From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 11 Nov 2008 04:24:45 +0000 (+0000)
Subject: swapped bedSort with bed_sort
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=723277f72af951aa96053167dd7378a83d0f2350;p=biopieces.git

swapped bedSort with bed_sort

git-svn-id: http://biopieces.googlecode.com/svn/trunk@301 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index 0af3b64..8fdc6a4 100644
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -2753,7 +2753,10 @@ sub script_calc_fixedstep
 
     foreach $chr ( sort keys %fh_hash )
     {
-        Maasha::Common::run( "bedSort", "$BP_TMP/$chr $BP_TMP/$chr" );
+        #Maasha::Common::run( "bedSort", "$BP_TMP/$chr $BP_TMP/$chr" );
+        Maasha::Common::run( "bed_sort", "--sort 3 --cols 5 $BP_TMP/$chr > $BP_TMP/$chr.sort" );
+
+        rename "$BP_TMP/$chr.sort", "$BP_TMP/$chr";
 
         $fh_in = Maasha::Common::read_open( "$BP_TMP/$chr" );