Add FILTER and QUAL fields to SVCallRecord

src/main/java/org/broadinstitute/hellbender/tools/sv/SVCallRecord.java

@@ -52,6 +52,8 @@ public class SVCallRecord implements SVLocatable {
     private final List<Allele> altAlleles;
     private final GenotypesContext genotypes;
     private final Map<String,Object> attributes;
+    private final Set<String> filters;
+    private final Double log10PError;
 
     // CPX related fields
     private final GATKSVVCFConstants.ComplexVariantSubtype cpxSubtype;
@@ -70,8 +72,10 @@ public SVCallRecord(final String id,
                         final List<Allele> alleles,
                         final List<Genotype> genotypes,
                         final Map<String,Object> attributes,
+                        final Set<String> filters,
+                        final Double log10PError,
                         final SAMSequenceDictionary dictionary) {
-        this(id, contigA, positionA, strandA, contigB, positionB, strandB, type, cpxSubtype, length, algorithms, alleles, genotypes, attributes);
+        this(id, contigA, positionA, strandA, contigB, positionB, strandB, type, cpxSubtype, length, algorithms, alleles, genotypes, attributes, filters, log10PError);
         validateCoordinates(dictionary);
     }
 
@@ -88,11 +92,14 @@ protected SVCallRecord(final String id,
                            final List<String> algorithms,
                            final List<Allele> alleles,
                            final List<Genotype> genotypes,
-                           final Map<String, Object> attributes) {
+                           final Map<String, Object> attributes,
+                           final Set<String> filters,
+                           final Double log10PError) {
         Utils.nonNull(algorithms);
         Utils.nonNull(alleles);
         Utils.nonNull(genotypes);
         Utils.nonNull(attributes);
+        Utils.nonNull(filters);
         this.id = Utils.nonNull(id);
         this.contigA = contigA;
         this.positionA = positionA;
@@ -112,6 +119,8 @@ protected SVCallRecord(final String id,
         final Pair<Boolean, Boolean> strands = inferStrands(type, strandA, strandB);
         this.strandA = strands.getLeft();
         this.strandB = strands.getRight();
+        this.filters = filters;
+        this.log10PError = log10PError;
     }
 
     /**
@@ -366,4 +375,16 @@ public SimpleInterval getPositionAInterval() {
     public SimpleInterval getPositionBInterval() {
         return new SimpleInterval(contigB, positionB, positionB);
     }
+
+    public Set<String> getFilters() {
+        return filters;
+    }
+
+    public Double getLog10PError() {
+        return log10PError;
+    }
+
+    public GATKSVVCFConstants.ComplexVariantSubtype getCpxSubtype() {
+        return cpxSubtype;
+    }
 }

src/main/java/org/broadinstitute/hellbender/tools/sv/SVCallRecordUtils.java

@@ -100,6 +100,13 @@ public static VariantContextBuilder getVariantBuilder(final SVCallRecord record)
                 && record.getStrandA() != null && record.getStrandB() != null) {
             builder.attribute(GATKSVVCFConstants.STRANDS_ATTRIBUTE, getStrandString(record));
         }
+        if (!record.getFilters().isEmpty()) {
+            builder.filters(record.getFilters());
+        }
+        if (record.getLog10PError() != null) {
+            builder.log10PError(record.getLog10PError());
+        }
+
         // htsjdk vcf encoder does not allow genotypes to have empty alleles
         builder.genotypes(record.getGenotypes().stream().map(SVCallRecordUtils::sanitizeEmptyGenotype).collect(Collectors.toList()));
         sanitizeNullAttributes(builder);
@@ -176,12 +183,12 @@ public static GenotypesContext populateGenotypesForMissingSamplesWithAlleles(fin
     public static SVCallRecord copyCallWithNewGenotypes(final SVCallRecord record, final GenotypesContext genotypes) {
         return new SVCallRecord(record.getId(), record.getContigA(), record.getPositionA(), record.getStrandA(), record.getContigB(),
                 record.getPositionB(), record.getStrandB(), record.getType(), record.getComplexSubtype(), record.getLength(), record.getAlgorithms(), record.getAlleles(),
-                genotypes, record.getAttributes());
+                genotypes, record.getAttributes(), record.getFilters(), record.getLog10PError());
     }
     public static SVCallRecord copyCallWithNewAttributes(final SVCallRecord record, final Map<String, Object> attr) {
         return new SVCallRecord(record.getId(), record.getContigA(), record.getPositionA(), record.getStrandA(), record.getContigB(),
                 record.getPositionB(), record.getStrandB(), record.getType(), record.getComplexSubtype(), record.getLength(), record.getAlgorithms(), record.getAlleles(),
-                record.getGenotypes(), attr);
+                record.getGenotypes(), attr, record.getFilters(), record.getLog10PError());
     }
 
