From 55af15f853a3ad594e0b45dea0f8b4dce210722d Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Mon, 12 Jan 2004 16:44:49 +0000
Subject: [PATCH] avoid a couple of warnings
---
modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm
index 6fb9690ecc..4f75755998 100644
--- a/modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm
@@ -123,7 +123,7 @@ sub store {
$sequence = uc($sequence);
- my $bvector;
+ my $bvector = '';
#convert sequence to 0s,1s,2s and 3s
$sequence =~ tr/ACTG/0123/;
@@ -136,10 +136,11 @@ sub store {
my $len = length($sequence);
for(my $i=0; $i < $len; $i++) {
- #pack the
my $char = substr($sequence,$i,1);
- if(($char+0) eq $char) { #fast way to check if an int
+ #quickly check if this character was an A,C,T or G (and was converted to
+ # a 0,1,2,3)
+ if($char =~ /[0-3]/) {
vec($bvector, $i,2) = $char;
if($nline_char) {
#end of an nline
@@ -167,6 +168,7 @@ sub store {
$nline_len = 1;
$nline_off = $i+1;
}
+ $char = 0; #need to put numeric val into bitvector despite nline
}
vec($bvector, $i,2) = $char;
--
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