54d6ab32e0cb1c5868b41cbfa52781f265598d55,deepvariant/make_examples.py,RegionProcessor,create_pileup_examples,#RegionProcessor#Any#,1695

Before Change

            dv_call.variant.reference_name, dv_call.variant.start,
            dv_call.variant.reference_bases))

    if self.options.pic_options.alt_aligned_pileup != "none":
      // Align the reads against each alternate allele, saving the sequences of
      // those alleles along with the alignments for pileup images.
      alt_info_for_samples = [
          self.align_to_all_haplotypes(dv_call.variant, reads)
          for reads in reads_for_samples
      ]
      // Each sample has different reads and thus different alt-alignments.
      haplotype_alignments_for_samples = [
          sample["alt_alignments"] for sample in alt_info_for_samples
      ]

      // All samples share the same alt sequences, so select the first one.
      haplotype_sequences = alt_info_for_samples[0]["alt_sequences"]
      pileup_images = self.pic.create_pileup_images(
          dv_call=dv_call,
          reads_for_samples=reads_for_samples,
          haplotype_alignments_for_samples=haplotype_alignments_for_samples,
          haplotype_sequences=haplotype_sequences)

    else:
      pileup_images = self.pic.create_pileup_images(
          dv_call=dv_call, reads_for_samples=reads_for_samples)

    if pileup_images is None:
      // We cannot build a PileupImage for dv_call, issue a warning.
      logging.warning("Could not create PileupImage for candidate at %s:%s",
                      dv_call.variant.reference_name, dv_call.variant.start)

After Change

            dv_call.variant.reference_bases))

    // Decide whether each candidate needs ALT-alignment.
    alt_align_this_variant = False
    if self.options.pic_options.alt_aligned_pileup != "none":
      if self.options.pic_options.types_to_alt_align == "indels":
        alt_align_this_variant = variant_utils.is_indel(dv_call.variant)
      else:  // types_to_alt_align can only be "all" or "indels".
        alt_align_this_variant = True

    haplotype_alignments_for_samples = None
    haplotype_sequences = None
    if alt_align_this_variant:
      // Align the reads against each alternate allele, saving the sequences of
      // those alleles along with the alignments for pileup images.
      alt_info_for_samples = [
          self.align_to_all_haplotypes(dv_call.variant, reads)
          for reads in reads_for_samples
      ]
      // Each sample has different reads and thus different alt-alignments.
      haplotype_alignments_for_samples = [
          sample["alt_alignments"] for sample in alt_info_for_samples
      ]
      // All samples share the same alt sequences, so select the first one.
      haplotype_sequences = alt_info_for_samples[0]["alt_sequences"]

    pileup_images = self.pic.create_pileup_images(
        dv_call=dv_call,
        reads_for_samples=reads_for_samples,
        haplotype_alignments_for_samples=haplotype_alignments_for_samples,

Instances