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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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Move rather than delete GVS BigQuery classes
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@mcovarr
mcovarr committed Jun 26, 2023
commit e7edf9eef22c902fc4c4216b202982d6a6e145cd
2 changes: 1 addition & 1 deletion ...bigquery/BigQueryResultAndStatistics.java → ...bigquery/BigQueryResultAndStatistics.java
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package org.broadinstitute.hellbender.utils.bigquery;
package org.broadinstitute.hellbender.utils.gvs.bigquery;

import com.google.cloud.bigquery.JobStatistics;
import com.google.cloud.bigquery.TableResult;
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2 changes: 1 addition & 1 deletion ...lbender/utils/bigquery/BigQueryUtils.java → ...der/utils/gvs/bigquery/BigQueryUtils.java
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package org.broadinstitute.hellbender.utils.bigquery;
package org.broadinstitute.hellbender.utils.gvs.bigquery;

import com.google.cloud.bigquery.*;
import io.grpc.StatusRuntimeException;
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2 changes: 1 addition & 1 deletion ...bender/utils/bigquery/GATKAvroReader.java → ...er/utils/gvs/bigquery/GATKAvroReader.java
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package org.broadinstitute.hellbender.utils.bigquery;
package org.broadinstitute.hellbender.utils.gvs.bigquery;

import htsjdk.samtools.util.CloseableIterator;
import org.apache.avro.generic.GenericRecord;
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2 changes: 1 addition & 1 deletion .../utils/bigquery/StorageAPIAvroReader.java → ...ls/gvs/bigquery/StorageAPIAvroReader.java
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package org.broadinstitute.hellbender.utils.bigquery;
package org.broadinstitute.hellbender.utils.gvs.bigquery;

import com.google.cloud.bigquery.storage.v1.AvroRows;
import com.google.cloud.bigquery.storage.v1.BigQueryReadClient;
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2 changes: 1 addition & 1 deletion ...geAPIAvroReaderAndBigQueryStatistics.java → ...geAPIAvroReaderAndBigQueryStatistics.java
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package org.broadinstitute.hellbender.utils.bigquery;
package org.broadinstitute.hellbender.utils.gvs.bigquery;

import com.google.cloud.bigquery.JobStatistics;

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2 changes: 1 addition & 1 deletion ...bender/utils/bigquery/TableReference.java → ...er/utils/gvs/bigquery/TableReference.java
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package org.broadinstitute.hellbender.utils.bigquery;
package org.broadinstitute.hellbender.utils.gvs.bigquery;

import com.google.common.collect.ImmutableList;

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2 changes: 1 addition & 1 deletion ...utils/bigquery/BigQueryUtilsUnitTest.java → ...s/gvs/bigquery/BigQueryUtilsUnitTest.java
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package org.broadinstitute.hellbender.utils.bigquery;
package org.broadinstitute.hellbender.utils.gvs.bigquery;

import com.google.cloud.bigquery.FieldValueList;
import org.apache.avro.generic.GenericRecord;
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