     /**
@@ -293,10 +300,10 @@ public static Stream<SVCallRecord> convertInversionsToBreakends(final SVCallReco
         Utils.validateArg(record.isIntrachromosomal(), "Inversion " + record.getId() + " is not intrachromosomal");
         final SVCallRecord positiveBreakend = new SVCallRecord(record.getId(), record.getContigA(),
                 record.getPositionA(), true, record.getContigB(), record.getPositionB(), true, GATKSVVCFConstants.StructuralVariantAnnotationType.BND, null,null,
-                record.getAlgorithms(), record.getAlleles(), record.getGenotypes(), record.getAttributes(), dictionary);
+                record.getAlgorithms(), record.getAlleles(), record.getGenotypes(), record.getAttributes(), record.getFilters(), record.getLog10PError(), dictionary);
         final SVCallRecord negativeBreakend = new SVCallRecord(record.getId(), record.getContigA(),
                 record.getPositionA(), false, record.getContigB(), record.getPositionB(), false, GATKSVVCFConstants.StructuralVariantAnnotationType.BND, null,null,
-                record.getAlgorithms(), record.getAlleles(), record.getGenotypes(), record.getAttributes(), dictionary);
+                record.getAlgorithms(), record.getAlleles(), record.getGenotypes(), record.getAttributes(), record.getFilters(), record.getLog10PError(), dictionary);
         return Stream.of(positiveBreakend, negativeBreakend);
     }
 
@@ -385,10 +392,11 @@ public static SVCallRecord create(final VariantContext variant, boolean keepVari
                 positionB = variant.getEnd();
             }
         }
+        final Double log10PError = variant.hasLog10PError() ? variant.getLog10PError() : null;
 
         final Map<String, Object> sanitizedAttributes = sanitizeAttributes(attributes);
         return new SVCallRecord(id, contigA, positionA, strand1, contigB, positionB, strand2, type, cpxSubtype, length, algorithms,
-                variant.getAlleles(), variant.getGenotypes(), sanitizedAttributes);
+                variant.getAlleles(), variant.getGenotypes(), sanitizedAttributes, variant.getFilters(), log10PError);
     }
 
     private static Map<String, Object> sanitizeAttributes(final Map<String, Object> attributes) {

src/main/java/org/broadinstitute/hellbender/tools/sv/cluster/CanonicalSVCollapser.java

@@ -182,8 +182,12 @@ public SVCallRecord collapse(final SVClusterEngine.OutputCluster cluster) {
         final Boolean strandA = type == GATKSVVCFConstants.StructuralVariantAnnotationType.CNV ? null : representative.getStrandA();
         final Boolean strandB = type == GATKSVVCFConstants.StructuralVariantAnnotationType.CNV ? null : representative.getStrandB();
 
+        final Set<String> filters = collapseFilters(items);
+        final Double quality = collapseQuality(items);
+
         return new SVCallRecord(representative.getId(), representative.getContigA(), start, strandA, representative.getContigB(),
-                end, strandB, type, representative.getComplexSubtype(), length, algorithms, alleles, genotypes, attributes, dictionary);
+                end, strandB, type, representative.getComplexSubtype(), length, algorithms, alleles, genotypes, attributes,
+                filters, quality, dictionary);
     }
 
     protected List<Allele> collapseAlleles(final List<Allele> altAlleles, final Allele refAllele) {
@@ -193,6 +197,21 @@ protected List<Allele> collapseAlleles(final List<Allele> altAlleles, final Alle
         return alleles;
     }
 
+    protected Set<String> collapseFilters(final List<SVCallRecord> items) {
+        return items.stream()
+                .map(SVCallRecord::getFilters)
+                .flatMap(Collection::stream)
+                .collect(Collectors.toSet());
+    }
+
+    protected Double collapseQuality(final List<SVCallRecord> items) {
+        if (items.size() == 1) {
+            return items.get(0).getLog10PError();
+        } else {
+            return null;
+        }
+    }
+
     /**
      * Asserts that the given records are valid for collapsing.
      */

