fixed bowtie_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@593 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/bowtie_seq b/bp_bin/bowtie_seq
index 3505771466ccdecd4e0f50d12e290984d63b6bb0..f6de2c5da01cc980fc2ce5e8628d884aeadc4c06 100755 (executable)
--- 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 3f4784a69059a1b3848232c2c34893053b6df62d..6bfa590b364d486f8202ddc454793b24d5fbc21d 100644 (file)
--- 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;
     }