INNER CODE UNIT · Python

addtags

timoast/sinto · sinto/addtags.py:40

def addtags(bam, tagfile, output, sam=False, trim_suffix=True, mode="tag", nproc=1):
    """Add tags to reads from individual cells

    Copies BAM entries to a new file, adding a read tag to cells matching an input table

    Parameters
    ----------
    bam : str
        Path to BAM file.
    tagfile : str
        Tab-delimited file containing cell barcode, read tag to be added, tag information
    output : str
        Name for output BAM file.
    sam : bool, optional
        Output SAM format. Default is BAM format.
    trim_suffix: bool, optional
        Remove trailing 2 characters from cell barcode in bam file (sometimes needed to match 10x barcodes).
    nproc : int, optional

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