Closed JaneliaSciComp closed 12 years ago
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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
See email:
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