sam_utils.py 文件源码

def load_samfile(sam_file):
    """To load an indexed bam file"""
    ftype = sam_file.split(".")[-1]
    if ftype != "bam" and ftype != "sam":
        print("Error: file type need suffix of bam or sam.")
        sys.exit(1)
    # print("Loading a %s" %ftype + " with file name: %s" %sam_file)
    if ftype == "bam":
        samfile = pysam.Samfile(sam_file, "rb")
    else:
        samfile = pysam.Samfile(sam_file, "r")
    return samfile