ReblockGVCFs cleanup

src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCF.java

@@ -108,6 +108,7 @@ public final class ReblockGVCF extends MultiVariantWalker {
     public static final String RGQ_THRESHOLD_SHORT_NAME = "rgq-threshold";
     public static final String TREE_SCORE_THRESHOLD_LONG_NAME = "tree-score-threshold-to-no-call";
     public static final String ANNOTATIONS_TO_KEEP_LONG_NAME = "annotations-to-keep";
+    public static final String ANNOTATIONS_TO_REMOVE_LONG_NAME = "format-annotations-to-remove";
     public static final String KEEP_ALL_ALTS_ARG_NAME = "keep-all-alts";
     public static final String QUAL_APPROX_LONG_NAME = "do-qual-score-approximation";
     public static final String QUAL_APPROX_SHORT_NAME = "do-qual-approx";
@@ -154,6 +155,10 @@ public final class ReblockGVCF extends MultiVariantWalker {
     @Argument(fullName=ANNOTATIONS_TO_KEEP_LONG_NAME, doc="Annotations that are not recognized by GATK to keep, that should be kept in final GVCF at variant sites.", optional = true)
     private List<String> annotationsToKeep = new ArrayList<>();
 
+    @Advanced
+    @Argument(fullName=ANNOTATIONS_TO_REMOVE_LONG_NAME, doc="FORMAT level annotations to remove from all genotypes in final GVCF.", optional = true)
+    private List<String> annotationsToRemove = new ArrayList<>();
+
     @Advanced
     @Argument(fullName=QUAL_APPROX_LONG_NAME, shortName=QUAL_APPROX_SHORT_NAME, doc="Add necessary INFO field annotation to perform QUAL approximation downstream; required for GnarlyGenotyper", optional = true)
     protected boolean doQualApprox = false;
@@ -227,6 +232,9 @@ public void onTraversalStart() {
                 + ", but the " + GATKVCFConstants.TREE_SCORE + " annotation is not present in the input GVCF.");
         }
 
+        List<String> missingAnnotationsToRemove = annotationsToRemove.stream().filter(a -> inputHeader.getFormatHeaderLine(a)==null).toList();
+        missingAnnotationsToRemove.forEach(a -> logger.warn("FORMAT level annotation " + a + ", which was requested to be removed by --" + ANNOTATIONS_TO_REMOVE_LONG_NAME + ", not found in input GVCF header."));
+
         final Set<VCFHeaderLine> inputHeaders = inputHeader.getMetaDataInSortedOrder();
 
         final Set<VCFHeaderLine> headerLines = new HashSet<>(inputHeaders);
@@ -317,7 +325,27 @@ protected void createAnnotationEngine() {
     // get VariantContexts from input gVCFs and regenotype
     @Override
     public void apply(VariantContext variant, ReadsContext reads, ReferenceContext ref, FeatureContext features) {
-        regenotypeVC(variant);
+        if (!variant.hasAllele(Allele.NON_REF_ALLELE)) {
+            throw new GATKException("Variant Context at " + variant.getContig() + ":" + variant.getStart() + " does not contain a <NON-REF> allele. This tool is only intended for use with GVCFs.");
+        }
+        VariantContext newVC = annotationsToRemove.size() > 0 ? vcFormatAnnotationsRemoved(variant) : variant;
+        regenotypeVC(newVC);
+    }
+
+    /**
+     * Remove format level annotations from genotype in variant context.
+     *
+     * @param vc variant context to remove format annotations from
+     * @return variant context with format annotations removed from genotype
+     */
+    private VariantContext vcFormatAnnotationsRemoved(final VariantContext vc) {
+        final Genotype genotype = vc.getGenotype(0);
+        Map<String, Object> extendedAttributes = genotype.getExtendedAttributes();
+        for (String annotation : annotationsToRemove) {
+            extendedAttributes.remove(annotation);
+        }
+        final Genotype newGenotype = new GenotypeBuilder(genotype).noAttributes().attributes(extendedAttributes).make();
+        return new VariantContextBuilder(vc).genotypes(newGenotype).make();
     }
 
     /**

src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/ReblockGVCFIntegrationTest.java

@@ -9,6 +9,7 @@
 import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
 import org.broadinstitute.hellbender.engine.FeatureDataSource;
+import org.broadinstitute.hellbender.exceptions.GATKException;
 import org.broadinstitute.hellbender.exceptions.UserException;
 import org.broadinstitute.hellbender.testutils.ArgumentsBuilder;
 import org.broadinstitute.hellbender.testutils.CommandLineProgramTester;
@@ -575,4 +576,35 @@ public void testFilters() throws IOException {
         Assert.assertFalse(filteredRefBlockVC.isFiltered()); // Ref block is unfiltered even though the input RefBlock and low qual variant were both filtered
         Assert.assertEquals(filteredRefBlockVC.getGenotype(0).getDP(), 12); // Ref block is combination of filtered variant with depth 22 and filtered ref block with depth 1
     }
+
+    @Test
+    public void testRemovingFormatAnnotations() {
+        final File input = getTestFile("dragen.g.vcf");
+        final File output = createTempFile("reblockedgvcf", ".vcf");
+        final String priKey = "PRI";
+
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.addReference(new File(hg38Reference))
+                .add("V", input)
+                .add(ReblockGVCF.ANNOTATIONS_TO_REMOVE_LONG_NAME, priKey)
+                .addOutput(output);
+        runCommandLine(args);
+
+        final List<VariantContext> outVCs = VariantContextTestUtils.readEntireVCFIntoMemory(output.getAbsolutePath()).getRight();
+        for(VariantContext vc : outVCs){
+            Assert.assertNull(vc.getGenotype(0).getExtendedAttribute(priKey));
+        }
+    }
+
+    @Test
+    public void testNonGVCFInput() {
+        final File output = createTempFile("reblockedgvcf", ".vcf");
+
+        final ArgumentsBuilder args = new ArgumentsBuilder();
+        args.addReference(new File(b37_reference_20_21))
+                .add("V", "src/test/resources/large/NA12878.HiSeq.WGS.b37_decoy.indel.recalibrated.chr20.vcf")
+                .addOutput(output);
+
+        Assert.assertThrows(GATKException.class, () -> runCommandLine(args));
+    }
 }