From 873e2f6c35f794b572568b97aca67d2b7476f992 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 23 Jul 2009 19:17:16 +0000
Subject: [PATCH] fixed bowtie_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@593 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/bowtie_seq            | 2 +-
 code_perl/Maasha/UCSC/BED.pm | 2 --
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index 3505771..f6de2c5 100755
--- a/bp_bin/bowtie_seq
+++ b/bp_bin/bowtie_seq
@@ -158,7 +158,7 @@ sub bowtie2biopiece
     $record->{ 'S_BEG' }      = $entry->[ 3 ];
     $record->{ 'SEQ' }        = $entry->[ 4 ];
     $record->{ 'SCORES' }     = $entry->[ 5 ];
-    $record->{ 'MAP_COUNT' }  = $entry->[ 6 ];
+    $record->{ 'SCORE' }      = $entry->[ 6 ] + 1;
     $record->{ 'DESCRIPTOR' } = $entry->[ 7 ];
 
     $record->{ 'SEQ_LEN' }    = length $entry->[ 4 ];
diff --git a/code_perl/Maasha/UCSC/BED.pm b/code_perl/Maasha/UCSC/BED.pm
index 3f4784a..6bfa590 100644
--- a/code_perl/Maasha/UCSC/BED.pm
+++ b/code_perl/Maasha/UCSC/BED.pm
@@ -506,8 +506,6 @@ sub biopiece2bed
 
     if ( exists $bp_record->{ "SCORE" } ) {
         $bed_entry[ score ] = $bp_record->{ "SCORE" };
-    } elsif ( exists $bp_record->{ "SCORE_MEAN" } ) {
-        $bed_entry[ score ] = sprintf( "%.0f", $bp_record->{ "SCORE_MEAN" } );
     } else {
         return wantarray ? @bed_entry : \@bed_entry;
     }
-- 
2.39.2