[glu-genetics] push by bioinformed@gmail.com - Send loci with equal SNP alleles back as A,B -- that is the best we ca... on 2012-10-31 22:52 GMT

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

Revision: e96ee1da3128
Branch: default
Author: Kevin B. Jacobs <jac...@bioinformed.com>
Date: Wed Oct 31 15:52:00 2012
Log: Send loci with equal SNP alleles back as A,B -- that is the best
we can do.
http://code.google.com/p/glu-genetics/source/detail?r=e96ee1da3128

Modified:
/glu/lib/illumina.py

=======================================
--- /glu/lib/illumina.py Mon Aug 13 11:23:11 2012
+++ /glu/lib/illumina.py Wed Oct 31 15:52:00 2012
@@ -394,7 +394,7 @@
validstrand = set(('top','bot','p','plus','m','minus'))
plusminus = set(('p','plus','m','minus'))

- assert targetstrand in ('ab','top','bottom','forward','reverse', \
+ assert targetstrand in ('ab','top','bottom','forward','reverse',
'real_forward','real_reverse',
'customer','anticustomer','design','antidesign')

@@ -455,7 +455,7 @@
if loc:
loc = int(loc)

- if targetstrand=='ab':
+ if targetstrand=='ab' or a==b:
yield lname,chrom,loc,STRAND_UNKNOWN,AB
continue