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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

[docs]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()