Mercurial > repos > romaingred > pirna_pipeline

comparison bin/align.pm @ 24:08bbde9d0c9d draft

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Uploaded
author romaingred
date Mon, 23 Oct 2017 08:16:22 -0400
parents 39b039d82743
children bd4b30bff219
comparison
equal deleted inserted replaced
23:7dd78ad2875f 24:08bbde9d0c9d
13 our @ISA = qw( Exporter ); 13 our @ISA = qw( Exporter );
14 our @EXPORT = qw( &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam ); 14 our @EXPORT = qw( &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam );
15 15
16 sub to_build 16 sub to_build
17 { 17 {
18 my $toBuildHashP = shift; my $log = shift; 18 my ( $toBuildTabP, $log, $newdir ) = @_;
19 19
20 while ( my ( $k, $v ) = each %{ $toBuildHashP } ) 20 foreach my $pairs ( @{ $toBuildTabP } )
21 { 21 {
22 build_index ( $k, $log ) if $v == 1; 22 if ( $pairs->[0] == 1 )
23 } 23 {
24 my $sym = $newdir.basename(${$pairs->[1]}).'_symlink.fa';
25 symlink( ${$pairs->[1]}, $sym );
26 ${$pairs->[1]} = $sym;
27 build_index ( ${$pairs->[1]}, $log );
28 }
29 }
24 } 30 }
25 31
26 sub build_index 32 sub build_index
27 { 33 {
28 my $to_index = shift; 34 my $to_index = shift;