phc-ingestion 0.8.28__py3-none-any.whl → 0.8.29__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (5) hide show
  1. ingestion/caris/util/structural.py +1 -0
  2. ingestion/nextgen/util/process_structural.py +2 -0
  3. {phc_ingestion-0.8.28.dist-info → phc_ingestion-0.8.29.dist-info}/METADATA +1 -1
  4. {phc_ingestion-0.8.28.dist-info → phc_ingestion-0.8.29.dist-info}/RECORD +5 -5
  5. {phc_ingestion-0.8.28.dist-info → phc_ingestion-0.8.29.dist-info}/WHEEL +0 -0
ingestion/caris/util/structural.py CHANGED
@@ -33,6 +33,7 @@ def extract_structural(prefix, data, log: Logger):
33
33
  "no result",
34
34
  "indeterminate",
35
35
  "wild type",
36
+ "hlaVD",
36
37
  ]:
37
38
  structural_variant_tests.append(this_result)
38
39
  if not structural_variant_tests:
ingestion/nextgen/util/process_structural.py CHANGED
@@ -187,6 +187,8 @@ def process_structural(
187
187
  chr1, chr2 = int(translocation["position1"][0][3:]), int(
188
188
  translocation["position2"][0][3:]
189
189
  )
190
+ if chr1 == chr2:
191
+ continue
190
192
  # Ensure chromosomes are in ascending order
191
193
  if chr1 > chr2:
192
194
  chr1, chr2 = chr2, chr1
{phc_ingestion-0.8.28.dist-info → phc_ingestion-0.8.29.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: phc-ingestion
3
- Version: 0.8.28
3
+ Version: 0.8.29
4
4
  Summary: Functions for LifeOmic PHC genomic ingestions
5
5
  License: MIT
6
6
  Author-email: LifeOmic Development <development@lifeomic.com>
{phc_ingestion-0.8.28.dist-info → phc_ingestion-0.8.29.dist-info}/RECORD RENAMED
@@ -11,7 +11,7 @@ ingestion/caris/util/interpretation.py,sha256=CghNurqeVA5VTBBorU8-ZTN-PVNPnR8wrm
11
11
  ingestion/caris/util/json.py,sha256=xVEfwKOwyRCEXZWKr9zXooPIrxGkUtSxcAYuDUHkAxw,4706
12
12
  ingestion/caris/util/metadata.py,sha256=629-yPh_qIZKJCJzJHEvo6EUGxIBW3Gw31RSytF4v08,9541
13
13
  ingestion/caris/util/specimen_details.py,sha256=R3uKHlLR056XcQbUPI6IO2dLr-z5Z5AJi866DJ379Qw,2105
14
- ingestion/caris/util/structural.py,sha256=409HwEUbzlnhtAjBco6Dx13L2RTj9hZGG68P-N3LNT8,4599
14
+ ingestion/caris/util/structural.py,sha256=yE-okF59OoIULBB7JQHHcrRHghiPoNyG2LCtknm0C2E,4628
15
15
  ingestion/caris/util/tar.py,sha256=BGR_2vBbxyMgF-GzJ3SrihsPdOzII4SFVz9tvKV5vo0,482
16
16
  ingestion/caris/util/tests.py,sha256=mcG3A8TW81_sn2Bfoa-Gd6Q1sR3_R4FX2BNskD4DkJk,372
17
17
  ingestion/caris/util/tmb.py,sha256=DVi1wPSjVr_32ZCc6Yb51tGqUlcxUx40yCvuqvNuDx4,1027
@@ -37,7 +37,7 @@ ingestion/nextgen/util/nextgen_specific_genes.py,sha256=II_E2AgAqv35u_ga25geRn6U
37
37
  ingestion/nextgen/util/pre_filter_somatic_vcf.py,sha256=K_gH4EnUXrKB22u_f8FqQVGrOS5LxXNsNO3VBn381eY,2301
38
38
  ingestion/nextgen/util/process_cnv.py,sha256=m-AhsXFlYw4LTzgJJaj5vXYbK5n3H7cImzBxD2To6M0,2598
39
39
  ingestion/nextgen/util/process_manifest.py,sha256=FOa-m78layb5TFTktaDHkHT9hAGUeH9ZPGeqgBncz64,8585
40
- ingestion/nextgen/util/process_structural.py,sha256=sdAMcsgXm1lUbvNN6URSTwMfRoKDuOzPG2NFtKyhL0I,7593
40
+ ingestion/nextgen/util/process_structural.py,sha256=56wVGmZIfQwqNYthCZ4OdFAaqkoZKZvIpJtf-wekzg4,7647
41
41
  ingestion/nextgen/util/process_vcf.py,sha256=TvyV5wyXXSpFy2lc6h3ljqVQ5VeDPGxihHl2_K6LalQ,8432
42
42
  ingestion/nextgen/util/types.py,sha256=SSzt5gv-kss1PR45eQUelypWrGI-dAfQMO3GSD-T-Wg,22
43
43
  ingestion/resources/GRCh37_map.csv.gz,sha256=JOEkjtbYrJpIdyoZdCvfJhvvz2dNfkSve7lXSXkCCD8,408290
@@ -54,6 +54,6 @@ ingestion/vcf_standardization/util/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQe
54
54
  ingestion/vcf_standardization/util/af_helpers.py,sha256=dpTzoeIQVeBRt0ETF3a9rp5ojZqznHg4x_hCZ8OPcOg,1061
55
55
  ingestion/vcf_standardization/util/dp_helpers.py,sha256=Nq8oLOLObu4_pv16qwwgpALRlUoJVCULrd9cFOD-eoI,823
56
56
  ingestion/vcf_standardization/util/read_write.py,sha256=IQotJ27To1MoQcRstc5AbHZtUuJz5cqkkZiHsDNaBvI,2471
57
- phc_ingestion-0.8.28.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
58
- phc_ingestion-0.8.28.dist-info/METADATA,sha256=sNMcZ4aHN1IukmJRigUx9yGU-QMfnN9a7im0ULXoUcA,552
59
- phc_ingestion-0.8.28.dist-info/RECORD,,
57
+ phc_ingestion-0.8.29.dist-info/WHEEL,sha256=B19PGBCYhWaz2p_UjAoRVh767nYQfk14Sn4TpIZ-nfU,87
58
+ phc_ingestion-0.8.29.dist-info/METADATA,sha256=yaQSargO2FJ9_mR6PJ5mRTTYXPhUIailySSuH-wBsxg,552
59
+ phc_ingestion-0.8.29.dist-info/RECORD,,