7ed8c6bbcfb2dc0da9b1011ba21d12791239de79,deepvariant/postprocess_variants.py,,main,#Any#,932

Before Change

    header = dv_vcf_constants.deepvariant_header(
        contigs=contigs, sample_names=[sample_name])
    use_csi = _decide_to_use_csi(contigs)
    with tempfile.NamedTemporaryFile() as temp:
      start_time = time.time()
      postprocess_variants_lib.process_single_sites_tfrecords(
          contigs, paths, temp.name)
      logging.info("CVO sorting took %s minutes",
                   (time.time() - start_time) / 60)

      logging.info("Transforming call_variants_output to variants.")
      start_time = time.time()
      independent_variants = _transform_call_variants_output_to_variants(
          input_sorted_tfrecord_path=temp.name,
          qual_filter=FLAGS.qual_filter,
          multi_allelic_qual_filter=FLAGS.multi_allelic_qual_filter,
          sample_name=sample_name,
          group_variants=FLAGS.group_variants)
      variant_generator = haplotypes.maybe_resolve_conflicting_variants(
          independent_variants)

      start_time = time.time()
      if not FLAGS.nonvariant_site_tfrecord_path:
        logging.info("Writing variants to VCF.")
        write_variants_to_vcf(
            variant_iterable=variant_generator,
            output_vcf_path=FLAGS.outfile,
            header=header)
        if FLAGS.outfile.endswith(".gz"):
          build_index(FLAGS.outfile, use_csi)
        logging.info("VCF creation took %s minutes",
                     (time.time() - start_time) / 60)
      else:
        logging.info("Merging and writing variants to VCF and gVCF.")
        lessthanfn = _get_contig_based_lessthan(contigs)
        with vcf.VcfWriter(
            FLAGS.outfile, header=header, round_qualities=True) as vcf_writer, \
            vcf.VcfWriter(
                FLAGS.gvcf_outfile, header=header, round_qualities=True) \
            as gvcf_writer:
          nonvariant_generator = tfrecord.read_shard_sorted_tfrecords(
              FLAGS.nonvariant_site_tfrecord_path,
              key=_get_contig_based_variant_sort_keyfn(contigs),
              proto=variants_pb2.Variant)
          merge_and_write_variants_and_nonvariants(
              variant_generator, nonvariant_generator, lessthanfn, fasta_reader,
              vcf_writer, gvcf_writer)
        if FLAGS.outfile.endswith(".gz"):
          build_index(FLAGS.outfile, use_csi)
        if FLAGS.gvcf_outfile.endswith(".gz"):
          build_index(FLAGS.gvcf_outfile, use_csi)
        logging.info("Finished writing VCF and gVCF in %s minutes.",
                     (time.time() - start_time) / 60)
      if FLAGS.vcf_stats_report:
        outfile_base = _get_base_path(FLAGS.outfile)
        with vcf.VcfReader(FLAGS.outfile) as reader:
          vcf_stats.create_vcf_report(
              variants=reader.iterate(),
              output_basename=outfile_base,
              sample_name=sample_name,
              vcf_reader=reader)


if __name__ == "__main__":
  flags.mark_flags_as_required(["infile", "outfile", "ref"])
  tf.app.run()

After Change

    if record is None:
      logging.info("call_variants_output is empty. Writing out empty VCF.")
      sample_name = dv_constants.DEFAULT_SAMPLE_NAME
      variant_generator = iter([])
    else:
      sample_name = _extract_single_sample_name(record)
      temp = tempfile.NamedTemporaryFile()
      start_time = time.time()

Instances