From bae451c54e206a343f9bed5c3d2ed64087b823ca Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Tue, 3 Dec 2024 12:15:13 -0500 Subject: [PATCH 01/14] move reference data fixtures --- hail_search/constants.py | 1 - .../clinvar_path_variants.ht/.README.txt.crc | Bin 12 -> 0 bytes .../.metadata.json.gz.crc | Bin 16 -> 0 bytes .../clinvar_path_variants.ht/README.txt | 3 --- .../globals/.metadata.json.gz.crc | Bin 16 -> 0 bytes .../globals/metadata.json.gz | Bin 615 -> 0 bytes .../globals/parts/.part-0.crc | Bin 28 -> 0 bytes .../globals/parts/part-0 | Bin 2155 -> 0 bytes .../.index.crc | Bin 12 -> 0 bytes .../.metadata.json.gz.crc | Bin 12 -> 0 bytes .../index | Bin 53 -> 0 bytes .../metadata.json.gz | Bin 183 -> 0 bytes .../clinvar_path_variants.ht/metadata.json.gz | Bin 537 -> 0 bytes .../rows/.metadata.json.gz.crc | Bin 16 -> 0 bytes .../rows/metadata.json.gz | Bin 587 -> 0 bytes ...-0-51057efb-1c1f-4d03-a0bc-ec8d7b2c6525.crc | Bin 12 -> 0 bytes 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.../clinvar_path_variants.ht/.README.txt.crc | Bin 12 -> 0 bytes .../.metadata.json.gz.crc | Bin 12 -> 0 bytes .../clinvar_path_variants.ht/README.txt | 3 --- .../globals/.metadata.json.gz.crc | Bin 12 -> 0 bytes .../globals/metadata.json.gz | Bin 240 -> 0 bytes .../globals/parts/.part-0.crc | Bin 12 -> 0 bytes .../globals/parts/part-0 | Bin 11 -> 0 bytes .../.index.crc | Bin 12 -> 0 bytes .../.metadata.json.gz.crc | Bin 12 -> 0 bytes .../index | Bin 57 -> 0 bytes .../metadata.json.gz | Bin 184 -> 0 bytes .../clinvar_path_variants.ht/metadata.json.gz | Bin 309 -> 0 bytes .../rows/.metadata.json.gz.crc | Bin 16 -> 0 bytes .../rows/metadata.json.gz | Bin 604 -> 0 bytes ...-0-23b3a09d-4799-4bcb-9e13-c2812c6915c5.crc | Bin 12 -> 0 bytes ...part-0-23b3a09d-4799-4bcb-9e13-c2812c6915c5 | Bin 28 -> 0 bytes .../high_af_variants.ht/.README.txt.crc | Bin 12 -> 0 bytes .../high_af_variants.ht/.metadata.json.gz.crc | Bin 12 -> 0 bytes .../high_af_variants.ht/README.txt | 3 --- 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.../clinvar_path_variants.ht/metadata.json.gz | Bin 0 -> 314 bytes .../rows/.metadata.json.gz.crc | Bin 0 -> 16 bytes .../rows/metadata.json.gz | Bin 0 -> 603 bytes ...-0-1a5db544-8945-4dad-8452-05d09631b4a9.crc | Bin 0 -> 12 bytes ...part-0-1a5db544-8945-4dad-8452-05d09631b4a9 | Bin 0 -> 52 bytes .../high_af_variants.ht/.README.txt.crc | Bin 0 -> 12 bytes .../high_af_variants.ht/._SUCCESS.crc | Bin .../high_af_variants.ht/.metadata.json.gz.crc | Bin 0 -> 12 bytes .../SNV_INDEL/high_af_variants.ht/README.txt | 3 +++ .../high_af_variants.ht/_SUCCESS | 0 .../globals/.metadata.json.gz.crc | Bin 0 -> 12 bytes .../globals/metadata.json.gz | Bin 0 -> 254 bytes .../globals/parts/.part-0.crc | Bin 0 -> 12 bytes .../high_af_variants.ht/globals/parts/part-0 | Bin 0 -> 40 bytes .../.index.crc | Bin .../.metadata.json.gz.crc | Bin .../index | Bin .../metadata.json.gz | Bin .../high_af_variants.ht/metadata.json.gz | Bin 0 -> 320 bytes .../rows/.metadata.json.gz.crc | Bin 0 -> 16 bytes .../high_af_variants.ht/rows/metadata.json.gz | Bin 0 -> 611 bytes ...0-31b75ec4-c1eb-49e3-9fc7-14d081ffc79b.crc} | Bin ...art-0-31b75ec4-c1eb-49e3-9fc7-14d081ffc79b} | Bin hail_search/queries/base.py | 2 +- hail_search/queries/mito.py | 17 +++++++---------- hail_search/queries/snv_indel_37.py | 11 ++++------- 100 files changed, 21 insertions(+), 28 deletions(-) delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/.README.txt.crc delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/.metadata.json.gz.crc delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/README.txt delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/globals/.metadata.json.gz.crc delete mode 100644 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hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/index/part-0-51057efb-1c1f-4d03-a0bc-ec8d7b2c6525.idx/index delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/index/part-0-51057efb-1c1f-4d03-a0bc-ec8d7b2c6525.idx/metadata.json.gz delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/metadata.json.gz delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/rows/.metadata.json.gz.crc delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/rows/metadata.json.gz delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/rows/parts/.part-0-51057efb-1c1f-4d03-a0bc-ec8d7b2c6525.crc delete mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/rows/parts/part-0-51057efb-1c1f-4d03-a0bc-ec8d7b2c6525 create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/.README.txt.crc rename hail_search/fixtures/reference_data/GRCh38/MITO/{cached_reference_dataset_queries => }/clinvar_path_variants.ht/._SUCCESS.crc (100%) create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/README.txt rename hail_search/fixtures/reference_data/GRCh38/MITO/{cached_reference_dataset_queries => }/clinvar_path_variants.ht/_SUCCESS (100%) create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/globals/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/globals/metadata.json.gz create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/globals/parts/.part-0.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/globals/parts/part-0 create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/index/part-0-99954840-d192-45cb-bbbc-043ef6047be9.idx/.index.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/index/part-0-99954840-d192-45cb-bbbc-043ef6047be9.idx/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/index/part-0-99954840-d192-45cb-bbbc-043ef6047be9.idx/index create mode 100644 hail_search/fixtures/reference_data/GRCh38/MITO/clinvar_path_variants.ht/index/part-0-99954840-d192-45cb-bbbc-043ef6047be9.idx/metadata.json.gz create mode 100644 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hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/cached_reference_dataset_queries/high_af_variants.ht/globals/.metadata.json.gz.crc delete mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/cached_reference_dataset_queries/high_af_variants.ht/globals/metadata.json.gz delete mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/cached_reference_dataset_queries/high_af_variants.ht/globals/parts/.part-0.crc delete mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/cached_reference_dataset_queries/high_af_variants.ht/globals/parts/part-0 delete mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/cached_reference_dataset_queries/high_af_variants.ht/metadata.json.gz delete mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/cached_reference_dataset_queries/high_af_variants.ht/rows/.metadata.json.gz.crc delete mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/cached_reference_dataset_queries/high_af_variants.ht/rows/metadata.json.gz create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/.README.txt.crc rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries => }/clinvar_path_variants.ht/._SUCCESS.crc (100%) create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/README.txt rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries => }/clinvar_path_variants.ht/_SUCCESS (100%) create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/globals/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/globals/metadata.json.gz create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/globals/parts/.part-0.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/globals/parts/part-0 create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/index/part-0-1a5db544-8945-4dad-8452-05d09631b4a9.idx/.index.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/index/part-0-1a5db544-8945-4dad-8452-05d09631b4a9.idx/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/index/part-0-1a5db544-8945-4dad-8452-05d09631b4a9.idx/index create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/index/part-0-1a5db544-8945-4dad-8452-05d09631b4a9.idx/metadata.json.gz create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/metadata.json.gz create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/rows/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/rows/metadata.json.gz create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/rows/parts/.part-0-1a5db544-8945-4dad-8452-05d09631b4a9.