From: Diane Trout <diane@caltech.edu>
Date: Sat, 10 May 2008 04:32:25 +0000 (+0000)
Subject: make it possible to include all alignments, not just the ones that match
X-Git-Tag: stanford.caltech-merged-database-2009-jan-15~66
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=8ebc08c518d47bdbab9c89b073fe66bc8a0b1f91

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

diff --git a/gaworkflow/util/makebed.py b/gaworkflow/util/makebed.py
index d2389ba..738b815 100755
--- 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])