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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
ampliconnoise-1.29/Scripts/RunBoth.sh-282- if [ ! -f ${sstub}_cd.fa ]; then
ampliconnoise-1.29/Scripts/RunBoth.sh:283: scount=`grep -ce ">" ${pstub}_cd.fa`
ampliconnoise-1.29/Scripts/RunBoth.sh-284- if [ $scount -lt 100 ]; then
##############################################
ampliconnoise-1.29/Scripts/RunBoth.sh-438- if [ -f ${stub}.raw ] ; then
ampliconnoise-1.29/Scripts/RunBoth.sh:439: tr=`grep -ce ">" ${stub}.raw`
ampliconnoise-1.29/Scripts/RunBoth.sh-440- else
##############################################
ampliconnoise-1.29/Scripts/RunBoth.sh-444- if [ -f ${stub}.dat ]; then
ampliconnoise-1.29/Scripts/RunBoth.sh:445: pf=`head -1 ${stub}.dat`
ampliconnoise-1.29/Scripts/RunBoth.sh-446- pf=${pf//" "*}
##############################################
ampliconnoise-1.29/Scripts/RunBoth.sh-451- if [ -f ${stub}_F.fa ]; then
ampliconnoise-1.29/Scripts/RunBoth.sh:452: us=`grep -ce ">" ${stub}_F.fa`
ampliconnoise-1.29/Scripts/RunBoth.sh-453- else
##############################################
ampliconnoise-1.29/Scripts/RunBoth.sh-457- if [ -f ${stub}_F_Chi.fa ]; then
ampliconnoise-1.29/Scripts/RunBoth.sh:458: cs=`grep -ce ">" ${stub}_F_Chi.fa`
ampliconnoise-1.29/Scripts/RunBoth.sh-459- else
##############################################
ampliconnoise-1.29/Scripts/RunBoth.sh-463- if [ -f ${stub}_F_Good.fa ]; then
ampliconnoise-1.29/Scripts/RunBoth.sh:464: rus=`grep -ce ">" ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunBoth.sh:465: ccread=`CountFasta.pl < ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunBoth.sh-466- cat ${stub}_F_Good.fa >> All_Good.fa
##############################################
ampliconnoise-1.29/Scripts/RunBothFLX.sh-282- if [ ! -f ${sstub}_cd.fa ]; then
ampliconnoise-1.29/Scripts/RunBothFLX.sh:283: scount=`grep -ce ">" ${pstub}_cd.fa`
ampliconnoise-1.29/Scripts/RunBothFLX.sh-284- if [ $scount -lt 100 ]; then
##############################################
ampliconnoise-1.29/Scripts/RunBothFLX.sh-438- if [ -f ${stub}.raw ] ; then
ampliconnoise-1.29/Scripts/RunBothFLX.sh:439: tr=`grep -ce ">" ${stub}.raw`
ampliconnoise-1.29/Scripts/RunBothFLX.sh-440- else
##############################################
ampliconnoise-1.29/Scripts/RunBothFLX.sh-444- if [ -f ${stub}.dat ]; then
ampliconnoise-1.29/Scripts/RunBothFLX.sh:445: pf=`head -1 ${stub}.dat`
ampliconnoise-1.29/Scripts/RunBothFLX.sh-446- pf=${pf//" "*}
##############################################
ampliconnoise-1.29/Scripts/RunBothFLX.sh-451- if [ -f ${stub}_F.fa ]; then
ampliconnoise-1.29/Scripts/RunBothFLX.sh:452: us=`grep -ce ">" ${stub}_F.fa`
ampliconnoise-1.29/Scripts/RunBothFLX.sh-453- else
##############################################
ampliconnoise-1.29/Scripts/RunBothFLX.sh-457- if [ -f ${stub}_F_Chi.fa ]; then
ampliconnoise-1.29/Scripts/RunBothFLX.sh:458: cs=`grep -ce ">" ${stub}_F_Chi.fa`
ampliconnoise-1.29/Scripts/RunBothFLX.sh-459- else
##############################################
ampliconnoise-1.29/Scripts/RunBothFLX.sh-463- if [ -f ${stub}_F_Good.fa ]; then
ampliconnoise-1.29/Scripts/RunBothFLX.sh:464: rus=`grep -ce ">" ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunBothFLX.sh:465: ccread=`CountFasta.pl < ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunBothFLX.sh-466- cat ${stub}_F_Good.fa >> All_Good.fa
##############################################
ampliconnoise-1.29/Scripts/RunFLX.sh-279- if [ ! -f ${sstub}_cd.fa ]; then
ampliconnoise-1.29/Scripts/RunFLX.sh:280: scount=`grep -ce ">" ${pstub}_cd.fa`
ampliconnoise-1.29/Scripts/RunFLX.sh-281- if [ $scount -lt 100 ]; then
##############################################
ampliconnoise-1.29/Scripts/RunFLX.sh-423- if [ -f ${stub}.raw ] ; then
ampliconnoise-1.29/Scripts/RunFLX.sh:424: tr=`grep -ce ">" ${stub}.raw`
ampliconnoise-1.29/Scripts/RunFLX.sh-425- else
##############################################
ampliconnoise-1.29/Scripts/RunFLX.sh-429- if [ -f ${stub}.dat ]; then
ampliconnoise-1.29/Scripts/RunFLX.sh:430: pf=`head -1 ${stub}.dat`
ampliconnoise-1.29/Scripts/RunFLX.sh-431- pf=${pf//" "*}
##############################################
ampliconnoise-1.29/Scripts/RunFLX.sh-436- if [ -f ${stub}_F.fa ]; then
ampliconnoise-1.29/Scripts/RunFLX.sh:437: us=`grep -ce ">" ${stub}_F.fa`
ampliconnoise-1.29/Scripts/RunFLX.sh-438- else
##############################################
