Disentangle non-GVS code from GVS code [VS-834]

broadinstitute · Mar 1, 2023 · 5976e35 · 5976e35
1 parent 6f747d0
commit 5976e35
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Showing 2 changed files with 1 addition and 16 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/bigquery/BigQueryUtils.java
@@ -6,7 +6,6 @@
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.broadinstitute.hellbender.exceptions.GATKException;
-import org.broadinstitute.hellbender.tools.gvs.common.SchemaUtils;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -451,19 +450,6 @@ public static StorageAPIAvroReaderAndBigQueryStatistics executeQueryWithStorageA
         return new StorageAPIAvroReaderAndBigQueryStatistics(new StorageAPIAvroReader(tr), bigQueryResultAndStatistics.queryStatistics);
     }
 
-    public static boolean doRowsExistFor(String projectID, String datasetName, String tableName, String sampleId) {
-        String template = "SELECT COUNT(*) FROM `%s.%s.%s` WHERE %s = %s";
-        String query = String.format(template, projectID, datasetName, tableName, SchemaUtils.SAMPLE_ID_FIELD_NAME, sampleId);
-
-        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 sample id %s",
-                projectID, datasetName, tableName, sampleId));
-    }
-
     private static StatusRuntimeException extractCausalStatusRuntimeExceptionOrThrow(Throwable original, Throwable current) {
         if (current == null) {
             throw new GATKException("No causal StatusRuntimeException found", original);

diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVCFHeaderLines.java
@@ -2,7 +2,6 @@
 
 import htsjdk.variant.vcf.*;
 
-import org.broadinstitute.hellbender.tools.gvs.common.CommonCode;
 import org.broadinstitute.hellbender.tools.walkers.annotator.*;
 import org.broadinstitute.hellbender.utils.Utils;
 
@@ -77,7 +76,7 @@ public static VCFFormatHeaderLine getEquivalentFormatHeaderLine(final String inf
         addFilterLine(new VCFFilterHeaderLine(VCFConstants.PASSES_FILTERS_v4, "Site contains at least one allele that passes filters"));
 
         addFilterLine(new VCFFilterHeaderLine(NAY_FROM_YNG, "Considered a NAY in the Yay, Nay, Grey table"));
-        addFilterLine(new VCFFilterHeaderLine(EXCESS_ALLELES,"Site has an excess of alternate alleles based on the input threshold (default is " + CommonCode.EXCESS_ALLELES_THRESHOLD + ")"));
+        addFilterLine(new VCFFilterHeaderLine(EXCESS_ALLELES,"Site has an excess of alternate alleles based on the input threshold"));
         addFilterLine(new VCFFilterHeaderLine(NO_HQ_GENOTYPES, "Site has no high quality variant genotypes"));
         addFilterLine(new VCFFilterHeaderLine(EXCESS_HET_KEY, "Site has excess het value larger than the threshold"));