*1.fq.gz | awk '{print $NF}' | cut -d'/' -f2 | cut -d'.' -f1`; do echo $i; ./hisatgenotype_locus.py --locus-list A --aligner-list hisat2.graph --num-editdist 2 --reads ILMN/$i.extracted.1.fq.gz,ILMN/$i.extracted.2.fq.gz --assembly-base assembly_graph_$i 2> $i.tmp; done
hisat2-2.2.1/evaluation/tests/CODIS/README-21-
##############################################
hisat2-2.2.1/evaluation/tests/HLA_novel/ILMN_StrandSeq/README-1-Download SRA reads in the FASTQ format
hisat2-2.2.1/evaluation/tests/HLA_novel/ILMN_StrandSeq/README:2: for i in `awk '{if(NR != 1) print $4}' SraRunInfo.txt`; do fastq-dump --gzip $i; done
hisat2-2.2.1/evaluation/tests/HLA_novel/ILMN_StrandSeq/README-3-
##############################################
hisat2-2.2.1/evaluation/tests/HLA_novel/ILMN_StrandSeq_original/README-1-Download SRA reads in the FASTQ format
hisat2-2.2.1/evaluation/tests/HLA_novel/ILMN_StrandSeq_original/README:2: for i in `awk '{if(NR != 1) print $4}' SraRunInfo.txt`; do fastq-dump --gzip $i; done
hisat2-2.2.1/evaluation/tests/HLA_novel/ILMN_StrandSeq_original/README-3-
##############################################
hisat2-2.2.1/evaluation/tests/HLA_novel/README-2-
hisat2-2.2.1/evaluation/tests/HLA_novel/README:3: for i in `ls -l CP_80/LP*1.fq.gz | awk '{print $NF}' | cut -d'/' -f2 | cut -d'.' -f1`; do echo $i; ./hisatgenotype_locus.py --locus-list A --num-editdist 2 --assembly --reads CP_80/$i.extracted.1.fq.gz,CP_80/$i.extracted.2.fq.gz --assembly-base assembly_graph_$i 2> $i.tmp; done
hisat2-2.2.1/evaluation/tests/HLA_novel/README-4-
##############################################
hisat2-2.2.1/fast_mutex.h-35- efficient access to the xchg assembler instruction than implementing the code as
hisat2-2.2.1/fast_mutex.h:36: a function in a separate .asm file. MSC does not support in line assembler for 64 bit builds.
hisat2-2.2.1/fast_mutex.h-37-
hisat2-2.2.1/fast_mutex.h:38: c) The NO_FAST_MUTEX_ASM option has been introduced
hisat2-2.2.1/fast_mutex.h-39-
##############################################
hisat2-2.2.1/fast_mutex.h-58-// revert to the system API)
hisat2-2.2.1/fast_mutex.h:59:#if !defined NO_FAST_MUTEX_ASM && ((defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))) || \
hisat2-2.2.1/fast_mutex.h-60- (defined(_MSC_VER) && (defined(_M_IX86) || defined(_M_X64))) || \
##############################################
hisat2-2.2.1/fast_mutex.h-187- #if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
hisat2-2.2.1/fast_mutex.h:188: asm volatile (
hisat2-2.2.1/fast_mutex.h-189- "movl $1,%%eax\n\t"
##############################################
hisat2-2.2.1/fast_mutex.h-198- int *ptrLock = &mLock;
hisat2-2.2.1/fast_mutex.h:199: __asm {
hisat2-2.2.1/fast_mutex.h-200- mov eax, 1
##############################################
hisat2-2.2.1/fast_mutex.h-209- int newLock = 1;
hisat2-2.2.1/fast_mutex.h:210: asm volatile (
hisat2-2.2.1/fast_mutex.h-211- "\n1:\n\t"
##############################################
hisat2-2.2.1/fast_mutex.h-240- #if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
hisat2-2.2.1/fast_mutex.h:241: asm volatile (
hisat2-2.2.1/fast_mutex.h-242- "movl $0,%%eax\n\t"
##############################################
hisat2-2.2.1/fast_mutex.h-250- int *ptrLock = &mLock;
hisat2-2.2.1/fast_mutex.h:251: __asm {
hisat2-2.2.1/fast_mutex.h-252- mov eax,0
##############################################
hisat2-2.2.1/fast_mutex.h-259- #elif defined(__GNUC__) && (defined(__ppc__))
hisat2-2.2.1/fast_mutex.h:260: asm volatile (
hisat2-2.2.1/fast_mutex.h-261- "sync\n\t" // Replace with lwsync where possible?
