Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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

from pysam import ctabix


[docs]def main(): # Read options, args. parser = optparse.OptionParser() (options, args) = parser.parse_args() input_fname, output_fname = args ctabix.tabix_compress(input_fname, output_fname, force=True)
if __name__ == "__main__": main()