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/ /_/ > | \// __ \| | / /_/ | | || |
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
reapr-1.0.18+dfsg/src/task_preprocess.pl-426- my $cmd = shift;
reapr-1.0.18+dfsg/src/task_preprocess.pl:427: if (system($cmd)) {
reapr-1.0.18+dfsg/src/task_preprocess.pl-428- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/src/task_perfectfrombam.pl-205- my $cmd = shift;
reapr-1.0.18+dfsg/src/task_perfectfrombam.pl:206: if (system($cmd)) {
reapr-1.0.18+dfsg/src/task_perfectfrombam.pl-207- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/src/task_perfectmap.pl-138- my $cmd = shift;
reapr-1.0.18+dfsg/src/task_perfectmap.pl:139: if (system($cmd)) {
reapr-1.0.18+dfsg/src/task_perfectmap.pl-140- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/src/task_plots.pl-125- my $cmd = shift;
reapr-1.0.18+dfsg/src/task_plots.pl:126: if (system($cmd)) {
reapr-1.0.18+dfsg/src/task_plots.pl-127- print STDERR "Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/src/task_pipeline.pl-98- $commands{fcdrate} = "$reapr fcdrate " . hash_to_ops($options{fcdrate}) . " ./ $stats_prefix $fcdrate_prefix\n"
reapr-1.0.18+dfsg/src/task_pipeline.pl:99: . "fcdcutoff=`tail -n 1 $fcdrate_prefix.info.txt | cut -f 1`";
reapr-1.0.18+dfsg/src/task_pipeline.pl-100-}
##############################################
reapr-1.0.18+dfsg/src/task_smaltmap.pl-101-my $cmd = "$reapr facheck $assembly";
reapr-1.0.18+dfsg/src/task_smaltmap.pl:102:if (system($cmd)) {
reapr-1.0.18+dfsg/src/task_smaltmap.pl-103- print STDERR "
##############################################
reapr-1.0.18+dfsg/src/task_smaltmap.pl-118- my $cmd = "$samtools faidx $assembly";
reapr-1.0.18+dfsg/src/task_smaltmap.pl:119: if (system($cmd)) {
reapr-1.0.18+dfsg/src/task_smaltmap.pl-120- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n\n";
##############################################
reapr-1.0.18+dfsg/src/task_smaltmap.pl-183- print "$ERROR_PREFIX Running: $cmd\n";
reapr-1.0.18+dfsg/src/task_smaltmap.pl:184: if (system($cmd)) {
reapr-1.0.18+dfsg/src/task_smaltmap.pl-185- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_preprocess.pl-426- my $cmd = shift;
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_preprocess.pl:427: if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_preprocess.pl-428- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_perfectfrombam.pl-205- my $cmd = shift;
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_perfectfrombam.pl:206: if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_perfectfrombam.pl-207- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_perfectmap.pl-138- my $cmd = shift;
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_perfectmap.pl:139: if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_perfectmap.pl-140- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_plots.pl-125- my $cmd = shift;
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_plots.pl:126: if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_plots.pl-127- print STDERR "Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_pipeline.pl-98- $commands{fcdrate} = "$reapr fcdrate " . hash_to_ops($options{fcdrate}) . " ./ $stats_prefix $fcdrate_prefix\n"
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_pipeline.pl:99: . "fcdcutoff=`tail -n 1 $fcdrate_prefix.info.txt | cut -f 1`";
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_pipeline.pl-100-}
##############################################
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl-101-my $cmd = "$reapr facheck $assembly";
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl:102:if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl-103- print STDERR "
##############################################
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl-118- my $cmd = "$samtools faidx $assembly";
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl:119: if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl-120- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n\n";
##############################################
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl-183- print "$ERROR_PREFIX Running: $cmd\n";
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl:184: if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/use_shared_libs/src/task_smaltmap.pl-185- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";
##############################################
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl-101-my $cmd = "$reapr facheck $assembly";
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl:102:if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl-103- print STDERR "
##############################################
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl-118- my $cmd = "$samtools faidx $assembly";
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl:119: if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl-120- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n\n";
##############################################
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl-183- print "$ERROR_PREFIX Running: $cmd\n";
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl:184: if (system($cmd)) {
reapr-1.0.18+dfsg/.pc/fix_sort_samtools13/src/task_smaltmap.pl-185- print STDERR "$ERROR_PREFIX Error in system call:\n$cmd\n";