37651fcb98ae564f95c28fbbe3401f48731f7a0d,deepvariant/realigner/window_selector.py,,_candidates_from_reads,#Any#Any#Any#Any#,42

Before Change

  return {
      expanded_region.start + i: count
      for i, count in enumerate(counts_vec)
      if count > 0 and ranges.position_overlaps(
          region.reference_name, expanded_region.start + i, region)
  }

After Change

    allele_counter.add(read)

  model_type = config.window_selector_model.model_type
  if model_type == realigner_pb2.WindowSelectorModel.VARIANT_READS:
    return _variant_reads_threshold_selector(
        allele_counter, config.window_selector_model.variant_reads_model,
        region, expanded_region)
  elif model_type == realigner_pb2.WindowSelectorModel.ALLELE_COUNT_LINEAR:
    return _allele_count_linear_selector(
        allele_counter, config.window_selector_model.allele_count_linear_model,
        region, expanded_region)
  else:
    raise ValueError("Unknown enum option "{}" for "
                     "WindowSelectorModel.model_type"
                     .format(config.window_selector_model.model_type))


def _variant_reads_threshold_selector(allele_counter, model_conf, region,
                                      expanded_region):
  Returns a list of candidate positions.

Instances