added VMATCH support to get_genome_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@534 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
index 737469d4476aef7e0df6a1a13182d21815785362..c2874e391671d8d8e067e49b1202a5c05a4ef00f 100755 (executable)
--- a/bp_bin/get_genome_seq
+++ b/bp_bin/get_genome_seq
@@ -104,7 +104,6 @@ if ( $options->{ "genome" } )
     }   
 }
 
-
 while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
     if ( $options->{ "genome" } and not $record->{ "SEQ" } )
@@ -123,6 +122,13 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
             $beg = $record->{ "S_BEG" } + $index_beg;
             $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
         }
+        elsif ( $record->{ "REC_TYPE" } eq "VMATCH" and exists $lookup_hash{ $record->{ "S_ID" } } )
+        {
+            ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };
+        
+            $beg = $record->{ "S_BEG" } + $index_beg;
+            $len = $record->{ "S_END" } - $record->{ "S_BEG" } + 1;
+        }
         elsif ( $record->{ "REC_TYPE" } eq "BLAST" and exists $lookup_hash{ $record->{ "S_ID" } } )
         {
             ( $index_beg, $index_len ) = @{ $lookup_hash{ $record->{ "S_ID" } } };