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performance problem :using find method of pysam.IndexedReads to get AlignedSegment object #984

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weir12 opened this issue Jan 19, 2021 · 0 comments

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@weir12
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weir12 commented Jan 19, 2021

Hi:
I tried to use pysam to extract the alignment informations(like base-quality,cigar) of specific reads(about a million reads)
Therefore, I have tried to fetch each read(by read_id) of BAM files in a single process environment.
The time consumption is not satisfactory.
Is there a high performance method to extraction alignment information of many reads?

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