From cc0a96584e410fc7ebc1c7a41ace31e7b6f20ed4 Mon Sep 17 00:00:00 2001
From: Daniel Rios <dr2@sanger.ac.uk>
Date: Mon, 15 Jan 2007 16:16:02 +0000
Subject: [PATCH] fixed bug when mapping indels
---
modules/Bio/EnsEMBL/Mapper.pm | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index fe652d249f..766710bc06 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -665,7 +665,7 @@ sub map_indel {
$mid_idx = ($start_idx+$end_idx)>>1;
$pair = $lr->[$mid_idx];
$self_coord = $pair->{$from};
- if( $self_coord->{'end'} < $start ) {
+ if( $self_coord->{'end'} <= $start ) {
$start_idx = $mid_idx;
} else {
$end_idx = $mid_idx;
@@ -678,7 +678,13 @@ sub map_indel {
my $target_coord = $pair->{$to};
if (exists $pair->{'indel'}){
- push @indel_coordinates, $target_coord;
+ #need to return unit coordinate
+ my $to =
+ Bio::EnsEMBL::Mapper::Unit->new($target_coord->{'id'},
+ $target_coord->{'start'},
+ $target_coord->{'end'},
+ );
+ push @indel_coordinates, $to;
last;
}
$last_used_pair = $pair;
--
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