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/clinvar_path_variants.ht/rows/parts/part-0-1a5db544-8945-4dad-8452-05d09631b4a9 create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/.README.txt.crc rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries => }/high_af_variants.ht/._SUCCESS.crc (100%) create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/README.txt rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries => }/high_af_variants.ht/_SUCCESS (100%) create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/globals/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/globals/metadata.json.gz create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/globals/parts/.part-0.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/globals/parts/part-0 rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries/high_af_variants.ht/index/part-0-fbbd1d66-9016-474d-b435-c7d356e21767.idx => high_af_variants.ht/index/part-0-31b75ec4-c1eb-49e3-9fc7-14d081ffc79b.idx}/.index.crc (100%) rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries/high_af_variants.ht/index/part-0-fbbd1d66-9016-474d-b435-c7d356e21767.idx => high_af_variants.ht/index/part-0-31b75ec4-c1eb-49e3-9fc7-14d081ffc79b.idx}/.metadata.json.gz.crc (100%) rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries/high_af_variants.ht/index/part-0-fbbd1d66-9016-474d-b435-c7d356e21767.idx => high_af_variants.ht/index/part-0-31b75ec4-c1eb-49e3-9fc7-14d081ffc79b.idx}/index (100%) rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries/high_af_variants.ht/index/part-0-fbbd1d66-9016-474d-b435-c7d356e21767.idx => high_af_variants.ht/index/part-0-31b75ec4-c1eb-49e3-9fc7-14d081ffc79b.idx}/metadata.json.gz (100%) create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/metadata.json.gz create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/rows/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/high_af_variants.ht/rows/metadata.json.gz rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries/high_af_variants.ht/rows/parts/.part-0-fbbd1d66-9016-474d-b435-c7d356e21767.crc => high_af_variants.ht/rows/parts/.part-0-31b75ec4-c1eb-49e3-9fc7-14d081ffc79b.crc} (100%) rename hail_search/fixtures/reference_data/GRCh38/SNV_INDEL/{cached_reference_dataset_queries/high_af_variants.ht/rows/parts/part-0-fbbd1d66-9016-474d-b435-c7d356e21767 => high_af_variants.ht/rows/parts/part-0-31b75ec4-c1eb-49e3-9fc7-14d081ffc79b} (100%) diff --git a/hail_search/constants.py b/hail_search/constants.py index ea46c0fe0f..a3037f919d 100644 --- a/hail_search/constants.py +++ b/hail_search/constants.py @@ -19,7 +19,6 @@ MOTIF_FEATURES_KEY = 'motif_feature' REGULATORY_FEATURES_KEY = 'regulatory_feature' CLINVAR_KEY = 'clinvar' -CLINVAR_MITO_KEY = 'clinvar_mito' HGMD_KEY = 'hgmd' STRUCTURAL_ANNOTATION_FIELD = 'structural' FAMILY_GUID_FIELD = 'familyGuids' diff --git a/hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/.README.txt.crc b/hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/.README.txt.crc deleted file mode 100644 index 5b283ca11048b84e9d36fee0ac8f0fcf15b8fabf..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12 TcmYc;N@ieSU}89@FS8B+5-S4& diff --git a/hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/.metadata.json.gz.crc b/hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/.metadata.json.gz.crc deleted file mode 100644 index 8b224cfeda836da46531ed1ce0ce624921e05757..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 16 XcmYc;N@ieSU}6xHuf5xN_Qop!A~^-x diff --git a/hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/README.txt b/hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/README.txt deleted file mode 100644 index fdae50be31..0000000000 --- a/hail_search/fixtures/reference_data/GRCh38/MITO/cached_reference_dataset_queries/clinvar_path_variants.ht/README.txt +++ /dev/null @@ -1,3 +0,0 @@ -This folder comprises a Hail (www.hail.is) native Table or MatrixTable. - Written with version 0.2.115-10932c754edb - Created at 2023/09/13 16:58:49 \ No newline at end of file diff --git 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hail_search.constants import CLINVAR_KEY, CLINVAR_MITO_KEY, HGMD_KEY, HGMD_PATH_RANGES, \ +from hail_search.constants import CLINVAR_KEY, HGMD_KEY, HGMD_PATH_RANGES, \ GNOMAD_GENOMES_FIELD, PREFILTER_FREQ_CUTOFF, PATH_FREQ_OVERRIDE_CUTOFF, PATHOGENICTY_SORT_KEY, PATHOGENICTY_HGMD_SORT_KEY, \ SPLICE_AI_FIELD, GENOME_VERSION_GRCh37 from hail_search.queries.base import PredictionPath, QualityFilterFormat @@ -28,10 +28,10 @@ class SnvIndelHailTableQuery37(MitoHailTableQuery): GNOMAD_GENOMES_FIELD: {'filter_af': 'AF_POPMAX_OR_GLOBAL', 'het': None, 'sort': 'gnomad'}, } PREDICTION_FIELDS_CONFIG = { - 'cadd': PredictionPath('cadd', 'PHRED'), + 'cadd': PredictionPath('dbnsfp', 'CADD_phred'), 'eigen': PredictionPath('eigen', 'Eigen_phred'), - 'mpc': PredictionPath('mpc', 'MPC'), - 'primate_ai': PredictionPath('primate_ai', 'score'), + 'mpc': PredictionPath('dbnsfp', 'MPC_score'), + 'primate_ai': PredictionPath('dbnsfp', 'PrimateAI_score'), SPLICE_AI_FIELD: PredictionPath(SPLICE_AI_FIELD, 'delta_score'), 'splice_ai_consequence': PredictionPath(SPLICE_AI_FIELD, 'splice_consequence'), 'mut_taster': PredictionPath('dbnsfp', 'MutationTaster_pred'), @@ -43,7 +43,6 @@ class SnvIndelHailTableQuery37(MitoHailTableQuery): **MitoHailTableQuery.PATHOGENICITY_FILTERS, HGMD_KEY: ('class', HGMD_PATH_RANGES), } - PATHOGENICITY_FIELD_MAP = {} ANNOTATION_OVERRIDE_FIELDS = [SPLICE_AI_FIELD] CORE_FIELDS = MitoHailTableQuery.CORE_FIELDS + ['CAID'] @@ -60,11 +59,9 @@ class SnvIndelHailTableQuery37(MitoHailTableQuery): 'format_value': lambda value: value.region_types.first(), }, } - ENUM_ANNOTATION_FIELDS[CLINVAR_KEY] = ENUM_ANNOTATION_FIELDS.pop(CLINVAR_MITO_KEY) SORTS = { **MitoHailTableQuery.SORTS, - PATHOGENICTY_SORT_KEY: lambda r: [MitoHailTableQuery.CLINVAR_SORT(CLINVAR_KEY, r)], PATHOGENICTY_HGMD_SORT_KEY: lambda r: [MitoHailTableQuery.CLINVAR_SORT(CLINVAR_KEY, r), r.hgmd.class_id], } From 2e98539b9c7f7270aa367c04667b499a9ea833fa Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Tue, 3 Dec 2024 17:46:50 -0500 Subject: [PATCH 02/14] Update mito table --- .../MITO/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../MITO/annotations.ht/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../GRCh38/MITO/annotations.ht/README.txt | 4 ++-- .../globals/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../annotations.ht/globals/metadata.json.gz | Bin 619 -> 581 bytes .../annotations.ht/globals/parts/.part-0.crc | Bin 24 -> 20 bytes .../MITO/annotations.ht/globals/parts/part-0 | Bin 1692 -> 1335 bytes .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin .../index | Bin 0 -> 95 bytes .../metadata.json.gz | Bin .../.index.crc | Bin 12 -> 0 bytes .../index | Bin 95 -> 0 bytes .../MITO/annotations.ht/metadata.json.gz | Bin 839 -> 809 bytes .../annotations.ht/rows/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../MITO/annotations.ht/rows/metadata.json.gz | Bin 1185 -> 1170 bytes ...0-093d669c-7af2-4de6-8090-96dd59ff0b00.crc | Bin 0 -> 12 bytes 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zk!f3v=DZX^Gpt1F(>O{sJ51r(KvD%ntF-s0L8HEXP0WtdkeA01%#PwYf`Mn$BLe;Q gA3a>J-s~jPo*ctf4FCWD00000D77#BAOHaX0F_!N82|tP From 14920fbcf2896438fd6fe6b9b79a224a8aacebf5 Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Tue, 3 Dec 2024 18:20:54 -0500 Subject: [PATCH 04/14] missed one --- hail_search/queries/mito.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/hail_search/queries/mito.py b/hail_search/queries/mito.py index c6479959a5..0cfe9fbdbb 100644 --- a/hail_search/queries/mito.py +++ b/hail_search/queries/mito.py @@ -5,7 +5,7 @@ import logging import os -from hail_search.constants import ABSENT_PATH_SORT_OFFSET, CLINVAR_KEY, CLINVAR_MITO_KEY, CLINVAR_LIKELY_PATH_FILTER, \ +from hail_search.constants import ABSENT_PATH_SORT_OFFSET, CLINVAR_KEY, CLINVAR_LIKELY_PATH_FILTER, \ CLINVAR_PATH_FILTER, \ CLINVAR_PATH_RANGES, CLINVAR_PATH_SIGNIFICANCES, ALLOWED_TRANSCRIPTS, ALLOWED_SECONDARY_TRANSCRIPTS, \ PATHOGENICTY_SORT_KEY, CONSEQUENCE_SORT, \ @@ -84,7 +84,7 @@ class MitoHailTableQuery(BaseHailTableQuery): **BaseHailTableQuery.BASE_ANNOTATION_FIELDS, } ENUM_ANNOTATION_FIELDS = { - CLINVAR_MITO_KEY: { + CLINVAR_KEY: { 'response_key': CLINVAR_KEY, 'include_version': True, 'annotate_value': lambda value, enum: { From 0ace1ea3858ba5db7858d8e1d09aba6f15a6287e Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Wed, 4 Dec 2024 09:45:39 -0500 Subject: [PATCH 05/14] Update fixtures with emptry struct --- .../SNV_INDEL/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../SNV_INDEL/annotations.ht/README.txt | 2 +- .../globals/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../annotations.ht/globals/metadata.json.gz | Bin 588 -> 589 bytes .../annotations.ht/globals/parts/.part-0.crc | Bin 20 -> 20 bytes .../annotations.ht/globals/parts/part-0 | Bin 1303 -> 1302 bytes .../.index.crc | Bin .../.metadata.json.gz.crc | Bin .../index | Bin .../metadata.json.gz | Bin .../annotations.ht/rows/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../annotations.ht/rows/metadata.json.gz | Bin 1218 -> 1218 bytes ...