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yhoogstrate / flaimapper

:honeybee: Fragment Location Annotation Identification Mapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data
GNU General Public License v3.0
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Pysam has a parallelization bug #17

Closed yhoogstrate closed 7 years ago

yhoogstrate commented 7 years ago 
alignment = pysam.alignment_file(...,'rb')
for region in alignment.fetch(chr):
    for read in alignment.fetch(region[0],region[1],region[2])
         ....

this goes wrong if the results of the first loop are yielded and exceed a certain size (probably chunk limit of pysam)

Both 0.8.2 and most recent 0.9 are affected