From 793ad13ab64a6778386a638f33a0cd7ba0002a9b Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 17 Dec 2008 23:53:33 +0000
Subject: [PATCH] fixed BED BUG

git-svn-id: http://biopieces.googlecode.com/svn/trunk@357 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/Biopieces.pm |  2 ++
 code_perl/Maasha/UCSC/BED.pm  | 19 +++++++++++++------
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index 4cbf81b..8260d09 100644
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -6700,6 +6700,8 @@ sub clean_tmp
             $sid  = $2;
             $pid  = $3;
 
+            next if $user eq "m.hansen";
+
             if ( $user eq Maasha::Common::get_user() )
             {
                 if ( not Maasha::Common::process_running( $pid ) )
diff --git a/code_perl/Maasha/UCSC/BED.pm b/code_perl/Maasha/UCSC/BED.pm
index b259086..a7a878f 100644
--- a/code_perl/Maasha/UCSC/BED.pm
+++ b/code_perl/Maasha/UCSC/BED.pm
@@ -523,17 +523,24 @@ sub biopiece2bed
          defined $bp_record->{ "THICK_END" } )
     {
         $bed_entry[ thickStart ] = $bp_record->{ "THICK_BEG" };
-        $bed_entry[ thickEnd ]   = $bp_record->{ "THICK_END" };
+        $bed_entry[ thickEnd ]   = $bp_record->{ "THICK_END" } + 1;
     }
-    else
+    elsif ( defined $bp_record->{ "BLOCK_COUNT" } )
     {
         $bed_entry[ thickStart ] = $bed_entry[ chromStart ];
-        $bed_entry[ thickEnd ]   = $bed_entry[ chromEnd ] - 1;
+        $bed_entry[ thickEnd ]   = $bed_entry[ chromEnd ];
     }
 
     return wantarray ? @bed_entry : \@bed_entry if $cols == 8;
 
-    $bed_entry[ itemRgb ] = $bp_record->{ "COLOR" } || 0;
+    if ( defined $bp_record->{ "COLOR" } )
+    {
+        $bed_entry[ itemRgb ] = $bp_record->{ "COLOR" };
+    }
+    elsif ( defined $bp_record->{ "BLOCK_COUNT" } )
+    {
+        $bed_entry[ itemRgb ] = 0;
+    }
 
     return wantarray ? @bed_entry : \@bed_entry if $cols == 9;
 
@@ -547,7 +554,7 @@ sub biopiece2bed
         $bed_entry[ blockCount ]  = $bp_record->{ "BLOCK_COUNT" };
         $bed_entry[ blockSizes ]  = $bp_record->{ "BLOCK_LENS" };
         $bed_entry[ blockStarts ] = join ",", @begs;
-        $bed_entry[ thickEnd ]++;
+        $bed_entry[ thickEnd ];
     }
     elsif ( defined $bp_record->{ "BLOCK_COUNT" } and
          defined $bp_record->{ "BLOCK_LENS" }  and
@@ -556,7 +563,7 @@ sub biopiece2bed
         $bed_entry[ blockCount ]  = $bp_record->{ "BLOCK_COUNT" };
         $bed_entry[ blockSizes ]  = $bp_record->{ "BLOCK_LENS" };
         $bed_entry[ blockStarts ] = $bp_record->{ "Q_BEGS" };
-        $bed_entry[ thickEnd ]++;
+        $bed_entry[ thickEnd ];
     }
 
     return wantarray ? @bed_entry : \@bed_entry;
-- 
2.39.5