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Merge branch 'devel' of https://github.com/wtsi-npg/npg_qc into maste…
…r to create release 69.8.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -50,10 +50,10 @@ sub find_or_save_composition { | |
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| sub write_samtools_script { | ||
| my ($script_path, $b1) = @_; | ||
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| open my $fh, '>', $script_path or croak "Cannot open $script_path for writing"; | ||
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| print $fh '#!/usr/local/bin/bash'; | ||
| print $fh '#!/usr/bin/env bash'; | ||
| print $fh "\n"; | ||
| print $fh '# Script to fake samtools in testing. Automatically generated by npg at ' . time; | ||
| print $fh "\n"; | ||
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@@ -65,34 +65,31 @@ sub write_samtools_script { | |
| } | ||
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| close $fh or carp "Cannot close $script_path"; | ||
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| chmod 0775, $script_path; | ||
| return 1; | ||
| } | ||
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| sub write_fastx_script { | ||
| sub write_seqtk_script { | ||
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| my ($script_path, $b1) = @_; | ||
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| my $fh; | ||
| open($fh, '>', $script_path) or croak "Cannot open $script_path for writing"; | ||
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| print $fh '#!/usr/local/bin/bash'; | ||
| print $fh "\n"; | ||
| print $fh '# Script to fake fastx in testing. Automatically generated by npg at ' . time; | ||
| print $fh '# Script to fake seqtk in testing. Automatically generated by npg at ' . time; | ||
| print $fh "\n"; | ||
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| # echo the first argument $1; | ||
| # echo number of arguments: $#; | ||
| if (!defined $b1) { | ||
| my $out = q[usage: fastx_reverse_complement [-h] [-r] [-z] [-v] [-i INFILE] [-o OUTFILE] | ||
| Part of FASTX Toolkit 0.0.12 by A. Gordon ([email protected]) | ||
| [-h] = This helpful help screen. | ||
| [-z] = Compress output with GZIP. | ||
| [-i INFILE] = FASTA/Q input file. default is STDIN. | ||
| [-o OUTFILE] = FASTA/Q output file. default is STDOUT. | ||
| my $out = q[ | ||
| Usage: seqtk <command> <arguments> | ||
| Version: 1.3 | ||
| Command: seq common transformation of FASTA/Q | ||
| ]; | ||
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| print $fh "echo '$out'"; | ||
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@@ -107,7 +104,7 @@ Part of FASTX Toolkit 0.0.12 by A. Gordon ([email protected]) | |
| sub write_bwa_script { | ||
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| my ($script_path, $s1, $bwa_version) = @_; | ||
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| my $fh; | ||
| open($fh, '>', $script_path) or croak "Cannot open $script_path for writing"; | ||
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@@ -133,7 +130,7 @@ sub write_bwa_script { | |
| } | ||
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| close $fh; | ||
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| chmod 0775, $script_path; | ||
| return 1; | ||
| } | ||
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