-2312032e-c9b8-4f11-988f-41b15165d4c3.crc} | Bin ...rt-0-2312032e-c9b8-4f11-988f-41b15165d4c3} | Bin .../SNV_INDEL/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../SNV_INDEL/annotations.ht/README.txt | 2 +- .../globals/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../annotations.ht/globals/metadata.json.gz | Bin 811 -> 812 bytes .../annotations.ht/globals/parts/.part-0.crc | Bin 24 -> 24 bytes .../annotations.ht/globals/parts/part-0 | Bin 2001 -> 2000 bytes .../.index.crc | Bin .../.metadata.json.gz.crc | Bin .../index | Bin .../metadata.json.gz | Bin .../annotations.ht/rows/.metadata.json.gz.crc | Bin 24 -> 24 bytes .../annotations.ht/rows/metadata.json.gz | Bin 1800 -> 1798 bytes ...-15287d8d-6e50-4c34-bd8d-e995fb40c368.crc} | Bin ...rt-0-15287d8d-6e50-4c34-bd8d-e995fb40c368} | Bin 28 files changed, 2 insertions(+), 2 deletions(-) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/{part-0-3c91f58b-224c-49b4-aff8-35b7bc5c0682.idx => part-0-2312032e-c9b8-4f11-988f-41b15165d4c3.idx}/.index.crc (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/{part-0-3c91f58b-224c-49b4-aff8-35b7bc5c0682.idx => part-0-2312032e-c9b8-4f11-988f-41b15165d4c3.idx}/.metadata.json.gz.crc (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/{part-0-3c91f58b-224c-49b4-aff8-35b7bc5c0682.idx => part-0-2312032e-c9b8-4f11-988f-41b15165d4c3.idx}/index (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/{part-0-3c91f58b-224c-49b4-aff8-35b7bc5c0682.idx => part-0-2312032e-c9b8-4f11-988f-41b15165d4c3.idx}/metadata.json.gz (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/rows/parts/{.part-0-3c91f58b-224c-49b4-aff8-35b7bc5c0682.crc => .part-0-2312032e-c9b8-4f11-988f-41b15165d4c3.crc} (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/rows/parts/{part-0-3c91f58b-224c-49b4-aff8-35b7bc5c0682 => part-0-2312032e-c9b8-4f11-988f-41b15165d4c3} (100%) rename hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/{part-0-432951f9-3028-4d34-881f-75f89ca2adc2.idx => part-0-15287d8d-6e50-4c34-bd8d-e995fb40c368.idx}/.index.crc (100%) rename hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/{part-0-432951f9-3028-4d34-881f-75f89ca2adc2.idx => part-0-15287d8d-6e50-4c34-bd8d-e995fb40c368.idx}/.metadata.json.gz.crc (100%) rename hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/{part-0-432951f9-3028-4d34-881f-75f89ca2adc2.idx => part-0-15287d8d-6e50-4c34-bd8d-e995fb40c368.idx}/index (100%) rename hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/{part-0-432951f9-3028-4d34-881f-75f89ca2adc2.idx => part-0-15287d8d-6e50-4c34-bd8d-e995fb40c368.idx}/metadata.json.gz (100%) rename hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/rows/parts/{.part-0-432951f9-3028-4d34-881f-75f89ca2adc2.crc => .part-0-15287d8d-6e50-4c34-bd8d-e995fb40c368.crc} (100%) rename hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/rows/parts/{part-0-432951f9-3028-4d34-881f-75f89ca2adc2 => part-0-15287d8d-6e50-4c34-bd8d-e995fb40c368} (100%) diff --git a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/.README.txt.crc b/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/.README.txt.crc index 4ad103df03335d2dca5a2ecf539ad8668a3e6a47..83c3c7f53d420879eddb0c6162a5a2353f6beda5 100644 GIT binary patch literal 12 TcmYc;N@ieSU}9LWZoC!