Process Sample gVCF headers during Ingest [VS-836]

broadinstitute · Jun 23, 2023 · 91de082 · 91de082
1 parent 03612e7
commit 91de082
Showing 1 changed file with 13 additions and 0 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/gvs/bigquery/BigQueryUtils.java
@@ -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);