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Source code for galaxy.datatypes.converters.vcf_to_vcf_bgzip

#!/usr/bin/env python

"""
Uses pysam to bgzip a vcf file as-is.
Headers, which are important, are kept.
Original ordering, which may be specifically needed  by tools or external display applications, is also maintained.

usage: %prog in_file out_file
"""
import optparse

import pysam


def main():
    # Read options, args.
    parser = optparse.OptionParser()
    (options, args) = parser.parse_args()
    input_fname, output_fname = args

    pysam.tabix_compress(input_fname, output_fname, force=True)


if __name__ == "__main__":
    main()