JaneliaSciComp/msg — Issue #17: Update Code with Tina's changes
Author: JaneliaSciComp
Created: 2011-10-25 13:52:36+00:00
State: open

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Hi David,

FYI, I made a minor change to two scripts (filter-sam.py and extract-ref-alleles.py) to check the XT tag status in cases where the X1 tag is not reported:

Replacing
no_subpoptimal_matches = read.opt('X1') == 0
indels = read.opt('XO') > 0 or read.opt('XG') > 0

with
no_subpoptimal_matches = False
try: no_subpoptimal_matches = read.opt('X1') == 0
except: no_subpoptimal_matches = read.opt('XT')=='U'

Hope this is clear,
Tina