##############################################
hisat2-2.2.1/gfm.h-551-#else
hisat2-2.2.1/gfm.h:552: asm ("popcntq %[x],%[count]\n": [count] "=&r" (count): [x] "r" (x));
hisat2-2.2.1/gfm.h-553-#endif
##############################################
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1008- "BUILD_TIME=\"\\\"`date\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj:1009: "COMPILER_VERSION=\"\\\"`$(CXX) -v 2>&1 | tail -1`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1010- "COMPILER_OPTIONS=\"\\\"test\\\"\"",
##############################################
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1068- "BUILD_TIME=\"\\\"`date`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj:1069: "COMPILER_VERSION=\"\\\"`$(CXX) -v 2>&1 | tail -1`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1070- "COMPILER_OPTIONS=\"\\\"test\\\"\"",
##############################################
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1140- "BUILD_TIME=\"\\\"`date\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj:1141: "COMPILER_VERSION=\"\\\"`$(CXX) -v 2>&1 | tail -1`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1142- "COMPILER_OPTIONS=\"\\\"test\\\"\"",
##############################################
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1186- "BUILD_TIME=\"\\\"`date`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj:1187: "COMPILER_VERSION=\"\\\"`$(CXX) -v 2>&1 | tail -1`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1188- "COMPILER_OPTIONS=\"\\\"test\\\"\"",
##############################################
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1208- "BUILD_TIME=\"\\\"`date\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj:1209: "COMPILER_VERSION=\"\\\"`$(CXX) -v 2>&1 | tail -1`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1210- "COMPILER_OPTIONS=\"\\\"test\\\"\"",
##############################################
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1229- "BUILD_TIME=\"\\\"`date`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj:1230: "COMPILER_VERSION=\"\\\"`$(CXX) -v 2>&1 | tail -1`\\\"\"",
hisat2-2.2.1/hisat2.xcodeproj/project.pbxproj-1231- "COMPILER_OPTIONS=\"\\\"test\\\"\"",
##############################################
hisat2-2.2.1/scripts/infer_fraglen.pl-81-$index =~ s/^~/$ENV{HOME}/;
hisat2-2.2.1/scripts/infer_fraglen.pl:82:die "Bad bowtie path: $bowtie2" if system("$bowtie2 --version >/dev/null 2>/dev/null") != 0;
hisat2-2.2.1/scripts/infer_fraglen.pl-83-die "Bad index: $index" if !checkIndex($index);
##############################################
hisat2-2.2.1/scripts/infer_fraglen.pl-91-my $tot = 0;
hisat2-2.2.1/scripts/infer_fraglen.pl:92:system($cmd1) == 0 || die "Error running '$cmd1'";
hisat2-2.2.1/scripts/infer_fraglen.pl-93-open (M1, ".infer_fraglen.tmp") || die "Could not open '.infer_fraglen.tmp'";
##############################################
hisat2-2.2.1/scripts/make_a_thaliana_tair.sh-15- fi
hisat2-2.2.1/scripts/make_a_thaliana_tair.sh:16: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_a_thaliana_tair.sh-17- return $?
##############################################
hisat2-2.2.1/scripts/make_b_taurus_UMD3.sh-50- fi
hisat2-2.2.1/scripts/make_b_taurus_UMD3.sh:51: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_b_taurus_UMD3.sh-52- return $?
##############################################
hisat2-2.2.1/scripts/make_bdgp6.sh-27- fi
hisat2-2.2.1/scripts/make_bdgp6.sh:28: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_bdgp6.sh-29- return $?
##############################################
hisat2-2.2.1/scripts/make_bdgp6_tran.sh-29- fi
hisat2-2.2.1/scripts/make_bdgp6_tran.sh:30: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_bdgp6_tran.sh-31- return $?
