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Kc fix type #7620

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merged 3 commits into from
Dec 27, 2021
Merged

Kc fix type #7620

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bfb465a
fixed bug introduced with new BQ libraries
kcibul Dec 22, 2021
1c970f8
updated WDLs also
kcibul Dec 22, 2021
4449ac6
now with tests
kcibul Dec 23, 2021
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsExtractCallset.wdl
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Expand Up @@ -43,7 +43,7 @@ workflow GvsExtractCallset {

String output_file_base_name
String? output_gcs_dir
File? gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20211217/gatk-package-4.2.0.0-448-gff251d6-SNAPSHOT-local.jar"
File? gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/kc_fix_type_20211222/gatk-package-4.2.0.0-451-gbfb465a-SNAPSHOT-local.jar"
Int local_disk_for_extract = 150

String fq_samples_to_extract_table = "~{data_project}.~{default_dataset}.~{extract_table_prefix}__SAMPLES"
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2 changes: 1 addition & 1 deletion scripts/variantstore/wdl/GvsImportGenomes.wdl
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Expand Up @@ -17,7 +17,7 @@ workflow GvsImportGenomes {
Int batch_size = 1

Int? preemptible_tries
File? gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/ah_var_store_20211217/gatk-package-4.2.0.0-448-gff251d6-SNAPSHOT-local.jar"
File? gatk_override = "gs://broad-dsp-spec-ops/scratch/bigquery-jointcalling/jars/kc_fix_type_20211222/gatk-package-4.2.0.0-451-gbfb465a-SNAPSHOT-local.jar"
String? docker
}

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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/CreateVariantIngestFiles.java
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Expand Up @@ -279,7 +279,7 @@ public void onTraversalStart() {
private TableSchema getLoadStatusTableSchema() {
TableSchema.Builder builder = TableSchema.newBuilder();
builder.addFields(
TableFieldSchema.newBuilder().setName(SchemaUtils.SAMPLE_ID_FIELD_NAME).setType(TableFieldSchema.Type.NUMERIC).setMode(TableFieldSchema.Mode.REQUIRED).build()
TableFieldSchema.newBuilder().setName(SchemaUtils.SAMPLE_ID_FIELD_NAME).setType(TableFieldSchema.Type.INT64).setMode(TableFieldSchema.Mode.REQUIRED).build()
);
builder.addFields(
TableFieldSchema.newBuilder().setName(SchemaUtils.LOAD_STATUS_FIELD_NAME).setType(TableFieldSchema.Type.STRING).setMode(TableFieldSchema.Mode.REQUIRED).build()
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3 changes: 2 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/utils/bigquery/PendingBQWriter.java
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Expand Up @@ -3,6 +3,7 @@
import com.google.cloud.bigquery.storage.v1beta2.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.broadinstitute.hellbender.exceptions.GATKException;

public class PendingBQWriter extends CommittedBQWriter {
static final Logger logger = LogManager.getLogger(PendingBQWriter.class);
Expand All @@ -15,7 +16,7 @@ public void flushBuffer() {
try {
writeJsonArray(0);
} catch (Exception ex) {
logger.error("Caught exception writing last records on close", ex);
throw new GATKException("Caught exception writing last records on close of " + writeStream.getName(), ex);
}
}

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