%5yS%V literal 12 TcmYc;N@ieSU}AWb#dQk+6Ep*B diff --git a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/README.txt b/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/README.txt index 48a4631d3e..3b6747d4a8 100644 --- a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/README.txt +++ 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hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-093d669c-7af2-4de6-8090-96dd59ff0b00.crc rename to hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/.part-0-ca4e546b-69e0-4607-ae0a-efb3e860b406.crc diff --git a/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-093d669c-7af2-4de6-8090-96dd59ff0b00 b/hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-ca4e546b-69e0-4607-ae0a-efb3e860b406 similarity index 100% rename from hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-093d669c-7af2-4de6-8090-96dd59ff0b00 rename to hail_search/fixtures/GRCh38/MITO/annotations.ht/rows/parts/part-0-ca4e546b-69e0-4607-ae0a-efb3e860b406 From ee177eeeb9c5b75e83d491303e2cb37d1068f5a0 Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Wed, 4 Dec 2024 10:33:59 -0500 Subject: [PATCH 07/14] Revert to existing fixtures :/ --- .../SNV_INDEL/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../annotations.ht/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../SNV_INDEL/annotations.ht/README.txt | 4 ++-- .../globals/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../annotations.ht/globals/metadata.json.gz | Bin 589 -> 662 bytes .../annotations.ht/globals/parts/.part-0.crc | Bin 20 -> 24 bytes .../annotations.ht/globals/parts/part-0 | Bin 1302 -> 1705 bytes .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin 0 -> 12 bytes .../index | Bin 0 -> 65 bytes .../metadata.json.gz | Bin 0 -> 185 bytes .../SNV_INDEL/annotations.ht/metadata.json.gz | Bin 860 -> 888 bytes .../annotations.ht/rows/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../annotations.ht/rows/metadata.json.gz | Bin 1218 -> 1233 bytes ...0-b51ceb7d-c97c-431c-95a6-6a49862ec937.crc | Bin 0 -> 12 bytes ...art-0-b51ceb7d-c97c-431c-95a6-6a49862ec937 | Bin 0 -> 344 bytes .../MITO/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../MITO/annotations.ht/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../GRCh38/MITO/annotations.ht/README.txt | 4 ++-- .../globals/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../annotations.ht/globals/metadata.json.gz | Bin 581 -> 619 bytes .../annotations.ht/globals/parts/.part-0.crc | Bin 20 -> 24 bytes .../MITO/annotations.ht/globals/parts/part-0 | Bin 1335 -> 1692 bytes .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin 0 -> 12 bytes .../index | Bin 0 -> 95 bytes .../metadata.json.gz | Bin 0 -> 185 bytes .../MITO/annotations.ht/metadata.json.gz | Bin 809 -> 839 bytes .../annotations.ht/rows/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../MITO/annotations.ht/rows/metadata.json.gz | Bin 1170 -> 1185 bytes ...0-636edbd3-d0a9-410f-b5fe-03749bbbd8db.crc | Bin 0 -> 12 bytes ...art-0-636edbd3-d0a9-410f-b5fe-03749bbbd8db | Bin 0 -> 484 bytes .../SNV_INDEL/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../annotations.ht/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../SNV_INDEL/annotations.ht/README.txt | 4 ++-- .../globals/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../annotations.ht/globals/metadata.json.gz | Bin 812 -> 809 bytes .../annotations.ht/globals/parts/.part-0.crc | Bin 24 -> 28 bytes .../annotations.ht/globals/parts/part-0 | Bin 2000 -> 2062 bytes .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin 0 -> 12 bytes .../index | Bin 0 -> 139 bytes .../metadata.json.gz | Bin 0 -> 185 bytes .../SNV_INDEL/annotations.ht/metadata.json.gz | Bin 1321 -> 1318 bytes .../annotations.ht/rows/.metadata.json.gz.crc | Bin 24 -> 24 bytes .../annotations.ht/rows/metadata.json.gz | Bin 1798 -> 1818 bytes ...0-664fe3f2-7823-4853-8938-a28f441df7a5.crc | Bin 0 -> 24 bytes ...art-0-664fe3f2-7823-4853-8938-a28f441df7a5 | Bin 0 -> 1634 bytes .../clinvar_path_variants.ht/.README.txt.crc | Bin 0 -> 12 bytes .../clinvar_path_variants.ht/._SUCCESS.crc | Bin 0 -> 8 bytes .../.metadata.json.gz.crc | Bin 0 -> 16 bytes .../clinvar_path_variants.ht/README.txt | 3 +++ .../clinvar_path_variants.ht/_SUCCESS | 0 .../globals/.metadata.json.gz.crc | Bin 0 -> 16 bytes .../globals/metadata.json.gz | Bin 0 -> 615 bytes .../globals/parts/.part-0.crc | Bin 0 -> 28 bytes .../globals/parts/part-0 | Bin 0 -> 2155 bytes .