##############################################
hisat2-2.2.1/scripts/make_canFam2.sh-11- BASE_CHRS="$BASE_CHRS chr$i"
hisat2-2.2.1/scripts/make_canFam2.sh:12: i=`expr $i + 1`
hisat2-2.2.1/scripts/make_canFam2.sh-13-done
##############################################
hisat2-2.2.1/scripts/make_canFam2.sh-25- fi
hisat2-2.2.1/scripts/make_canFam2.sh:26: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_canFam2.sh-27- return $?
##############################################
hisat2-2.2.1/scripts/make_ce10.sh-12- fi
hisat2-2.2.1/scripts/make_ce10.sh:13: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_ce10.sh-14- return $?
hisat2-2.2.1/scripts/make_ce10.sh-15- else
hisat2-2.2.1/scripts/make_ce10.sh:16: wget -O `basename $1` $1
hisat2-2.2.1/scripts/make_ce10.sh-17- return $?
##############################################
hisat2-2.2.1/scripts/make_dm6.sh-19- fi
hisat2-2.2.1/scripts/make_dm6.sh:20: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_dm6.sh-21- return $?
hisat2-2.2.1/scripts/make_dm6.sh-22- else
hisat2-2.2.1/scripts/make_dm6.sh:23: wget -O `basename $1` $1
hisat2-2.2.1/scripts/make_dm6.sh-24- return $?
##############################################
hisat2-2.2.1/scripts/make_grch37.sh-27- fi
hisat2-2.2.1/scripts/make_grch37.sh:28: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch37.sh-29- return $?
##############################################
hisat2-2.2.1/scripts/make_grch37_snp.sh-31- fi
hisat2-2.2.1/scripts/make_grch37_snp.sh:32: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch37_snp.sh-33- return $?
##############################################
hisat2-2.2.1/scripts/make_grch37_snp_tran.sh-33- fi
hisat2-2.2.1/scripts/make_grch37_snp_tran.sh:34: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch37_snp_tran.sh-35- return $?
##############################################
hisat2-2.2.1/scripts/make_grch37_snp_tran_ercc.sh-35- fi
hisat2-2.2.1/scripts/make_grch37_snp_tran_ercc.sh:36: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch37_snp_tran_ercc.sh-37- return $?
##############################################
hisat2-2.2.1/scripts/make_grch37_tran.sh-29- fi
hisat2-2.2.1/scripts/make_grch37_tran.sh:30: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch37_tran.sh-31- return $?
##############################################
hisat2-2.2.1/scripts/make_grch38.sh-27- fi
hisat2-2.2.1/scripts/make_grch38.sh:28: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch38.sh-29- return $?
##############################################
hisat2-2.2.1/scripts/make_grch38_rep.sh-27- fi
hisat2-2.2.1/scripts/make_grch38_rep.sh:28: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch38_rep.sh-29- return $?
##############################################
hisat2-2.2.1/scripts/make_grch38_snp.sh-31- fi
hisat2-2.2.1/scripts/make_grch38_snp.sh:32: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch38_snp.sh-33- return $?
##############################################
hisat2-2.2.1/scripts/make_grch38_snp_rep.sh-31- fi
hisat2-2.2.1/scripts/make_grch38_snp_rep.sh:32: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch38_snp_rep.sh-33- return $?
##############################################
hisat2-2.2.1/scripts/make_grch38_snp_tran.sh-33- fi
hisat2-2.2.1/scripts/make_grch38_snp_tran.sh:34: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch38_snp_tran.sh-35- return $?
##############################################
hisat2-2.2.1/scripts/make_grch38_snp_tran_ercc.sh-35- fi
hisat2-2.2.1/scripts/make_grch38_snp_tran_ercc.sh:36: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch38_snp_tran_ercc.sh-37- return $?
##############################################
hisat2-2.2.1/scripts/make_grch38_tran.sh-29- fi
hisat2-2.2.1/scripts/make_grch38_tran.sh:30: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grch38_tran.sh-31- return $?
##############################################
hisat2-2.2.1/scripts/make_grcm38.sh-22- fi
hisat2-2.2.1/scripts/make_grcm38.sh:23: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grcm38.sh-24- return $?
