From b83e50334f76d2a509bc5cb223b17604abf8f908 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 5 Dec 2008 06:02:53 +0000
Subject: [PATCH] fixed CHR_BEG=0 bug

git-svn-id: http://biopieces.googlecode.com/svn/trunk@335 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/UCSC/BED.pm | 20 ++++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/code_perl/Maasha/UCSC/BED.pm b/code_perl/Maasha/UCSC/BED.pm
index c95c930..9d48daa 100644
--- a/code_perl/Maasha/UCSC/BED.pm
+++ b/code_perl/Maasha/UCSC/BED.pm
@@ -480,13 +480,21 @@ sub biopiece2bed
                                $bp_record->{ "S_ID" }    ||
                                return undef;
 
-    $bed_entry[ chromStart ] = $bp_record->{ "CHR_BEG" } || 
-                               $bp_record->{ "S_BEG" }   ||
-                               return undef;
+    if ( defined $bp_record->{ "CHR_BEG" } ) {
+        $bed_entry[ chromStart ] = $bp_record->{ "CHR_BEG" };
+    } elsif ( defined $bp_record->{ "S_BEG" } ) {
+        $bed_entry[ chromStart ] = $bp_record->{ "S_BEG" };
+    } else {
+        return undef;
+    }
 
-    $bed_entry[ chromEnd ]   = $bp_record->{ "CHR_END" } || 
-                               $bp_record->{ "S_END" }   ||
-                               return undef;
+    if ( defined $bp_record->{ "CHR_END" } ) {
+        $bed_entry[ chromEnd ] = $bp_record->{ "CHR_END" };
+    } elsif ( defined $bp_record->{ "S_END" }) {
+        $bed_entry[ chromEnd ] = $bp_record->{ "S_END" };
+    } else {
+        return undef;
+    }
 
     $bed_entry[ chromEnd ]++;
 
-- 
2.39.5