[Bioperl-guts-l] [14839] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Fixed bug: not using gapped length to calculate LocatableSeq-> end in _overlap_alignment.

[Florent E Angly]

Revision: 14839
Author:   fangly
Date:     2008-08-29 10:58:09 -0400 (Fri, 29 Aug 2008)

Log Message:
-----------
Fixed bug: not using gapped length to calculate LocatableSeq->end in _overlap_alignment. Letting the default behavior use ungapped length instead

Modified Paths:
--------------
    bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm

Modified: bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm
===================================================================
--- bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm	2008-08-29 14:49:32 UTC (rev 14838)
+++ bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm	2008-08-29 14:58:09 UTC (rev 14839)
@@ -1521,7 +1521,6 @@
         -id       => 1,
         -seq      => $qstring,
         -start    => 1,
-        -end      => $overlap,
         -alphabet => 'dna'
   );
   $aln->add_seq($qalseq);
@@ -1529,7 +1528,6 @@
         -id       => 2,
         -seq      => $tstring,
         -start    => 1,
-        -end      => $overlap,
         -alphabet => 'dna'
   );
   $aln->add_seq($talseq);