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Source code for galaxy.datatypes.converters.bcf_bgzip_to_bcf_converter

#!/usr/bin/env python

Uses bcftools to extract a bcf from a bcf.gz

usage: %prog in_file out_file
import optparse
import subprocess

[docs]def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args subprocess.call(["bcftools", "view", input_fname, "-o", output_fname, "-O", "u"])
if __name__ == "__main__": main()