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optional column call_ps #9025

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optional column call_ps #9025

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e1357a3
optional column
yonghaoy Oct 30, 2024
4bbbb82
one more missing place
yonghaoy Oct 30, 2024
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsExtractAvroFilesForHail.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -279,7 +279,7 @@ task ExtractFromSuperpartitionedTables {
EXPORT DATA OPTIONS(
uri='${avro_prefix}/vets/vet_${str_table_index}/vet_${str_table_index}_*.avro', format='AVRO', compression='SNAPPY') AS
SELECT location, v.sample_id, ref, REPLACE(alt,',<NON_REF>','') alt, call_GT as GT, call_AD as AD, call_GQ as GQ, cast(SPLIT(call_pl,',')[OFFSET(0)] as int64) as RGQ,
call_PS as PS
SAFE_CAST(call_PS AS INT64) AS PS
FROM \`~{project_id}.~{dataset_name}.vet_${str_table_index}\` v
INNER JOIN \`~{project_id}.~{dataset_name}.sample_info\` s ON s.sample_id = v.sample_id
WHERE withdrawn IS NULL AND
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/extract/create_ranges_cohort_extract_data_table.py
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Expand Up @@ -263,7 +263,7 @@ def get_ref_subselect(fq_vet_table, samples, id):

if len(partition_samples) > 0:
subs = {}
insert = f"\nINSERT INTO `{fq_destination_table_data}` (location, sample_id, ref, alt, call_GT, call_GQ, call_AD, AS_QUALapprox, QUALapprox, CALL_PL, CALL_PGT, CALL_PID, CALL_PS) \n WITH \n"
insert = f"\nINSERT INTO `{fq_destination_table_data}` (location, sample_id, ref, alt, call_GT, call_GQ, call_AD, AS_QUALapprox, QUALapprox, CALL_PL, CALL_PGT, CALL_PID, SAFE_CAST(CALL_PS AS INT64) AS CALL_PS) \n WITH \n"
fq_vet_table = f"{fq_ranges_dataset}.{VET_TABLE_PREFIX}{i:03}"
j = 1

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