##############################################
hisat2-2.2.1/scripts/make_grcm38_snp.sh-26- fi
hisat2-2.2.1/scripts/make_grcm38_snp.sh:27: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grcm38_snp.sh-28- return $?
##############################################
hisat2-2.2.1/scripts/make_grcm38_snp_tran.sh-28- fi
hisat2-2.2.1/scripts/make_grcm38_snp_tran.sh:29: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grcm38_snp_tran.sh-30- return $?
##############################################
hisat2-2.2.1/scripts/make_grcm38_tran.sh-25- fi
hisat2-2.2.1/scripts/make_grcm38_tran.sh:26: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_grcm38_tran.sh-27- return $?
##############################################
hisat2-2.2.1/scripts/make_hg19.sh-24- fi
hisat2-2.2.1/scripts/make_hg19.sh:25: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_hg19.sh-26- return $?
##############################################
hisat2-2.2.1/scripts/make_hg38.sh-24- fi
hisat2-2.2.1/scripts/make_hg38.sh:25: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_hg38.sh-26- return $?
##############################################
hisat2-2.2.1/scripts/make_hg38_allsnp.sh-28- fi
hisat2-2.2.1/scripts/make_hg38_allsnp.sh:29: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_hg38_allsnp.sh-30- return $?
##############################################
hisat2-2.2.1/scripts/make_hg38_snp.sh-28- fi
hisat2-2.2.1/scripts/make_hg38_snp.sh:29: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_hg38_snp.sh-30- return $?
##############################################
hisat2-2.2.1/scripts/make_hg38_snp_tran.sh-24- fi
hisat2-2.2.1/scripts/make_hg38_snp_tran.sh:25: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_hg38_snp_tran.sh-26- return $?
##############################################
hisat2-2.2.1/scripts/make_mm10.sh-24- fi
hisat2-2.2.1/scripts/make_mm10.sh:25: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_mm10.sh-26- return $?
##############################################
hisat2-2.2.1/scripts/make_mm9.sh-67- fi
hisat2-2.2.1/scripts/make_mm9.sh:68: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_mm9.sh-69- return $?
##############################################
hisat2-2.2.1/scripts/make_r64.sh-27- fi
hisat2-2.2.1/scripts/make_r64.sh:28: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_r64.sh-29- return $?
##############################################
hisat2-2.2.1/scripts/make_r64_tran.sh-29- fi
hisat2-2.2.1/scripts/make_r64_tran.sh:30: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_r64_tran.sh-31- return $?
##############################################
hisat2-2.2.1/scripts/make_rn4.sh-21- BASE_CHRS="$BASE_CHRS chr$i"
hisat2-2.2.1/scripts/make_rn4.sh:22: i=`expr $i + 1`
hisat2-2.2.1/scripts/make_rn4.sh-23-done
##############################################
hisat2-2.2.1/scripts/make_rn4.sh-60- fi
hisat2-2.2.1/scripts/make_rn4.sh:61: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_rn4.sh-62- return $?
##############################################
hisat2-2.2.1/scripts/make_rn6.sh-27- fi
hisat2-2.2.1/scripts/make_rn6.sh:28: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_rn6.sh-29- return $?
##############################################
hisat2-2.2.1/scripts/make_rnor6.sh-27- fi
hisat2-2.2.1/scripts/make_rnor6.sh:28: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_rnor6.sh-29- return $?
##############################################
hisat2-2.2.1/scripts/make_rnor6_tran.sh-29- fi
hisat2-2.2.1/scripts/make_rnor6_tran.sh:30: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_rnor6_tran.sh-31- return $?
##############################################
hisat2-2.2.1/scripts/make_sc3.sh-12- fi
hisat2-2.2.1/scripts/make_sc3.sh:13: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_sc3.sh-14- return $?
##############################################
hisat2-2.2.1/scripts/make_wbcel235.sh-27- fi
hisat2-2.2.1/scripts/make_wbcel235.sh:28: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_wbcel235.sh-29- return $?
