INNER CODE UNIT · Python

getBasename

nf-core/eager · bin/filter_bam_fragment_length.py:47

def getBasename(file_name):
    if ("/") in file_name:
        basename = file_name.split("/")[-1].split(".")[0]
    else:
        basename = file_name.split(".")[0]
    return basename


def filter_bam(infile, outfile, fraglen, allreads):
    """Write bam to file

    Args:
        infile (stream): pysam stream
        outfile (str): Path to output bam
        fraglen(int): Minimum fragment length to keep
        allreads(bool): Apply on all reads, not only mapped
    """
    bamfile = pysam.AlignmentFile(infile, "rb")

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