From bf79ce0b0e0458a64e922b5f9cd2583f4aa76239 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 5 May 2016 14:18:09 +0100
Subject: [PATCH] test some coordinate shifting
---
modules/Bio/EnsEMBL/TranscriptMapper.pm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/TranscriptMapper.pm b/modules/Bio/EnsEMBL/TranscriptMapper.pm
index a9a6f9e59f..78576a033f 100644
--- a/modules/Bio/EnsEMBL/TranscriptMapper.pm
+++ b/modules/Bio/EnsEMBL/TranscriptMapper.pm
@@ -157,8 +157,8 @@ sub _load_mapper {
foreach my $ex (@{$transcript->get_all_Exons}) {
- my $gen_start = $ex->start();
- my $gen_end = $ex->end();
+ my $gen_start = $ex->seq_region_start();
+ my $gen_end = $ex->seq_region_end();
$cdna_start = $cdna_end + 1;
$cdna_end = $cdna_start + $ex->length() - 1;
--
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