##############################################
hisat2-2.2.1/scripts/make_wbcel235_tran.sh-29- fi
hisat2-2.2.1/scripts/make_wbcel235_tran.sh:30: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_wbcel235_tran.sh-31- return $?
##############################################
hisat2-2.2.1/scripts/make_zm3_snp_tran_ercc.sh-31- fi
hisat2-2.2.1/scripts/make_zm3_snp_tran_ercc.sh:32: curl -o `basename $1` $1
hisat2-2.2.1/scripts/make_zm3_snp_tran_ercc.sh-33- return $?
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-423- print STDERR "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:424: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-425- $? == 0 || mydie("Error running '$cmd'; exitlevel=$?");
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-430- print STDERR "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:431: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-432- $? == 0 || mydie("Error running '$cmd'; exitlevel=$?");
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-927- print "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:928: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-929- $? == 0 ||
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-932- print "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:933: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-934- $? == 0 ||
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-944- print "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:945: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-946- $? == 0 ||
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-951- print "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:952: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-953- $? == 0 ||
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-958- print "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:959: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-960- $? == 0 ||
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-963- print "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:964: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-965- $? == 0 ||
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-976- print "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:977: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-978- $? == 0 || mydie("Command '$cmd' failed with exitlevel $?");
##############################################
hisat2-2.2.1/scripts/sim/Sim.pm-980- print "$cmd\n";
hisat2-2.2.1/scripts/sim/Sim.pm:981: system($cmd);
hisat2-2.2.1/scripts/sim/Sim.pm-982- $? == 0 ||
##############################################
hisat2-2.2.1/scripts/sim/unit.sh-21-
hisat2-2.2.1/scripts/sim/unit.sh:22:d=`dirname $0`
hisat2-2.2.1/scripts/sim/unit.sh:23:for i in `ls $d/*.pm` ; do echo $i ; perl $i --test ; done
##############################################
hisat2-2.2.1/scripts/test/args.pl-30-my $bowtie2_d = "./bowtie2-debug";
hisat2-2.2.1/scripts/test/args.pl:31:if(system("$bowtie2 --version") != 0) {
hisat2-2.2.1/scripts/test/args.pl-32- print STDERR "Could not execute ./bowtie2; looking in PATH...\n";
##############################################
hisat2-2.2.1/scripts/test/args.pl-34- chomp($bowtie2);
hisat2-2.2.1/scripts/test/args.pl:35: if(system("$bowtie2 --version") != 0) {
hisat2-2.2.1/scripts/test/args.pl-36- die "Could not find bowtie2 in current directory or in PATH\n";
##############################################
hisat2-2.2.1/scripts/test/args.pl-38-}
hisat2-2.2.1/scripts/test/args.pl:39:if(system("$bowtie2_d --version") != 0) {
hisat2-2.2.1/scripts/test/args.pl-40- print STDERR "Could not execute ./bowtie2-debug; looking in PATH...\n";
##############################################
