From bb3041164cc86c3ec71419f5f4b43a6eab9ee972 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Sat, 24 Mar 2012 01:41:33 +0000
Subject: [PATCH] Switch to using $subsequence_slice than $self for the start
and end values. If we don't then we will try to retrieve all repeat features
for an entire chromosome.
---
modules/Bio/EnsEMBL/RepeatMaskedSlice.pm | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm b/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
index e75fac1296..445d67d706 100644
--- a/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
+++ b/modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
@@ -263,8 +263,8 @@ sub subseq {
my $seq_region_slice = $self->seq_region_Slice();
# The blocksize can be defined on the top of this module.
- my $block_min = ($self->start()-1) >> $BLOCK_PWR;
- my $block_max = ($self->end()-1) >> $BLOCK_PWR;
+ my $block_min = ($subsequence_slice->start()-1) >> $BLOCK_PWR;
+ my $block_max = ($subsequence_slice->end()-1) >> $BLOCK_PWR;
my $sub_start = ($block_min << $BLOCK_PWR)+1;
my $sub_end = ($block_max+1)<<$BLOCK_PWR;
--
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