Mercurial > repos > romaingred > pirna_pipeline

comparison bin/align.pm @ 44:bd4b30bff219 draft

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Uploaded
author romaingred
date Fri, 01 Dec 2017 08:02:00 -0500
parents 08bbde9d0c9d
children a03408665904
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43:0be8011b3d98 44:bd4b30bff219
38 print $log "Creating index for $to_index\n"; 38 print $log "Creating index for $to_index\n";
39 } 39 }
40 40
41 sub get_unique 41 sub get_unique
42 { 42 {
43 my ( $sam, $s_uni, $prefix, $details, $report ) = @_; 43 my ( $sam, $s_uni, $out_prefix, $col_prefix, $details, $report ) = @_;
44 44
45 my $fout = $prefix.'all.fastq'; 45 my $fout = $col_prefix.'all_mappers.fastq';
46 my $funi = $prefix.'unique.fastq'; 46 my $funi = $col_prefix.'unique_mappers.fastq';
47 my $frej = $prefix.'rejected.fastq'; 47 my $frej = $col_prefix.'unmapped.fastq';
48 48
49 my $repartition = $prefix.'distribution.txt'; 49 my $repartition = $prefix.'distribution.txt';
50 my $png_rep = $prefix.'distribution.png'; 50 my $png_rep = $prefix.'distribution.png';
51 my ( %duplicates, %genome_hits) ; 51 my ( %duplicates, %genome_hits) ;
52 52