make it possible to include all alignments, not just the ones that match

[htsworkflow.git] / gaworkflow / util / makebed.py

diff --git a/gaworkflow/util/makebed.py b/gaworkflow/util/makebed.py
index d2389ba0441fb2a7154d8c48919106efa59edd32..738b815b270d2d8352d6157a7b5e1948b437e3a3 100755 (executable)
--- a/gaworkflow/util/makebed.py
+++ b/gaworkflow/util/makebed.py
@@ -25,7 +25,9 @@ def make_bed_from_eland_stream(instream, outstream, name, description, chromosom
   for line in instream:
     fields = line.split()
     # we need more than the CHR field, and it needs to match a chromosome
-    if len(fields) <= CHR or fields[CHR][:3] != chromosome_prefix:
+    if len(fields) <= CHR or \
+          (chromosome_prefix is not None and \
+             fields[CHR][:3] != chromosome_prefix):
       continue
     start = fields[START]
     stop = int(start) + len(fields[SEQ])