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

import pysam


[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) pysam.sort("-@%s" % slots, '-o', output_fname, '-O', 'bam', '-T', '.', input_fname)
if __name__ == "__main__": main()