From 90e11c8eccedc5c82aff9d6b4cfdf454d6da9c10 Mon Sep 17 00:00:00 2001
From: premanand17 <prem.apa@gmail.com>
Date: Thu, 29 Sep 2016 11:26:48 +0100
Subject: [PATCH] Changes to include input coordinates in map out -
ENSCORESW-1481 - Further formatting updates
---
modules/Bio/EnsEMBL/Mapper.pm | 6 +++---
modules/Bio/EnsEMBL/TranscriptMapper.pm | 4 ++--
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Mapper.pm b/modules/Bio/EnsEMBL/Mapper.pm
index 3f6cf6b1b2..64fb5603c2 100644
--- a/modules/Bio/EnsEMBL/Mapper.pm
+++ b/modules/Bio/EnsEMBL/Mapper.pm
@@ -357,10 +357,10 @@ sub map_coordinates {
# new mapping Coordinate, the IndelCoordinate.
$target_start = $target_coord->{'start'};
$target_end = $target_coord->{'end'};
-
+
#original coordinates
- $ori_start = $self_coord->{'start'};
- $ori_end = $self_coord->{'end'};
+ $ori_start = $self_coord->{'start'};
+ $ori_end = $self_coord->{'end'};
#create a Gap object
my $gap = Bio::EnsEMBL::Mapper::Gap->new( $start,
diff --git a/modules/Bio/EnsEMBL/TranscriptMapper.pm b/modules/Bio/EnsEMBL/TranscriptMapper.pm
index 1538574680..3def4ab834 100644
--- a/modules/Bio/EnsEMBL/TranscriptMapper.pm
+++ b/modules/Bio/EnsEMBL/TranscriptMapper.pm
@@ -248,7 +248,7 @@ sub _load_mapper {
sub cdna2genomic {
- my ($self,$start,$end, $include_original_region, $cdna_coding_start) = @_;
+ my ($self, $start, $end, $include_original_region, $cdna_coding_start) = @_;
if( !defined $end ) {
throw("Must call with start/end");
@@ -257,7 +257,7 @@ sub cdna2genomic {
$cdna_coding_start = defined $cdna_coding_start ? $cdna_coding_start : 1;
my $mapper = $self->{'exon_coord_mapper'};
- return $mapper->map_coordinates( 'cdna', $start, $end, 1, "cdna", $include_original_region, $cdna_coding_start);
+ return $mapper->map_coordinates('cdna', $start, $end, 1, "cdna", $include_original_region, $cdna_coding_start);
}
--
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