Fix for revcom issues with MAF format from @dandaman, fixes #147"

bioperl · Sep 13, 2016 · 611e1c5 · 611e1c5
1 parent a16f466
commit 611e1c5
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/Bio/AlignIO/maf.pm b/Bio/AlignIO/maf.pm
@@ -172,8 +172,8 @@ sub next_aln {
     $strand = $strand eq '+' ? 1 : $strand eq '-' ? -1 : 0;
 	my $seq = Bio::LocatableSeq->new('-seq'          => $text,
 					 '-display_id'   => $src,
-					 '-start'        => $start,
-					 '-end'          => $start + $size - 1,
+					 '-start'        => $strand > 0 ? $start                : ($srcsize-($start+$size-2)),
+					 '-end'          => $strand > 0 ? ($start + $size - 1)  : ($srcsize-($start-1)) ,
 					 '-strand'       => $strand,
 					 '-alphabet'     => $self->alphabet,
 					);