Handle input BED files for conversion to interval lists

hyphaltip · Nov 1, 2010 · d33dffb · d33dffb
1 parent 3dc7d9f
commit d33dffb
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/nextgen/scripts/utils/sort_gatk_intervals.py b/nextgen/scripts/utils/sort_gatk_intervals.py
@@ -39,7 +39,10 @@ def read_intervals(in_handle):
         if len(parts) == 1:
             chr_name, loc = parts[0].split(":")
             start, end = loc.split("-")
-            yield [chr_name, start, end, "+", "interval_%s" % i]
+            yield (chr_name, start, end, "+", "interval_%s" % i)
+        elif len(parts) == 6:
+            chr_name, start, end, strand, name, _ = parts
+            yield (chr_name, start, end, strand, name)
         elif len(parts) == 5:
             yield parts
         else: