[glu-genetics] 2 new revisions pushed by bioinformed@gmail.com on 2013-06-30 15:25 GMT

[glu-ge...@googlecode.com]

2 new revisions:

Revision: 7cc88d007dfc
Branch: default
Author: Kevin Jacobs <kevin....@invitae.com>
Date: Sun Jun 30 08:23:37 2013
Log: Increase maximum CSV field size
http://code.google.com/p/glu-genetics/source/detail?r=7cc88d007dfc

Revision: 2c0080010835
Branch: default
Author: Kevin Jacobs <kevin....@invitae.com>
Date: Sun Jun 30 08:24:02 2013
Log: Fix alignment filter
http://code.google.com/p/glu-genetics/source/detail?r=2c0080010835

==============================================================================
Revision: 7cc88d007dfc
Branch: default
Author: Kevin Jacobs <kevin....@invitae.com>
Date: Sun Jun 30 08:23:37 2013
Log: Increase maximum CSV field size
http://code.google.com/p/glu-genetics/source/detail?r=7cc88d007dfc

Modified:
/glu/lib/seqlib/bed.py

=======================================
--- /glu/lib/seqlib/bed.py Fri Jul 20 09:59:31 2012
+++ /glu/lib/seqlib/bed.py Sun Jun 30 08:23:37 2013
@@ -47,6 +47,7 @@
if not filename:
return features

+ csv.field_size_limit(1024*1024)
bed = csv.reader(autofile(filename),dialect='excel-tab')

generic_names = ('feature_%06d' % i for i in count(1))

==============================================================================
Revision: 2c0080010835
Branch: default
Author: Kevin Jacobs <kevin....@invitae.com>
Date: Sun Jun 30 08:24:02 2013
Log: Fix alignment filter
http://code.google.com/p/glu-genetics/source/detail?r=2c0080010835

Modified:
/glu/lib/seqlib/filter.py

=======================================
--- /glu/lib/seqlib/filter.py Sun Jun 30 06:46:21 2013
+++ /glu/lib/seqlib/filter.py Sun Jun 30 08:24:02 2013
@@ -119,11 +119,11 @@
positive_flags |= pos
negative_flags |= neg

- if not positive_flags and not negative_flags:
+ if positive_flags or negative_flags or min_mapq:
+ return _filter_alignments(alignments,positive_flags,negative_flags,
min_mapq)
+ else:
return alignments

- return _filter_alignments(alignments,positive_flags,negative_flags)
-

def alignment_filter_options(group):
opts = ', '.join(sorted(SUPPORTED_OPTIONS))