phc-ingestion 0.8.41__py3-none-any.whl → 0.8.42__py3-none-any.whl

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Files changed (4) hide show
  1. ingestion/generic/process.py +5 -1
  2. {phc_ingestion-0.8.41.dist-info → phc_ingestion-0.8.42.dist-info}/METADATA +1 -1
  3. {phc_ingestion-0.8.41.dist-info → phc_ingestion-0.8.42.dist-info}/RECORD +4 -4
  4. {phc_ingestion-0.8.41.dist-info → phc_ingestion-0.8.42.dist-info}/WHEEL +0 -0
ingestion/generic/process.py CHANGED
@@ -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-0.8.41.dist-info → phc_ingestion-0.8.42.dist-info}/METADATA 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: 0.8.41
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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-0.8.41.dist-info → phc_ingestion-0.8.42.dist-info}/RECORD RENAMED
@@ -26,7 +26,7 @@ ingestion/foundation/util/ga4gh.py,sha256=dn7uoQdnKHfIVCSHVEyPpR0jc1uRp1YB4P_9tL
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  ingestion/foundation/util/interpretation.py,sha256=LVVUmMyD6Un1rIKXqiyQDUC6oIJUd8cU3I9YHD5fsXg,405
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  ingestion/foundation/util/vcf_etl.py,sha256=ZBrX1XGRz-ymLUEiVcjjqmPZPb-AfD9On8UkZJDa1Dk,2133
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  ingestion/generic/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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- ingestion/generic/process.py,sha256=WJHV_-SKhrDZ3JS3fm9DVMoW3Zs2t50GiraSV3vlLHE,1548
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+ ingestion/generic/process.py,sha256=ZaVnZ_gx9faDUsuresI1A0oCegTa-dPQT7DBFMeZGyY,1777
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  ingestion/generic/utils.py,sha256=1MEIru7uq38IjUdL8lcHqDH0oTki9uWrz1f2e-pmRoU,2814
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  ingestion/nextgen/__init__.py,sha256=7LQ-h_Bvc5P1QcHMdzsqi1Qm4fTJn04-ozar2ty9wSc,59
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  ingestion/nextgen/process.py,sha256=5Z0RfclwTAYZruGDiLPutjPCYFh1DJpoWY9dnttghT4,3993
@@ -54,6 +54,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
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  ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
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  ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
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  ingestion/vcf_standardization/util/read_write.py,sha256=x3Pf6Dq8tmolblbCS5CrNmrcHS3FGfqBSFpFgvFGC4g,2526
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- phc_ingestion-0.8.41.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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- phc_ingestion-0.8.41.dist-info/METADATA,sha256=YefyKypDkMluRD6uKVTI1EObzXpr2JlkSpO_SfGh5SE,573
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- phc_ingestion-0.8.41.dist-info/RECORD,,
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+ phc_ingestion-0.8.42.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
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+ phc_ingestion-0.8.42.dist-info/METADATA,sha256=LB_E096gDykQT0yFc3_AP28VNff1Zi91Ltj971FZ8c0,573
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+ phc_ingestion-0.8.42.dist-info/RECORD,,