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Added functionality to filter BAM regions based on known chromosomes from VCF files and created a new function to read chromosome names from VCF.
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As discussed in #249, computing depth for the BAM regions is non-uniform and, for most scRNA-seq, will bottleneck on the MT chromosome if included. When using known or common variants, one can work around this by only computing depth on chromosomes that are included in the VCF(s). This PR implements that functionality.
In practice with common variants, I see this reduce the
get_bam_regionsstep from over an hour to under 10 mins.