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin 0 -> 12 bytes .../index | Bin 0 -> 53 bytes .../metadata.json.gz | Bin 0 -> 183 bytes .../clinvar_path_variants.ht/metadata.json.gz | Bin 0 -> 537 bytes .../rows/.metadata.json.gz.crc | Bin 0 -> 16 bytes .../rows/metadata.json.gz | Bin 0 -> 587 bytes ...0-51057efb-1c1f-4d03-a0bc-ec8d7b2c6525.crc | Bin 0 -> 12 bytes ...art-0-51057efb-1c1f-4d03-a0bc-ec8d7b2c6525 | Bin 0 -> 36 bytes .../clinvar_path_variants.ht/.README.txt.crc | Bin 0 -> 12 bytes .../clinvar_path_variants.ht/._SUCCESS.crc | Bin 0 -> 8 bytes .../.metadata.json.gz.crc | Bin 0 -> 12 bytes .../clinvar_path_variants.ht/README.txt | 3 +++ .../clinvar_path_variants.ht/_SUCCESS | 0 .../globals/.metadata.json.gz.crc | Bin 0 -> 12 bytes .../globals/metadata.json.gz | Bin 0 -> 240 bytes .../globals/parts/.part-0.crc | Bin 0 -> 12 bytes .../globals/parts/part-0 | Bin 0 -> 11 bytes .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin 0 -> 12 bytes .../index | Bin 0 -> 57 bytes .../metadata.json.gz | Bin 0 -> 184 bytes .../clinvar_path_variants.ht/metadata.json.gz | Bin 0 -> 309 bytes .../rows/.metadata.json.gz.crc | Bin 0 -> 16 bytes .../rows/metadata.json.gz | Bin 0 -> 604 bytes ...0-23b3a09d-4799-4bcb-9e13-c2812c6915c5.crc | Bin 0 -> 12 bytes ...art-0-23b3a09d-4799-4bcb-9e13-c2812c6915c5 | Bin 0 -> 28 bytes .../high_af_variants.ht/.README.txt.crc | Bin 0 -> 12 bytes .../high_af_variants.ht/._SUCCESS.crc | Bin 0 -> 8 bytes .../high_af_variants.ht/.metadata.json.gz.crc | Bin 0 -> 12 bytes .../high_af_variants.ht/README.txt | 3 +++ .../high_af_variants.ht/_SUCCESS | 0 .../globals/.metadata.json.gz.crc | Bin 0 -> 12 bytes .../globals/metadata.json.gz | Bin 0 -> 239 bytes .../globals/parts/.part-0.crc | Bin 0 -> 12 bytes .../high_af_variants.ht/globals/parts/part-0 | Bin 0 -> 36 bytes .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin 0 -> 12 bytes .../index | Bin 0 -> 112 bytes .../metadata.json.gz | Bin 0 -> 184 bytes .../high_af_variants.ht/metadata.json.gz | Bin 0 -> 315 bytes .../rows/.metadata.json.gz.crc | Bin 0 -> 16 bytes .../high_af_variants.ht/rows/metadata.json.gz | Bin 0 -> 613 bytes ...0-fbbd1d66-9016-474d-b435-c7d356e21767.crc | Bin 0 -> 12 bytes ...art-0-fbbd1d66-9016-474d-b435-c7d356e21767 | Bin 0 -> 101 bytes 102 files changed, 15 insertions(+), 6 deletions(-) create mode 100644 hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-b51ceb7d-c97c-431c-95a6-6a49862ec937.idx/.index.crc create mode 100644 hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-b51ceb7d-c97c-431c-95a6-6a49862ec937.idx/.metadata.json.gz.crc create mode 100644 hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-b51ceb7d-c97c-431c-95a6-6a49862ec937.idx/index create mode 100644 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Subject: [PATCH 12/14] Fix issue with coalesced missing values --- .../SNV_INDEL/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../annotations.ht/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../SNV_INDEL/annotations.ht/README.txt | 2 +- .../.index.crc | Bin 0 -> 12 bytes .../.metadata.json.gz.crc | Bin .../index | Bin 0 -> 139 bytes .../metadata.json.gz | Bin .../.index.crc | Bin 12 -> 0 bytes .../index | Bin 139 -> 0 bytes .../SNV_INDEL/annotations.ht/metadata.json.gz | Bin 1279 -> 1280 bytes .../annotations.ht/rows/.metadata.json.gz.crc | Bin 24 -> 24 bytes .../annotations.ht/rows/metadata.json.gz | Bin 1799 -> 1800 bytes ...0-2b10c852-02a2-426d-a0cf-961ae060d4c3.crc | Bin 0 -> 24 bytes ...0-53a22dd0-7e1b-47b0-a272-e89bc103abe8.crc | Bin 24 -> 0 bytes ...art-0-2b10c852-02a2-426d-a0cf-961ae060d4c3 | Bin 0 -> 1634 bytes ...art-0-53a22dd0-7e1b-47b0-a272-e89bc103abe8 | Bin 1613 -> 0 bytes 16 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/part-0-2b10c852-02a2-426d-a0cf-961ae060d4c3.idx/.index.crc rename hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/{part-0-53a22dd0-7e1b-47b0-a272-e89bc103abe8.idx => part-0-2b10c852-02a2-426d-a0cf-961ae060d4c3.idx}/.metadata.json.gz.crc (100%) create mode 100644 hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/part-0-2b10c852-02a2-426d-a0cf-961ae060d4c3.idx/index rename hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/{part-0-53a22dd0-7e1b-47b0-a272-e89bc103abe8.idx => part-0-2b10c852-02a2-426d-a0cf-961ae060d4c3.idx}/metadata.json.gz (100%) delete mode 100644 hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/part-0-53a22dd0-7e1b-47b0-a272-e89bc103abe8.idx/.index.crc delete mode 100644 hail_search/fixtures/GRCh38/SNV_INDEL/annotations.ht/index/part-0-53a22dd0-7e1b-47b0-a272-e89bc103abe8.idx/index create mode 100644 