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Modified pysam import to class attribute #418

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Modified pysam import to class attribute #418

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5 changes: 3 additions & 2 deletions checkm/coverage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@ def __init__(self, threads):
# pysam can be a challenge to install and most users
# will not use this functionality so importing pysam here
import pysam
self.pysam = pysam

self.logger = logging.getLogger('timestamp')
self.totalThreads = threads
Expand Down Expand Up @@ -128,7 +129,7 @@ def _processBam(self, bamFile, bAllReads, minAlignPer, maxEditDistPer, minQC, co
workerQueue = mp.Queue()
writerQueue = mp.Queue()

bamfile = pysam.Samfile(bamFile, 'rb')
bamfile = self.pysam.Samfile(bamFile, 'rb')
refSeqIds = bamfile.references
refSeqLens = bamfile.lengths

Expand Down Expand Up @@ -190,7 +191,7 @@ def __workerThread(self, bamFile, bAllReads, minAlignPer, maxEditDistPer, minQC,
if seqIds == None:
break

bamfile = pysam.Samfile(bamFile, 'rb')
bamfile = self.pysam.Samfile(bamFile, 'rb')

for seqId, seqLen in zip(seqIds, seqLens):
numReads = 0
Expand Down