Add in names.

define_short_transcripts.py

@@ -89,8 +89,11 @@ def tss_center(feature,assembly):
         stop = chromsizes[feature.chrom][1]
     feature.start = start
     feature.stop = stop
+    feature.name = feature[3]
+    feature.score = '0'
+    feature.strand = '.'
     return pybedtools.create_interval_from_list(
-            [feature.chrom, str(feature.start), str(feature.stop)])
+            [feature.chrom, str(feature.start), str(feature.stop), feature.name, feature.score, feature.strand ])
 
 
 def main():