ampliconnoise-1.29/Scripts/RunFLX.sh-442- if [ -f ${stub}_F_Chi.fa ]; then
ampliconnoise-1.29/Scripts/RunFLX.sh:443: cs=`grep -ce ">" ${stub}_F_Chi.fa`
ampliconnoise-1.29/Scripts/RunFLX.sh-444- else
##############################################
ampliconnoise-1.29/Scripts/RunFLX.sh-448- if [ -f ${stub}_F_Good.fa ]; then
ampliconnoise-1.29/Scripts/RunFLX.sh:449: rus=`grep -ce ">" ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunFLX.sh:450: ccread=`CountFasta.pl < ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunFLX.sh-451- cat ${stub}_F_Good.fa >> All_Good.fa
##############################################
ampliconnoise-1.29/Scripts/RunTitanium.sh-281- if [ ! -f ${sstub}_cd.fa ]; then
ampliconnoise-1.29/Scripts/RunTitanium.sh:282: scount=`grep -ce ">" ${pstub}_cd.fa`
ampliconnoise-1.29/Scripts/RunTitanium.sh-283- if [ $scount -lt 100 ]; then
##############################################
ampliconnoise-1.29/Scripts/RunTitanium.sh-426- if [ -f ${stub}.raw ] ; then
ampliconnoise-1.29/Scripts/RunTitanium.sh:427: tr=`grep -ce ">" ${stub}.raw`
ampliconnoise-1.29/Scripts/RunTitanium.sh-428- else
##############################################
ampliconnoise-1.29/Scripts/RunTitanium.sh-432- if [ -f ${stub}.dat ]; then
ampliconnoise-1.29/Scripts/RunTitanium.sh:433: pf=`head -1 ${stub}.dat`
ampliconnoise-1.29/Scripts/RunTitanium.sh-434- pf=${pf//" "*}
##############################################
ampliconnoise-1.29/Scripts/RunTitanium.sh-439- if [ -f ${stub}_F.fa ]; then
ampliconnoise-1.29/Scripts/RunTitanium.sh:440: us=`grep -ce ">" ${stub}_F.fa`
ampliconnoise-1.29/Scripts/RunTitanium.sh-441- else
##############################################
ampliconnoise-1.29/Scripts/RunTitanium.sh-445- if [ -f ${stub}_F_Chi.fa ]; then
ampliconnoise-1.29/Scripts/RunTitanium.sh:446: cs=`grep -ce ">" ${stub}_F_Chi.fa`
ampliconnoise-1.29/Scripts/RunTitanium.sh-447- else
##############################################
ampliconnoise-1.29/Scripts/RunTitanium.sh-451- if [ -f ${stub}_F_Good.fa ]; then
ampliconnoise-1.29/Scripts/RunTitanium.sh:452: rus=`grep -ce ">" ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunTitanium.sh:453: ccread=`CountFasta.pl < ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunTitanium.sh-454- cat ${stub}_F_Good.fa >> All_Good.fa
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-281- if [ ! -f ${sstub}_cd.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumA.sh:282: scount=`grep -ce ">" ${pstub}_cd.fa`
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-283- if [ $scount -lt 100 ]; then
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-426- if [ -f ${stub}.raw ] ; then
ampliconnoise-1.29/Scripts/RunTitaniumA.sh:427: tr=`grep -ce ">" ${stub}.raw`
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-428- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-432- if [ -f ${stub}.dat ]; then
ampliconnoise-1.29/Scripts/RunTitaniumA.sh:433: pf=`head -1 ${stub}.dat`
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-434- pf=${pf//" "*}
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-439- if [ -f ${stub}_F.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumA.sh:440: us=`grep -ce ">" ${stub}_F.fa`
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-441- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-445- if [ -f ${stub}_F_Chi.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumA.sh:446: cs=`grep -ce ">" ${stub}_F_Chi.fa`
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-447- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-451- if [ -f ${stub}_F_Good.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumA.sh:452: rus=`grep -ce ">" ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunTitaniumA.sh:453: ccread=`CountFasta.pl < ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunTitaniumA.sh-454- cat ${stub}_F_Good.fa >> All_Good.fa
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-297- echo $command
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:298: scount=`grep -ce ">" ${dir}_s${spyro}_T${length}.fa`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-299- if [ $scount -lt 100 ]; then
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-341-
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:342: scount=`grep -ce ">" ${sstub}_A.fa`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-343- if [ $scount -lt 100 ]; then
