reverted code for format_genome in order to make vmatch_seq work correctly

git-svn-id: http://biopieces.googlecode.com/svn/trunk@200 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/Match.pm b/code_perl/Maasha/Match.pm
index b4050a8fa971105e236b2b1bc690eaa02a1f12f3..c74d7195b8446c015749432f4ac03d92a4d12167 100644 (file)
--- a/code_perl/Maasha/Match.pm
+++ b/code_perl/Maasha/Match.pm
@@ -328,12 +328,12 @@ sub vmatch_index
 
     Maasha::Common::dir_create_if_not_exists( $dst_dir );
 
-    if ( Maasha::Common::file_size( $file ) < 200_000_000 )
-    {
-        &Maasha::Common::run( "mkvtree", "-db $src_dir/$file -dna -pl -allout -indexname $dst_dir/$file > /dev/null 3>&1" );
-    }
-    else
-    {
+#    if ( Maasha::Common::file_size( $file ) < 200_000_000 )
+#    {
+#        &Maasha::Common::run( "mkvtree", "-db $src_dir/$file -dna -pl -allout -indexname $dst_dir/$file > /dev/null 3>&1" );
+#    }
+#    else
+#    {
         $fh = Maasha::Common::read_open( "$src_dir/$file" );
 
         while ( $entry = Maasha::Fasta::get_entry( $fh ) )
@@ -345,7 +345,7 @@ sub vmatch_index
             &Maasha::Common::run( "mkvtree", "-db $tmp_dir/$tmp_file -dna -pl -allout -indexname $dst_dir/$tmp_file > /dev/null 3>&1" );
 
             unlink "$tmp_dir/$tmp_file";
-        }
+#        }
 
         close $fh;
     }