X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Ffind_gaps;h=ade831ad9c9e1d28060050bec35a850a8cb4572a;hb=658943d07afe151e66c8ddfa0fc1708a48515f9d;hp=b39b22b0dd0570189f75ce1506a7ae8891f87923;hpb=cd6541f8b0c481181ebcf55be5aecf82001744f1;p=biopieces.git

diff --git a/bp_bin/find_gaps b/bp_bin/find_gaps
index b39b22b..ade831a 100755
--- a/bp_bin/find_gaps
+++ b/bp_bin/find_gaps
@@ -47,6 +47,8 @@ $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) )
 {
+    Maasha::Biopieces::put_record( $record, $out );
+
     if ( exists $record->{ 'SEQ' } )
     {
         $gaps = find_gaps( $record->{ 'SEQ' }, $options->{ 'min_len' } );
@@ -58,8 +60,6 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
             Maasha::Biopieces::put_record( $gap, $out ); 
         }
     }
-
-    Maasha::Biopieces::put_record( $record, $out );
 }
 
 Maasha::Biopieces::close_stream( $in );
@@ -83,11 +83,13 @@ sub find_gaps
 
     # Returns a list.
 
-    my ( @gaps, $block, $beg, $end );
+    my ( $gap_char, @gaps, $block, $beg, $end );
+
+    $gap_char = 'N';
 
     $seq = uc $seq;
 
-    $block = 'N' x $min;
+    $block = $gap_char x $min;
 
     $beg = 0;
 
@@ -99,13 +101,14 @@ sub find_gaps
 
         $end = $beg;
 
-        while ( substr( $seq, $end, 1 ) eq 'N' ) {
+        while ( substr( $seq, $end, 1 ) eq $gap_char ) {
             $end++;
         }
 
         push @gaps, {
             S_BEG => $beg,
             S_END => $end - 1,
+            S_LEN => $end - $beg,
         };
 
         $beg = $end + 1;