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        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
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       /_____/            \/           \/           
              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
shovill-1.1.0/README.md-241----------|--------|------------
shovill-1.1.0/README.md:242:`$SHOVILL_CPUS` | `--cpus` | 8
shovill-1.1.0/README.md:243:`$SHOVILL_RAM` | `--ram` | 16
shovill-1.1.0/README.md:244:`$SHOVILL_ASSEMBLER` | `--assembler` | `spades`
shovill-1.1.0/README.md:245:`$TMPDIR` | `--tmpdir` | `/tmp`
shovill-1.1.0/README.md-246-
##############################################
shovill-1.1.0/bin/shovill-270-msg("Assembling reads with '$assembler'");
shovill-1.1.0/bin/shovill:271:my $asm = "$assembler.fasta";  # assembler result file to process further
shovill-1.1.0/bin/shovill-272-my $asmdir = $assembler;
##############################################
shovill-1.1.0/bin/shovill-289-    "skesa --gz $opts --fastq $PE1,$PE2 --use_paired_ends"
shovill-1.1.0/bin/shovill:290:   ." --contigs_out $asm --min_contig 1"
shovill-1.1.0/bin/shovill-291-   ." --memory $ram_int --cores $cpus"
##############################################
shovill-1.1.0/bin/shovill-321-# Check for zero output or failed assembly
shovill-1.1.0/bin/shovill:322:err("Assembly failed - $asm has zero contigs!") unless -s $asm;
shovill-1.1.0/bin/shovill-323-
##############################################
shovill-1.1.0/bin/shovill-327-unless ($nocorr) {
shovill-1.1.0/bin/shovill:328:  -r $asm or err("Can not see '$asm' file to correct!");
shovill-1.1.0/bin/shovill-329-  msg("Checking for assembly errors in $asm");
##############################################
shovill-1.1.0/bin/shovill-333-  my $sort_ram = int($half_ram * 1024 / $sort_cpus); # RAM per thread, in Mb
shovill-1.1.0/bin/shovill:334:  run_cmd("(bwa mem -v 3 -x intractg -t $cpus $asm R1.fq.gz R2.fq.gz"
shovill-1.1.0/bin/shovill-335-         ." | samclip --ref ${asm}.fai"
shovill-1.1.0/bin/shovill-336-         ." | samtools sort --threads $sort_cpus -m ${sort_ram}m"
shovill-1.1.0/bin/shovill:337:         ." --reference $asm -T $tmpdir -o $BAM)", "bwa+samtools-sort");
shovill-1.1.0/bin/shovill-338-  run_cmd("samtools index $BAM", "samtools-index");
##############################################
shovill-1.1.0/bin/shovill-340-  msg("Correcting errors in $asm");
shovill-1.1.0/bin/shovill:341:  run_cmd("pilon --genome $asm --frags $BAM --minmq $MIN_MQ --minqual $MIN_BQ"
shovill-1.1.0/bin/shovill-342-         ." --fix bases --output pilon --threads $cpus --changes --mindepth 0.25", "pilon");
##############################################
shovill-1.1.0/bin/shovill-504-  }
shovill-1.1.0/bin/shovill:505:  msg("Repaired", scalar(keys %$diff), "contigs from $asm at $total positions.");
shovill-1.1.0/bin/shovill-506-  return $diff;
##############################################
shovill-1.1.0/bin/shovill-566-  msg("Running: $cmd");
shovill-1.1.0/bin/shovill:567:  system($cmd)==0 or err("Error $? running command: $!");
shovill-1.1.0/bin/shovill-568-}
##############################################
shovill-1.1.0/debian/createmanpages-4-
shovill-1.1.0/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
shovill-1.1.0/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
##############################################
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-270-msg("Assembling reads with '$assembler'");
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:271:my $asm = "$assembler.fasta";  # assembler result file to process further
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-272-my $asmdir = $assembler;
##############################################
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-289-    "skesa --gz $opts --fastq $PE1,$PE2 --use_paired_ends"
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:290:   ." --contigs_out $asm --min_contig 1"
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-291-   ." --memory $ram_int --cores $cpus"
##############################################
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-321-# Check for zero output or failed assembly
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:322:err("Assembly failed - $asm has zero contigs!") unless -s $asm;
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-323-
##############################################
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-327-unless ($nocorr) {
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:328:  -r $asm or err("Can not see '$asm' file to correct!");
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-329-  msg("Checking for assembly errors in $asm");
##############################################
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-333-  my $sort_ram = int($half_ram * 1024 / $sort_cpus); # RAM per thread, in Mb
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:334:  run_cmd("(bwa mem -v 3 -x intractg -t $cpus $asm R1.fq.gz R2.fq.gz"
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-335-         ." | samclip --ref ${asm}.fai"
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-336-         ." | samtools sort --threads $sort_cpus -m ${sort_ram}m"
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:337:         ." --reference $asm -T $tmpdir -o $BAM)", "bwa+samtools-sort");
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-338-  run_cmd("samtools index $BAM", "samtools-index");
##############################################
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-340-  msg("Correcting errors in $asm");
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:341:  run_cmd("pilon --genome $asm --frags $BAM --minmq $MIN_MQ --minqual $MIN_BQ"
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-342-         ." --fix bases --output pilon --threads $cpus --changes --mindepth 0.25", "pilon");
##############################################
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-504-  }
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:505:  msg("Repaired", scalar(keys %$diff), "contigs from $asm at $total positions.");
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-506-  return $diff;
##############################################
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-566-  msg("Running: $cmd");
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill:567:  system($cmd)==0 or err("Error $? running command: $!");
shovill-1.1.0/.pc/fix-shebang.patch/bin/shovill-568-}