From b923598cfcfdcf89d307087e1cbd21ae115f5645 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 20 Jan 2011 09:33:41 +0000
Subject: [PATCH] slight cleanup of find_gaps

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1210 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/find_gaps | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/bp_bin/find_gaps b/bp_bin/find_gaps
index 300ae09..ade831a 100755
--- a/bp_bin/find_gaps
+++ b/bp_bin/find_gaps
@@ -83,11 +83,13 @@ sub find_gaps
 
     # Returns a list.
 
-    my ( @gaps, $block, $beg, $end );
+    my ( $gap_char, @gaps, $block, $beg, $end );
+
+    $gap_char = 'N';
 
     $seq = uc $seq;
 
-    $block = 'N' x $min;
+    $block = $gap_char x $min;
 
     $beg = 0;
 
@@ -99,7 +101,7 @@ sub find_gaps
 
         $end = $beg;
 
-        while ( substr( $seq, $end, 1 ) eq 'N' ) {
+        while ( substr( $seq, $end, 1 ) eq $gap_char ) {
             $end++;
         }
 
-- 
2.39.2