phc-ingestion 0.8.40__tar.gz → 0.8.42__tar.gz

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  1. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/PKG-INFO +1 -1
  2. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/util/ga4gh.py +1 -1
  3. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/generic/process.py +5 -1
  4. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/pyproject.toml +1 -1
  5. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/PYPI.md +0 -0
  6. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/__init__.py +0 -0
  7. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/__init__.py +0 -0
  8. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/process.py +0 -0
  9. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/__init__.py +0 -0
  10. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/cnv.py +0 -0
  11. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/detect_genome_ref.py +0 -0
  12. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/ga4gh.py +0 -0
  13. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/hla.py +0 -0
  14. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/ihc.py +0 -0
  15. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/interpretation.py +0 -0
  16. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/json.py +0 -0
  17. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/metadata.py +0 -0
  18. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/specimen_details.py +0 -0
  19. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/structural.py +0 -0
  20. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/tar.py +0 -0
  21. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/tests.py +0 -0
  22. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/tmb.py +0 -0
  23. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/tsv.py +0 -0
  24. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/caris/util/vcf.py +0 -0
  25. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/__init__.py +0 -0
  26. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/process.py +0 -0
  27. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/util/__init__.py +0 -0
  28. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/util/cnv.py +0 -0
  29. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/util/fnv.py +0 -0
  30. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/util/interpretation.py +0 -0
  31. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/util/vcf_etl.py +0 -0
  32. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/generic/__init__.py +0 -0
  33. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/generic/utils.py +0 -0
  34. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/__init__.py +0 -0
  35. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/process.py +0 -0
  36. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/alteration_table.py +0 -0
  37. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/interpretation.py +0 -0
  38. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/manifest_helpers.py +0 -0
  39. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/nextgen_specific_genes.py +0 -0
  40. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/pre_filter_somatic_vcf.py +0 -0
  41. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/process_cnv.py +0 -0
  42. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/process_manifest.py +0 -0
  43. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/process_structural.py +0 -0
  44. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/process_vcf.py +0 -0
  45. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/nextgen/util/types.py +0 -0
  46. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/resources/GRCh37_map.csv.gz +0 -0
  47. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/resources/GRCh38_map.csv.gz +0 -0
  48. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/shared_util/__init__.py +0 -0
  49. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/shared_util/coords_to_genes.py +0 -0
  50. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/shared_util/gene_to_coords.py +0 -0
  51. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/shared_util/open_maybe_gzipped.py +0 -0
  52. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/shared_util/types.py +0 -0
  53. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/vcf_standardization/Variant.py +0 -0
  54. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/vcf_standardization/__init__.py +0 -0
  55. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/vcf_standardization/standardize.py +0 -0
  56. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/vcf_standardization/util/__init__.py +0 -0
  57. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/vcf_standardization/util/af_helpers.py +0 -0
  58. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/vcf_standardization/util/dp_helpers.py +0 -0
  59. {phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/vcf_standardization/util/read_write.py +0 -0
{phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: phc-ingestion
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- Version: 0.8.40
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+ Version: 0.8.42
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  Summary: Functions for LifeOmic PHC genomic ingestions
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  License: MIT
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  Author-email: LifeOmic Development <development@lifeomic.com>
{phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/foundation/util/ga4gh.py RENAMED
@@ -92,7 +92,7 @@ def get_plasma_tumor_fraction(genes) -> Optional[str]:
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  ptf_val = ptf_entry.get("Alterations", {}).get("Alteration", {}).get("Name", "")
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  try:
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  # See https://github.com/lifeomic/phc-ingestion/pull/129
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- float_val = float(ptf_val)
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+ float_val = float(ptf_val.strip("%"))
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  if float_val > 0:
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  return "Elevated"
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  elif float_val == 0:
{phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/ingestion/generic/process.py RENAMED
@@ -19,8 +19,12 @@ def process(
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  vcf_final = base_vcf_file.replace(".vcf", ".modified.nrm.filtered.vcf")
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  if not vcf_final.endswith(".gz"):
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  vcf_final = vcf_final + ".gz"
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+ # All generic VCF ingestions are germline, so ensure the
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+ # sample name is prefixed with "germline_". This matches
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+ # the downstream logic in genomic-manifest
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+ sample_name = f"germline_{case_id}"
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  vcf_line_count = standardize_vcf(
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- vcf_file, vcf_out, out_path, case_id, log, compression=True
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+ vcf_file, vcf_out, out_path, sample_name, log, compression=True
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  )
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  # Add to manifest
{phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/pyproject.toml RENAMED
@@ -1,6 +1,6 @@
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  [project]
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  name = "phc-ingestion"
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- version = "0.8.40"
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+ version = "0.8.42"
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  description = "Functions for LifeOmic PHC genomic ingestions"
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  authors = [
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  { name = "LifeOmic Development", email = "development@lifeomic.com" },
{phc-ingestion-0.8.40 → phc-ingestion-0.8.42}/PYPI.md RENAMED
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