fa662d348e088ad1709f554aa5268e7a774a0fe8,cnvlib/coverage.py,,interval_coverages_count,#Any#Any#Any#,62

Before Change

                                    key=lambda r: r[0]):
        // Thunk and reshape this chromosome"s intervals
        echo("Processing chromosome", chrom, "of", os.path.basename(bam_fname))
        _chroms, starts, ends, names = zip(*rows_iter)
        counts_depths = [region_depth_count(bamfile, chrom, s, e, min_mapq)
                         for s, e in zip(starts, ends)]
        for start, end, name, (count, depth) in zip(starts, ends, names,

After Change

def interval_coverages_count(bed_fname, bam_fname, min_mapq):
    Calculate log2 coverages in the BAM file at each interval.
    bamfile = pysam.Samfile(bam_fname, "rb")
    for chrom, subregions in RA.read(bed_fname).by_chromosome():
        echo("Processing chromosome", chrom, "of", os.path.basename(bam_fname))
        for _chrom, start, end, name, in subregions.coords(["name"]):
            count, depth = region_depth_count(bamfile, chrom, start, end,

Instances