Mercurial > repos > romaingred > pirna_pipeline

comparison bin/piPipe.pl @ 47:851c8bbb3214 draft

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Uploaded
author romaingred
date Fri, 01 Dec 2017 08:48:57 -0500
parents 0be8011b3d98
children 71ac58e0d5be
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46:a03408665904 47:851c8bbb3214
117 mkdir $size_dir; 117 mkdir $size_dir;
118 118
119 my $fastq_resized = $dir_fq.$name.'_'.$min.'-'.$max.'.fastq'; 119 my $fastq_resized = $dir_fq.$name.'_'.$min.'-'.$max.'.fastq';
120 size_distribution ( $fastq[$child], $fastq_resized, $size_dir, $min, $max ); 120 size_distribution ( $fastq[$child], $fastq_resized, $size_dir, $min, $max );
121 121
122 my $sam_genome = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'_'.$ref_name.'.sam'; 122 my $sam_genome = $gen_dir.$fastq_n[$child].'_'.$min.'-'.max.'sam';
123 my $sam_genome_unique = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'_'.$ref_name.'_unique.sam'; 123 my $sam_genome_unique = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'_unique.sam';
124 my $fastq_prefix = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max; 124 my $fastq_prefix = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max;
125 125
126 BWA_call ( $ref, $fastq_resized, $sam_genome, $mis, $proc_child, $report ); 126 BWA_call ( $ref, $fastq_resized, $sam_genome, $mis, $proc_child, $report );
127 my ( $fai_ref_hashP, $ma, $ma_uni ) = get_unique ( $sam_genome, $sam_genome_unique, $gen_dir, $fq_collection.$fastq_n[$child], 1, $report ); 127 my ( $fai_ref_hashP, $ma, $ma_uni ) = get_unique ( $sam_genome, $sam_genome_unique, $gen_dir, $fq_collection.$fastq_n[$child], 1, $report );
128 128