hisat2-2.2.1/scripts/test/args.pl-42- chomp($bowtie2_d);
hisat2-2.2.1/scripts/test/args.pl:43: if(system("$bowtie2_d --version") != 0) {
hisat2-2.2.1/scripts/test/args.pl-44- die "Could not find bowtie2-debug in current directory or in PATH\n";
##############################################
hisat2-2.2.1/scripts/test/args.pl-50- my $bowtie2_build = "./bowtie2-build";
hisat2-2.2.1/scripts/test/args.pl:51: if(system("$bowtie2_build --version") != 0) {
hisat2-2.2.1/scripts/test/args.pl-52- print STDERR "Could not execute ./bowtie2-build; looking in PATH...\n";
hisat2-2.2.1/scripts/test/args.pl:53: $bowtie2_build = `which $bowtie2_build`;
hisat2-2.2.1/scripts/test/args.pl-54- chomp($bowtie2_build);
hisat2-2.2.1/scripts/test/args.pl:55: if(system("$bowtie2_build --version") != 0) {
hisat2-2.2.1/scripts/test/args.pl-56- die "Could not find bowtie2-build in current directory or in PATH\n";
##############################################
hisat2-2.2.1/scripts/test/args.pl-58- }
hisat2-2.2.1/scripts/test/args.pl:59: system("$bowtie2_build -C genomes/NC_008253.fna e_coli_c") && die;
hisat2-2.2.1/scripts/test/args.pl-60-} else {
##############################################
hisat2-2.2.1/scripts/test/args.pl-99- print "$cmd\n";
hisat2-2.2.1/scripts/test/args.pl:100: return system($cmd);
hisat2-2.2.1/scripts/test/args.pl-101-}
##############################################
hisat2-2.2.1/scripts/test/simple_tests.pl-46-if(! -x $bowtie2 || ! -x $bowtie2_build) {
hisat2-2.2.1/scripts/test/simple_tests.pl:47: my $bowtie2_dir = `dirname $bowtie2`;
hisat2-2.2.1/scripts/test/simple_tests.pl:48: my $bowtie2_exe = `basename $bowtie2`;
hisat2-2.2.1/scripts/test/simple_tests.pl:49: my $bowtie2_build_exe = `basename $bowtie2_build`;
hisat2-2.2.1/scripts/test/simple_tests.pl-50- chomp($bowtie2_dir);
##############################################
hisat2-2.2.1/scripts/test/simple_tests.pl-52- chomp($bowtie2_build_exe);
hisat2-2.2.1/scripts/test/simple_tests.pl:53: system("make -C $bowtie2_dir $bowtie2_exe $bowtie2_build_exe") && die;
hisat2-2.2.1/scripts/test/simple_tests.pl-54-}
##############################################
hisat2-2.2.1/scripts/test/simple_tests.pl-4120- print "$cmd\n";
hisat2-2.2.1/scripts/test/simple_tests.pl:4121: system($cmd);
hisat2-2.2.1/scripts/test/simple_tests.pl-4122- ($? == 0) || die "Bad exitlevel from bowtie2-build: $?";
##############################################
hisat2-2.2.1/third_party/cpuid.h-84-#else
hisat2-2.2.1/third_party/cpuid.h:85:/* Host GCCs older than 3.0 weren't supporting Intel asm syntax
hisat2-2.2.1/third_party/cpuid.h-86- nor alternatives in i386 code. */
##############################################
hisat2-2.2.1/third_party/cpuid.h-140-#else
hisat2-2.2.1/third_party/cpuid.h:141:/* Host GCCs older than 3.0 weren't supporting Intel asm syntax
hisat2-2.2.1/third_party/cpuid.h-142- nor alternatives in i386 code. */
##############################################
hisat2-2.2.1/debian/patches/python3-319- assert os.path.exists("SJ.out.tab")
hisat2-2.2.1/debian/patches/python3:320: os.system("awk 'BEGIN {OFS=\"\t\"; strChar[0]=\".\"; strChar[1]=\"+\"; strChar[2]=\"-\";} {if($5>0){print $1,$2,$3,strChar[$4]}}' SJ.out.tab > SJ.out.tab.Pass1.sjdb")
hisat2-2.2.1/debian/patches/python3-321-@@ -1517,18 +1517,18 @@
##############################################
hisat2-2.2.1/debian/patches/python3-770- assert os.path.exists("SJ.out.tab")
hisat2-2.2.1/debian/patches/python3:771: os.system("awk 'BEGIN {OFS=\"\t\"; strChar[0]=\".\"; strChar[1]=\"+\"; strChar[2]=\"-\";} {if($5>0){print $1,$2,$3,strChar[$4]}}' SJ.out.tab > SJ.out.tab.Pass1.sjdb")
hisat2-2.2.1/debian/patches/python3-772-@@ -2518,18 +2518,18 @@
##############################################