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PREFILTER_FREQ_CUTOFF, PATH_FREQ_OVERRIDE_CUTOFF, PATHOGENICTY_HGMD_SORT_KEY, \ SPLICE_AI_FIELD, GENOME_VERSION_GRCh37 from hail_search.queries.base import PredictionPath, QualityFilterFormat from hail_search.queries.mito import MitoHailTableQuery From 07e0d19b52aad5df026a7ca42e475452acfb87fd Mon Sep 17 00:00:00 2001 From: Benjamin Blankenmeister Date: Wed, 4 Dec 2024 13:07:53 -0500 Subject: [PATCH 14/14] Fix incorrectly annotated type :/ --- .../SNV_INDEL/annotations.ht/.README.txt.crc | Bin 12 -> 12 bytes .../annotations.ht/.metadata.json.gz.crc | Bin 16 -> 16 bytes .../SNV_INDEL/annotations.ht/README.txt | 2 +- .../.index.crc | Bin .../.metadata.json.gz.crc | Bin .../index | Bin .../metadata.json.gz | Bin .../SNV_INDEL/annotations.ht/metadata.json.gz | Bin 856 -> 856 bytes .../annotations.ht/rows/.metadata.json.gz.crc | Bin 20 -> 20 bytes .../annotations.ht/rows/metadata.json.gz | Bin 1219 -> 1219 bytes ...-32c79149-c8dd-4b54-8db9-097b88a68456.crc} | Bin ...rt-0-32c79149-c8dd-4b54-8db9-097b88a68456} | Bin 12 files changed, 1 insertion(+), 1 deletion(-) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/{part-0-a8249542-6225-499d-8aa1-1ceefd5488b8.idx => part-0-32c79149-c8dd-4b54-8db9-097b88a68456.idx}/.index.crc (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/{part-0-a8249542-6225-499d-8aa1-1ceefd5488b8.idx => part-0-32c79149-c8dd-4b54-8db9-097b88a68456.idx}/.metadata.json.gz.crc (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/{part-0-a8249542-6225-499d-8aa1-1ceefd5488b8.idx => part-0-32c79149-c8dd-4b54-8db9-097b88a68456.idx}/index (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/{part-0-a8249542-6225-499d-8aa1-1ceefd5488b8.idx => part-0-32c79149-c8dd-4b54-8db9-097b88a68456.idx}/metadata.json.gz (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/rows/parts/{.part-0-a8249542-6225-499d-8aa1-1ceefd5488b8.crc => .part-0-32c79149-c8dd-4b54-8db9-097b88a68456.crc} (100%) rename hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/rows/parts/{part-0-a8249542-6225-499d-8aa1-1ceefd5488b8 => part-0-32c79149-c8dd-4b54-8db9-097b88a68456} (100%) diff --git a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/.README.txt.crc b/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/.README.txt.crc index 3294815987696c08db6cf5f9c9215dcd7721cdb2..553ad190d009d55e302bce70271f0f9fe2959166 100644 GIT binary patch literal 12 TcmYc;N@ieSU}D%}GW87r69NOI literal 12 TcmYc;N@ieSU}6X^J5~$;5-kHg diff --git a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/.metadata.json.gz.crc b/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/.metadata.json.gz.crc index 507235e55ce07d12c7acf6e7dd2c66b1decdfc53..9a0672f9f31c5512a5847bb94816348ab8dcc825 100644 GIT binary patch literal 16 XcmYc;N@ieSU}8|;<0oyd`!fmv9?}Fp literal 16 XcmYc;N@ieSU}CTr{_@pM*3|(3A%g@~ diff --git a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/README.txt b/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/README.txt index a2649654d1..3be897fb74 100644 --- a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/README.txt +++ b/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/README.txt @@ -1,3 +1,3 @@ This folder comprises a Hail (www.hail.is) native Table or MatrixTable. Written with version 0.2.133-4c60fddb171a - Created at 2024/12/04 12:20:45 \ No newline at end of file + Created at 2024/12/04 13:07:33 \ No newline at end of file diff --git a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-a8249542-6225-499d-8aa1-1ceefd5488b8.idx/.index.crc b/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-32c79149-c8dd-4b54-8db9-097b88a68456.idx/.index.crc similarity index 100% rename from hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-a8249542-6225-499d-8aa1-1ceefd5488b8.idx/.index.crc rename to hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-32c79149-c8dd-4b54-8db9-097b88a68456.idx/.index.crc diff --git a/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-a8249542-6225-499d-8aa1-1ceefd5488b8.idx/.metadata.json.gz.crc b/hail_search/fixtures/GRCh37/SNV_INDEL/annotations.ht/index/part-0-32c79149-c8dd-4b54-8db9-097b88a68456.idx/.metadata.json.gz.crc similarity index 100% rename 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