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Handle CTX_PP/QQ and CTX_PQ/QP CPX_TYPE values in SVConcordance #8885

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merged 5 commits into from
Jul 1, 2024
Merged

Handle CTX_PP/QQ and CTX_PQ/QP CPX_TYPE values in SVConcordance #8885

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223a974
handle CTX_PP/QQ and CTX_PQ/QP CPX_TYPE values in SVConcordance
epiercehoffman Jun 21, 2024
62ed784
map cpx type back to string & delete redundant getCpxSubtype()
epiercehoffman Jun 24, 2024
0b779dd
capitalize map name
epiercehoffman Jun 27, 2024
36448cb
SVCallRecord add CPX_TYPE if exists, not just if SVTYPE==CPX
epiercehoffman Jun 28, 2024
808d708
add unit test for SVCallRecord create from CTX variant
epiercehoffman Jun 28, 2024
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6 changes: 5 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/sv/SVCallRecordUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -426,10 +426,14 @@ public static List<String> getAlgorithms(final VariantContext variant) {

public static GATKSVVCFConstants.ComplexVariantSubtype getComplexSubtype(final VariantContext variant) {
Utils.nonNull(variant);
final String subtypeString = variant.getAttributeAsString(GATKSVVCFConstants.CPX_TYPE, null);
String subtypeString = variant.getAttributeAsString(GATKSVVCFConstants.CPX_TYPE, null);
if (subtypeString == null) {
return null;
}
else {
// replace / in CTX_PP/QQ and CTX_PQ/QP with _ to match ComplexVariantSubtype constants which cannot contain slashes
subtypeString = subtypeString.replace("/", "_");
}
if (!VALID_CPX_SUBTYPES.contains(subtypeString)) {
throw new IllegalArgumentException("Invalid CPX subtype: " + subtypeString + ", valid values are: " +
String.join(", ", VALID_CPX_SUBTYPES));
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8 changes: 2 additions & 6 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVAnnotateEngine.java
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Expand Up @@ -9,6 +9,7 @@
import org.broadinstitute.hellbender.exceptions.UserException;
import org.broadinstitute.hellbender.tools.spark.sv.utils.GATKSVVCFConstants;
import org.broadinstitute.hellbender.tools.spark.sv.utils.SVUtils;
import org.broadinstitute.hellbender.tools.sv.SVCallRecordUtils;
import org.broadinstitute.hellbender.utils.SVInterval;
import org.broadinstitute.hellbender.utils.SVIntervalTree;
import org.broadinstitute.hellbender.utils.SimpleInterval;
Expand Down Expand Up @@ -862,12 +863,7 @@ protected static boolean includesDispersedDuplication(final GATKSVVCFConstants.C
protected Map<String, Object> annotateStructuralVariant(final VariantContext variant) {
final Map<String, Set<String>> variantConsequenceDict = new HashMap<>();
final GATKSVVCFConstants.StructuralVariantAnnotationType overallSVType = getSVType(variant);
final String complexTypeString = variant.getAttributeAsString(GATKSVVCFConstants.CPX_TYPE, null);
GATKSVVCFConstants.ComplexVariantSubtype complexType = null;
if (complexTypeString != null) {
// replace / in CTX_PP/QQ and CTX_PQ/QP with _ to match ComplexVariantSubtype constants which cannot contain slashes
complexType = GATKSVVCFConstants.ComplexVariantSubtype.valueOf(complexTypeString.replace("/", "_"));
}
final GATKSVVCFConstants.ComplexVariantSubtype complexType = SVCallRecordUtils.getComplexSubtype(variant);
final boolean includesDispersedDuplication = includesDispersedDuplication(complexType, COMPLEX_SUBTYPES_WITH_DISPERSED_DUP);
final List<SVSegment> svSegmentsForGeneOverlaps = getSVSegments(variant, overallSVType, maxBreakendLen, complexType);

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53 changes: 53 additions & 0 deletions src/test/java/org/broadinstitute/hellbender/tools/sv/SVCallRecordUtilsUnitTest.java
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Expand Up @@ -583,4 +583,57 @@ public void testCreate(final VariantContext variant, final SVCallRecord expected
final SVCallRecord resultKeepAttr = SVCallRecordUtils.create(variant, true);
SVTestUtils.assertEqualsExceptExcludedAttributes(resultKeepAttr, expected, Collections.emptyList());
}

@DataProvider(name = "testGetComplexSubtypeData")
public Object[][] testGetComplexSubtypeData() {
return new Object[][]{
{new VariantContextBuilder()
.source("source")
.id("id")
.chr("chr1")
.start(2000)
.stop(3000)
.alleles(Arrays.asList(Allele.REF_N, Allele.create("<CPX>", false)))
.attributes(Map.of(
GATKSVVCFConstants.SVTYPE, GATKSVVCFConstants.StructuralVariantAnnotationType.CPX,
GATKSVVCFConstants.CPX_TYPE, "dupINVdup"
))
.make(),
GATKSVVCFConstants.ComplexVariantSubtype.dupINVdup
},
{new VariantContextBuilder()
.source("source")
.id("id")
.chr("chr1")
.start(2000)
.stop(3000)
.alleles(Arrays.asList(Allele.REF_N, Allele.create("<CPX>", false)))
.attributes(Map.of(
GATKSVVCFConstants.SVTYPE, GATKSVVCFConstants.StructuralVariantAnnotationType.CPX,
GATKSVVCFConstants.CPX_TYPE, "CTX_PP/QQ"
))
.make(),
GATKSVVCFConstants.ComplexVariantSubtype.CTX_PP_QQ
},
{new VariantContextBuilder()
.source("source")
.id("id")
.chr("chr1")
.start(2000)
.stop(3000)
.alleles(Arrays.asList(Allele.REF_N, Allele.create("<DEL>", false)))
.attributes(Map.of(
GATKSVVCFConstants.SVTYPE, GATKSVVCFConstants.StructuralVariantAnnotationType.DEL
))
.make(),
null
}
};
}

@Test(dataProvider= "testGetComplexSubtypeData")
public void testGetComplexSubtype(final VariantContext variant, final GATKSVVCFConstants.ComplexVariantSubtype expected) {
final GATKSVVCFConstants.ComplexVariantSubtype actual = SVCallRecordUtils.getComplexSubtype(variant);
Assert.assertEquals(actual, expected);
}
}
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