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Add row_to_globals_check and update config #658

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Add row_to_globals_check and update config #658

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995f6be
add first draft log output
klaricch Feb 6, 2025
592a3ed
add ability to sort columns
klaricch Feb 6, 2025
e320987
add ability to filter by col values
klaricch Feb 6, 2025
9e05eab
simplify names
klaricch Feb 7, 2025
a391d22
small edits
klaricch Feb 7, 2025
588b8d8
add test ht and change re
klaricch Feb 7, 2025
fc8da4b
small edit
klaricch Feb 11, 2025
a2e65b3
small edit
klaricch Feb 11, 2025
ffd6900
add view table option
klaricch Feb 12, 2025
d889654
add test rows for missingness
klaricch Feb 12, 2025
647b530
add use-logtest-ht option
klaricch Feb 12, 2025
a2d6181
fix column sort
klaricch Feb 12, 2025
9e59c10
add to test dataset
klaricch Feb 13, 2025
137595d
remove bold
klaricch Feb 13, 2025
f85fe2b
isort
klaricch Feb 14, 2025
b35a792
small edits
klaricch Feb 14, 2025
23a601d
isort
klaricch Feb 14, 2025
b77cb1e
autopep
klaricch Feb 14, 2025
1b8a400
small edits
klaricch Feb 14, 2025
af04ab5
small edits
klaricch Feb 14, 2025
af96d98
add global len check and edit schema
klaricch Feb 20, 2025
31802b0
small edits
klaricch Feb 20, 2025
2cf370f
Merge remote-tracking branch 'origin/main' into kl/row_len
klaricch Feb 21, 2025
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6 changes: 3 additions & 3 deletions gnomad_qc/v5/configs/validity_inputs_config.json
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
{
"missingness_threshold": 0.5,
"indexed_array_annotations": {"faf": "faf_index_dict", "freq": "freq_index_dict"},
"struct_annotations_for_missingness": ["grpmax", "fafmax"],
"freq_meta_expr": "ht.freq_meta",
"freq_names": {"freq": "freq", "freq_meta": "freq_meta", "freq_index_dict": "freq_index_dict", "freq_meta_sample_count": "freq_meta_sample_count"},
"faf_names": {"faf": "faf", "faf_meta": "faf_meta", "faf_index_dict": "faf_index_dict"},
"freq_annotations_to_sum": ["AC", "AN", "homozygote_count"],
"freq_sort_order": ["gen_anc", "sex", "group"],
"nhomalt_metric": "homozygote_count",
"nhomalt_metric": "homozygote_count"
}
43 changes: 35 additions & 8 deletions gnomad_qc/v5/configs/validity_inputs_schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,24 +4,51 @@
"type": "object",
"properties": {
"missingness_threshold": {"type": "number"},
"indexed_array_annotations": {
"struct_annotations_for_missingness": {
"type": "array",
"items": {"type": "string"},
},
"freq_names": {
"type": "object",
"additionalProperties": {"type": "string"},
"properties": {
"freq": {"type": "string"},
"freq_meta": {"type": "string"},
"freq_index_dict": {"type": "string"},
"freq_meta_sample_count": {"type": "string"},
},
"required": [
"freq",
"freq_meta",
"freq_index_dict",
"freq_meta_sample_count",
],
"additionalProperties": False,
},
"struct_annotations_for_missingness": {
"faf_names": {
"type": "object",
"properties": {
"faf": {"type": "string"},
"faf_meta": {"type": "string"},
"faf_index_dict": {"type": "string"},
},
"required": ["faf", "faf_meta", "faf_index_dict"],
"additionalProperties": False,
},
"freq_annotations_to_sum": {
"type": "array",
"items": {"type": "string"},
},
"freq_sort_order": {
"type": "array",
"items": {"type": "string"},
},
"freq_meta_expr": {"type": "string"},
"freq_annotations_to_sum": {"type": "array", "items": {"type": "string"}},
"freq_sort_order": {"type": "array", "items": {"type": "string"}},
"nhomalt_metric": {"type": "string"},
},
"required": [
"missingness_threshold",
"indexed_array_annotations",
"struct_annotations_for_missingness",
"freq_meta_expr",
"freq_names",
"faf_names",
"freq_annotations_to_sum",
"freq_sort_order",
"nhomalt_metric",
Expand Down
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