From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 23 Jul 2009 14:07:04 +0000 (+0000)
Subject: fixed bowtie_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=e57006bd2608afd866968efbe1898a3153bbc49a;p=biopieces.git

fixed bowtie_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@588 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index f7229f1..3505771 100755
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -92,6 +92,7 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
 close $fh_out;
 
 push @args, "-n $options->{ 'mismatches' }";
+push @args, "-v $options->{ 'mismatches' }";  # DANGER: using seed mismatches as alignment mismatches - may work, may not!
 push @args, "-f" if $type eq "FASTA";
 
 if ( defined $options->{ 'max_hits' } ) {
@@ -151,13 +152,14 @@ sub bowtie2biopiece
 
     my ( $record, @scores );
 
-    $record->{ 'Q_ID' }     = $entry->[ 0 ];
-    $record->{ 'STRAND' }   = $entry->[ 1 ];
-    $record->{ 'S_ID' }     = $entry->[ 2 ];
-    $record->{ 'S_BEG' }    = $entry->[ 3 ];
-    $record->{ 'SEQ' }      = $entry->[ 4 ];
-    $record->{ 'SCORES' }   = $entry->[ 5 ];
-    $record->{ 'MISMATCH' } = $entry->[ 6 ];
+    $record->{ 'Q_ID' }       = $entry->[ 0 ];
+    $record->{ 'STRAND' }     = $entry->[ 1 ];
+    $record->{ 'S_ID' }       = $entry->[ 2 ];
+    $record->{ 'S_BEG' }      = $entry->[ 3 ];
+    $record->{ 'SEQ' }        = $entry->[ 4 ];
+    $record->{ 'SCORES' }     = $entry->[ 5 ];
+    $record->{ 'MAP_COUNT' }  = $entry->[ 6 ];
+    $record->{ 'DESCRIPTOR' } = $entry->[ 7 ];
 
     $record->{ 'SEQ_LEN' }    = length $entry->[ 4 ];
     $record->{ 'S_END' }      = $record->{ 'S_BEG' } + $record->{ 'SEQ_LEN' } - 1;