add error message for when tree-score-threshold is set in ReblockGVCF…

…s without TREE_SCORE present
broadinstitute · Feb 22, 2023 · b8c39dd · b8c39dd
1 parent b7f24ff
commit b8c39dd
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diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java
@@ -211,6 +211,12 @@ public void onTraversalStart() {
         }
 
         final VCFHeader inputHeader = getHeaderForVariants();
+
+        if (treeScoreThreshold > 0 && !inputHeader.getInfoHeaderLines().contains(GATKVCFConstants.TREE_SCORE)) {
+            throw new UserException("-" + TREE_SCORE_THRESHOLD_LONG_NAME + " is set to value greater than 0: " + treeScoreThreshold
+                + ", but the " + GATKVCFConstants.TREE_SCORE + " annotation is not present in the input GVCF.");
+        }
+
         final Set<VCFHeaderLine> inputHeaders = inputHeader.getMetaDataInSortedOrder();
 
         final Set<VCFHeaderLine> headerLines = new HashSet<>(inputHeaders);

diff --git a/.../org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java b/.../org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java
@@ -503,4 +503,18 @@ public void testFirstPositionOnContigNotDropped() {
         Assert.assertEquals(outVCs.get(1).getContig(), "chr13");
         Assert.assertEquals(outVCs.get(1).getStart(), 18173860);
     }
+
+    @Test
+    public void testTreeScoreWithNoAnnotation() {
+        final File output = createTempFile("reblockedgvcf", ".vcf");
+
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.add("V", largeFileTestDir + "NA12878.prod.chr20snippet.g.vcf.gz")
+                .addOutput(output)
+                .addReference(b37_reference_20_21)
+                .add(ReblockGVCF.TREE_SCORE_THRESHOLD_LONG_NAME, 0.3)
+                .add("do-qual-approx", true);
+
+        Assert.assertThrows(UserException.class, () -> runCommandLine(args));
+    }
 }