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Fix GQ error in 1000 genomes data #3

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ngcrawford opened this issue Jun 19, 2013 · 0 comments
Open

Fix GQ error in 1000 genomes data #3

ngcrawford opened this issue Jun 19, 2013 · 0 comments

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@ngcrawford
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Exception in thread Thread-2:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 504, in run
self.__target(_self.__args, *_self.__kwargs)
File "/usr/lib/python2.7/multiprocessing/pool.py", line 314, in _handle_tasks
for i, task in enumerate(taskseq):
File "/usr/lib/python2.7/multiprocessing/pool.py", line 236, in
self._taskqueue.put((((result._job, i, func, (x,), {})
File "/home/Programs/pypgen-master/doc/src/package/scripts/vcfSNVfstats", line 52, in vcf_iterator
vcf_line = parse_vcf_line(line, empty_vcf_line)
File "/home/Programs/pypgen-master/doc/src/package/pypgen/parser/VCF.py", line 302, in parse_vcf_line
genotype['GQ'] = float(genotype['GQ'])
KeyError: 'GQ'

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