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Source code for galaxy.datatypes.converters.cram_to_bam

#!/usr/bin/env python

"""
Uses pysam to convert a CRAM file to a sorted bam file.
usage: %prog in_file out_file
"""
import optparse
import os

from pysam import sort  # type: ignore[attr-defined]


[docs]def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args slots = os.getenv("GALAXY_SLOTS", 1) sort(f"-@{slots}", "-o", output_fname, "-O", "bam", "-T", ".", input_fname)
if __name__ == "__main__": main()