From a9520cc62627ff6b156245f3e8322e85346aa804 Mon Sep 17 00:00:00 2001
From: Jeremy Goecks <jeremy.goecks@emory.edu>
Date: Mon, 25 Oct 2010 13:26:06 -0400
Subject: [PATCH] When converting from GFF to BED, make all BED features with
 thick blocks.

---
 tools/filters/gff_to_bed_converter.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/tools/filters/gff_to_bed_converter.py b/tools/filters/gff_to_bed_converter.py
index 98e9e01a994..3c262aa76e9 100644
--- a/tools/filters/gff_to_bed_converter.py
+++ b/tools/filters/gff_to_bed_converter.py
@@ -41,8 +41,12 @@ def get_bed_line( chrom, name, strand, blocks ):
     # Bed format: chrom, chromStart, chromEnd, name, score, strand, \
     #               thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts
     #
+    # Render complete feature with thick blocks. There's no clear way to do this unless
+    # we analyze the block names, but making everything thick makes more sense than
+    # making everything thin.
+    #
     return "%s\t%i\t%i\t%s\t0\t%s\t%i\t%i\t0\t%i\t%s\t%s\n" % \
-            ( chrom, t_start, t_end, name, strand, t_start, t_start, len( block_starts ), 
+            ( chrom, t_start, t_end, name, strand, t_start, t_end, len( block_starts ), 
                 ",".join( block_sizes ), ",".join( block_starts ) )
 
 def __main__():