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Non-GVS bits required for GVS [VS-971] #8362

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merged 5 commits into from
Jun 27, 2023
+66 −13
Merged

Non-GVS bits required for GVS [VS-971] #8362

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1c25535
renamed VCF header
mcovarr Jun 8, 2023
1feea0f
Monitoring script support for VQSR Lite WDL JointVcfFiltering.wdl
mcovarr Jun 13, 2023
fdc09c7
run test with dummy monitoring script
mcovarr Jun 21, 2023
e7edf9e
Move rather than delete GVS BigQuery classes
mcovarr Jun 23, 2023
dc44285
Process Sample gVCF headers during Ingest [VS-836]
mcovarr Jun 23, 2023
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Process Sample gVCF headers during Ingest [VS-836]
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@mcovarr
mcovarr committed Jun 26, 2023
commit dc442857aaa5afb3c73303fe1a1fb4ecd0913c87
13 changes: 13 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtils.java
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Expand Up @@ -451,6 +451,19 @@ public static StorageAPIAvroReaderAndBigQueryStatistics executeQueryWithStorageA
}

public static boolean doRowsExistFor(String projectID, String datasetName, String tableName, String columnName, String value) {
String template = "SELECT COUNT(*) FROM `%s.%s.%s` WHERE %s = '%s'";
String query = String.format(template, projectID, datasetName, tableName, columnName, value);

BigQueryResultAndStatistics resultAndStatistics = BigQueryUtils.executeQuery(projectID, query, true, null);
for (final FieldValueList row : resultAndStatistics.result.iterateAll()) {
final long count = row.get(0).getLongValue();
return count != 0;
}
throw new GATKException(String.format("No rows returned from count of `%s.%s.%s` for %s = '%s'",
projectID, datasetName, tableName, columnName, value));
}

public static boolean doRowsExistFor(String projectID, String datasetName, String tableName, String columnName, Long value) {
String template = "SELECT COUNT(*) FROM `%s.%s.%s` WHERE %s = %s";
String query = String.format(template, projectID, datasetName, tableName, columnName, value);

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