INNER CODE UNIT · Python

run_fragments

timoast/sinto · sinto/cli.py:46

def run_fragments(options):
    """Wraps the sinto.fragments function for use on the command line
    """
    fragments.fragments(
        bam=options.bam,
        fragment_path=options.fragments,
        min_mapq=options.min_mapq,
        nproc=options.nproc,
        cellbarcode=options.barcodetag,
        readname_barcode=options.barcode_regex,
        chromosomes=options.use_chrom,
        cells=options.cells,
        max_distance=options.max_distance,
        min_distance=options.min_distance,
        chunksize=options.chunksize,
        shifts=[options.shift_plus, options.shift_minus],
        collapse_within=options.collapse_within
    )

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