bug fix for read duplication with nproc > 1#80
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…ndaries when running sinto with --nproc > 1
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Fixes #76.
The issue described by #76 was also present in my data, causing downstream
bamtofastqto error on my sinto-filtered bams.The bug happens when nproc > 1 and seems to be caused by
pysam.fetch(chrom, start, end)returning reads overlapping bothstartandendpositions, so reads spanning a chunk boundary are returned by both workers and written twice whennproc> 1.Fix: in
_iterate_reads, skip reads withreference_start < i[1], so that each chunk has a unique set of reads. The>= 0keeps unmapped reads which havereference_start == -1.