INNER CODE UNIT · Python

extract_mapped

nf-core/eager · bin/extract_map_reads.py:63

def extract_mapped(bamfile, merged):
    """Get mapped reads in parallel
    Args:
        threads(int): number of threads to use
        bam(str): path to bamfile
    Returns:
        bamfile(str): path to bam alignment file
        result(set): list of mapped reads name (str)
    """
    if bamfile.endswith(".bam") or bamfile.endswith(".gz"):
        read_mode = "rb"
    else:
        read_mode = "r"
    mapped_reads = set()
    bamfile = pysam.AlignmentFile(bamfile, mode=read_mode)
    for read in bamfile.fetch():
        if read.flag != 4:
            if merged:

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