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-386- if [ ! -f ${sstub}_cd.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:387: scount=`grep -ce ">" ${pstub}_cd.fa`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-388- if [ $scount -lt 100 ]; then
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-516- if [ -f ${stub}.raw ] ; then
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:517: tr=`grep -ce ">" ${stub}.raw`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-518- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-522- if [ -f ${stub}.dat ]; then
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:523: pf=`head -1 ${stub}.dat`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-524- pf=${pf//" "*}
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-529- if [ -f ${stub}_F.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:530: us=`grep -ce ">" ${stub}_F.fa`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-531- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-535- if [ -f ${stub}_F_Chi.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:536: cs=`grep -ce ">" ${stub}_F_Chi.fa`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-537- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-541- if [ -f ${stub}_F_Good.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:542: rus=`grep -ce ">" ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh:543: ccread=`CountFasta.pl < ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunTitaniumFast.sh-544- cat ${stub}_F_Good.fa >> All_Good.fa
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-198- if [ ! -f ${sstub}_cd.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:199: scount=`grep -ce ">" ${pstub}_cd.fa`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-200- echo "Counted $scount unique sequences after PyroNoise" >> AN_Progress.txt
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-323-
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:324: controlcount=`grep -ce ">" All_s${spyro}_cd.fa`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-325- echo "Counted $controlcount unique sequences after PyroNoise" >> ../AN_Progress.txt
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-376-
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:377: scount=`grep -ce ">" ${sstub}_A.fa`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-378-
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-423- if [ -f ${stub}.raw ] ; then
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:424: tr=`grep -ce ">" ${stub}.raw`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-425- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-429- if [ -f ${stub}.dat ]; then
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:430: pf=`head -1 ${stub}.dat`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-431- pf=${pf//" "*}
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-436- if [ -f ${stub}_F.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:437: us=`grep -ce ">" ${stub}_F.fa`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-438- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-442- if [ -f ${stub}_F_Chi.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:443: cs=`grep -ce ">" ${stub}_F_Chi.fa`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-444- else
##############################################
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-448- if [ -f ${stub}_F_Good.fa ]; then
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:449: rus=`grep -ce ">" ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh:450: ccread=`CountFasta.pl < ${stub}_F_Good.fa`
ampliconnoise-1.29/Scripts/RunTitaniumWeb.sh-451- cat ${stub}_F_Good.fa >> All_Good.fa
##############################################
ampliconnoise-1.29/debian/ampliconnoise.pod-1-#!/bin/bash
ampliconnoise-1.29/debian/ampliconnoise.pod:2:echo pod2man -c 'AmpliconNoise Documentation' "$0" ">" `basename "$0" .pod`.1
ampliconnoise-1.29/debian/ampliconnoise.pod:3:exec pod2man -c 'AmpliconNoise Documentation' "$0" > `basename "$0" .pod`.1
ampliconnoise-1.29/debian/ampliconnoise.pod-4-
##############################################
ampliconnoise-1.29/debian/rules-31- ( for f in bin/* ; do \
ampliconnoise-1.29/debian/rules:32: ln -s ampliconnoise.1 debian/ampliconnoise/usr/share/man/man1/`basename "$$f"`.1 ; \
ampliconnoise-1.29/debian/rules-33- done )