hisat2-2.2.1/debian/patches/reproducibile-68-+ -DBUILD_TIME="\"${BUILD_TIME}\"" \
hisat2-2.2.1/debian/patches/reproducibile:69: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
hisat2-2.2.1/debian/patches/reproducibile-70- $(FILE_FLAGS) \
##############################################
hisat2-2.2.1/.pc/hardening/Makefile-292- -DBUILD_TIME="\"`date`\"" \
hisat2-2.2.1/.pc/hardening/Makefile:293: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
hisat2-2.2.1/.pc/hardening/Makefile-294- $(FILE_FLAGS) \
##############################################
hisat2-2.2.1/.pc/reproducibile/Makefile-292- -DBUILD_TIME="\"`date`\"" \
hisat2-2.2.1/.pc/reproducibile/Makefile:293: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
hisat2-2.2.1/.pc/reproducibile/Makefile-294- $(FILE_FLAGS) \
##############################################
hisat2-2.2.1/.pc/fix-freebsd/hisat2-478- push @to_delete, $ofn;
hisat2-2.2.1/.pc/fix-freebsd/hisat2:479: system("$build_bin $ofn $ofn") == 0 ||
hisat2-2.2.1/.pc/fix-freebsd/hisat2-480- Fail("hisat2-build returned non-0 exit level.\n");
##############################################
hisat2-2.2.1/.pc/fix-freebsd/hisat2-645-} else {
hisat2-2.2.1/.pc/fix-freebsd/hisat2:646: $ret = system($cmd);
hisat2-2.2.1/.pc/fix-freebsd/hisat2-647-}
##############################################
hisat2-2.2.1/.pc/compilerflags/Makefile-295- -DBUILD_TIME="\"${BUILD_TIME}\"" \
hisat2-2.2.1/.pc/compilerflags/Makefile:296: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
hisat2-2.2.1/.pc/compilerflags/Makefile-297- $(FILE_FLAGS) \
##############################################
hisat2-2.2.1/.pc/simde/Makefile-295- -DBUILD_TIME="\"${BUILD_TIME}\"" \
hisat2-2.2.1/.pc/simde/Makefile:296: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
hisat2-2.2.1/.pc/simde/Makefile-297- $(FILE_FLAGS) \
##############################################
hisat2-2.2.1/.pc/python3/evaluation/real/calculate_read_cost.py-1513- assert os.path.exists("SJ.out.tab")
hisat2-2.2.1/.pc/python3/evaluation/real/calculate_read_cost.py:1514: os.system("awk 'BEGIN {OFS=\"\t\"; strChar[0]=\".\"; strChar[1]=\"+\"; strChar[2]=\"-\";} {if($5>0){print $1,$2,$3,strChar[$4]}}' SJ.out.tab > SJ.out.tab.Pass1.sjdb")
hisat2-2.2.1/.pc/python3/evaluation/real/calculate_read_cost.py-1515- for file in os.listdir("."):
##############################################
hisat2-2.2.1/.pc/python3/evaluation/simulation/calculate_read_cost.py-2513- assert os.path.exists("SJ.out.tab")
hisat2-2.2.1/.pc/python3/evaluation/simulation/calculate_read_cost.py:2514: os.system("awk 'BEGIN {OFS=\"\t\"; strChar[0]=\".\"; strChar[1]=\"+\"; strChar[2]=\"-\";} {if($5>0){print $1,$2,$3,strChar[$4]}}' SJ.out.tab > SJ.out.tab.Pass1.sjdb")
hisat2-2.2.1/.pc/python3/evaluation/simulation/calculate_read_cost.py-2515- for file in os.listdir("."):
##############################################
hisat2-2.2.1/.pc/fix-manual/Makefile-295- -DBUILD_TIME="\"${BUILD_TIME}\"" \
hisat2-2.2.1/.pc/fix-manual/Makefile:296: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
hisat2-2.2.1/.pc/fix-manual/Makefile-297- $(FILE_FLAGS) \
##############################################
hisat2-2.2.1/hisat2-478- push @to_delete, $ofn;
hisat2-2.2.1/hisat2:479: system("$build_bin $ofn $ofn") == 0 ||
hisat2-2.2.1/hisat2-480- Fail("hisat2-build returned non-0 exit level.\n");
##############################################
hisat2-2.2.1/hisat2-645-} else {
hisat2-2.2.1/hisat2:646: $ret = system($cmd);
hisat2-2.2.1/hisat2-647-}
##############################################
hisat2-2.2.1/Makefile-295- -DBUILD_TIME="\"${BUILD_TIME}\"" \
hisat2-2.2.1/Makefile:296: -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \
hisat2-2.2.1/Makefile-297- $(FILE_FLAGS) \