src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCluster.java

@@ -453,7 +453,8 @@ public VariantContext buildVariantContext(final SVCallRecord call) {
         // Build new variant
         final SVCallRecord finalCall = new SVCallRecord(newId, call.getContigA(), call.getPositionA(), call.getStrandA(),
                 call.getContigB(), call.getPositionB(), call.getStrandB(), call.getType(), call.getComplexSubtype(), call.getLength(),
-                call.getAlgorithms(), call.getAlleles(), filledGenotypes, call.getAttributes(), dictionary);
+                call.getAlgorithms(), call.getAlleles(), filledGenotypes, call.getAttributes(), call.getFilters(),
+                call.getLog10PError(), dictionary);
         final VariantContextBuilder builder = SVCallRecordUtils.getVariantBuilder(finalCall);
         if (omitMembers) {
             builder.rmAttribute(GATKSVVCFConstants.CLUSTER_MEMBER_IDS_KEY);

src/test/java/org/broadinstitute/hellbender/tools/sv/SVCallRecordUnitTest.java

@@ -1,6 +1,9 @@
 package org.broadinstitute.hellbender.tools.sv;
 
 import com.google.common.collect.Lists;
+import htsjdk.variant.variantcontext.Allele;
+import htsjdk.variant.variantcontext.GenotypeBuilder;
+import htsjdk.variant.variantcontext.GenotypesContext;
 import org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
@@ -73,7 +76,7 @@ public Object[][] testCreateInvalidCoordinatesData() {
     public void testCreateInvalidCoordinates(final String contigA, final int posA, final String contigB, final int posB) {
         new SVCallRecord("var1", contigA, posA, true, contigB, posB, false, GATKSVVCFConstants.StructuralVariantAnnotationType.BND,
                 null, null, SVTestUtils.PESR_ONLY_ALGORITHM_LIST, Collections.emptyList(), Collections.emptyList(),
-                Collections.emptyMap(), SVTestUtils.hg38Dict);
+                Collections.emptyMap(), Collections.emptySet(), null, SVTestUtils.hg38Dict);
         Assert.fail("Expected exception not thrown");
     }
 
@@ -90,6 +93,26 @@ public Object[][] testCreateValidCoordinatesData() {
     public void testCreateValidCoordinates(final String contigA, final int posA, final String contigB, final int posB) {
         new SVCallRecord("var1", contigA, posA, true, contigB, posB, false, GATKSVVCFConstants.StructuralVariantAnnotationType.BND,
                 null, null, SVTestUtils.PESR_ONLY_ALGORITHM_LIST, Collections.emptyList(), Collections.emptyList(),
-                Collections.emptyMap(), SVTestUtils.hg38Dict);
+                Collections.emptyMap(), Collections.emptySet(), null, SVTestUtils.hg38Dict);
+    }
+
+    public void testGetters() {
+        final SVCallRecord record = new SVCallRecord("var1", "chr1", 100, true, "chr1", 200, false, GATKSVVCFConstants.StructuralVariantAnnotationType.DEL,
+                GATKSVVCFConstants.ComplexVariantSubtype.dDUP, null, SVTestUtils.PESR_ONLY_ALGORITHM_LIST, Lists.newArrayList(Allele.REF_N, Allele.SV_SIMPLE_DEL),
+                GenotypesContext.create(GenotypeBuilder.create("sample1", Lists.newArrayList(Allele.SV_SIMPLE_DEL, Allele.SV_SIMPLE_DEL))),
+                Collections.singletonMap("TEST_KEY", "TEST_VALUE"), Collections.singleton("TEST_FILTER"), Double.valueOf(30), SVTestUtils.hg38Dict);
+        Assert.assertEquals(record.getId(), "var1");
+        Assert.assertEquals(record.getContigA(), "chr1");
+        Assert.assertEquals(record.getPositionA(), 100);
+        Assert.assertEquals(record.getStrandA(), Boolean.TRUE);
+        Assert.assertEquals(record.getContigB(), "chr1");
+        Assert.assertEquals(record.getPositionB(), 200);
+        Assert.assertEquals(record.getStrandA(), Boolean.FALSE);
+        Assert.assertEquals(record.getAlgorithms(), SVTestUtils.PESR_ONLY_ALGORITHM_LIST);
+        Assert.assertEquals(record.getGenotypes().get("sample1").getAlleles(), Lists.newArrayList(Allele.SV_SIMPLE_DEL, Allele.SV_SIMPLE_DEL));
+        Assert.assertEquals(record.getAttributes(), Collections.singletonMap("TEST_KEY", "TEST_VALUE"));
+        Assert.assertEquals(record.getAlleles(), Lists.newArrayList(Allele.REF_N, Allele.SV_SIMPLE_DEL));
+        Assert.assertEquals(record.getFilters(), Collections.singleton("TEST_FILTER"));
+        Assert.assertEquals(record.getLog10PError(), Double.valueOf(30));
     }
 }