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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()