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fix cnvpadding param. TEST FAILING #628

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fix cnvpadding param. TEST FAILING #628

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ef4d525
fix cnvpadding param. TEST FAILING
julie-sullivan Nov 16, 2022
defbfd2
pad overlaps query too
julie-sullivan Nov 16, 2022
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9 changes: 7 additions & 2 deletions ...b/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeCalculator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
import org.opencb.commons.datastore.core.QueryOptions;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.opencb.biodata.models.variant.avro.VariantType;

import java.util.*;

Expand Down Expand Up @@ -73,7 +74,9 @@ protected void parseQueryParam(QueryOptions queryOptions) {
}

protected int getStart(int extraPadding) {
if (imprecise && variant.getSv() != null) {
if (imprecise && VariantType.CNV.equals(variant.getType())) {
return variant.getStart() - extraPadding;
} else if (imprecise && variant.getSv() != null) {
return variant.getSv().getCiStartLeft() != null ? variant.getSv().getCiStartLeft() - extraPadding
: variant.getStart();
} else {
Expand All @@ -83,7 +86,9 @@ protected int getStart(int extraPadding) {
}

protected int getEnd(int extraPadding) {
if (imprecise && variant.getSv() != null) {
if (imprecise && VariantType.CNV.equals(variant.getType())) {
return variant.getEnd() + extraPadding;
} else if (imprecise && variant.getSv() != null) {
return variant.getSv().getCiEndRight() != null ? variant.getSv().getCiEndRight() + extraPadding
: variant.getEnd();
} else {
Expand Down
6 changes: 4 additions & 2 deletions ...va/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeGenericRegionCalculator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
import org.opencb.biodata.models.core.Gene;
import org.opencb.biodata.models.core.Transcript;
import org.opencb.biodata.models.variant.Variant;
import org.opencb.biodata.models.variant.avro.VariantType;
import org.opencb.biodata.models.variant.avro.ConsequenceType;
import org.opencb.biodata.models.variant.avro.ExonOverlap;
import org.opencb.cellbase.core.ParamConstants;
Expand All @@ -43,8 +44,9 @@ public List<ConsequenceType> run(Variant inputVariant, List<Gene> geneList, bool
parseQueryParam(queryOptions);
List<ConsequenceType> consequenceTypeList = new ArrayList<>();
variant = inputVariant;
variantEnd = getEnd(svExtraPadding);
variantStart = getStart(svExtraPadding);
int extraPadding = VariantType.CNV.equals(variant.getType()) ? cnvExtraPadding : svExtraPadding;
variantEnd = getEnd(extraPadding);
variantStart = getStart(extraPadding);
// isBigDeletion = ((variantEnd - variantStart) > BIG_VARIANT_SIZE_THRESHOLD);
boolean isIntergenic = true;
for (Gene currentGene : geneList) {
Expand Down
7 changes: 5 additions & 2 deletions ...src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -587,8 +587,8 @@ private List<VariantAnnotation> runAnnotationProcess(List<Variant> normalizedVar

if (annotatorSet.contains("consequenceType")) {
try {
List<ConsequenceType> consequenceTypeList = getConsequenceTypeList(variant, affectedGenes, true, QueryOptions.empty(),
dataRelease);
List<ConsequenceType> consequenceTypeList = getConsequenceTypeList(variant, affectedGenes, true,
new QueryOptions().append("imprecise", imprecise).append("cnvExtraPadding", cnvExtraPadding), dataRelease);
variantAnnotation.setConsequenceTypes(consequenceTypeList);
if (phased) {
checkAndAdjustPhasedConsequenceTypes(variant, variantBuffer, dataRelease);
Expand Down Expand Up @@ -1308,6 +1308,9 @@ private boolean[] getRegulatoryRegionOverlaps(Variant variant) throws QueryExcep
return getRegulatoryRegionOverlaps(variant.getChromosome(), variant.getStart());
} else if (VariantType.INDEL.equals(variant.getType()) && StringUtils.isBlank(variant.getReference())) {
return getRegulatoryRegionOverlaps(variant.getChromosome(), variant.getStart() - 1, variant.getEnd());
} else if (VariantType.CNV.equals(variant.getType())) {
return getRegulatoryRegionOverlaps(variant.getChromosome(), variant.getStart() - cnvExtraPadding,
variant.getEnd() + cnvExtraPadding);
// Short deletions and symbolic variants except breakends
} else if (!VariantType.BREAKEND.equals(variant.getType())) {
return getRegulatoryRegionOverlaps(variant.getChromosome(), variant.getStart(), variant.getEnd());
Expand Down
34 changes: 34 additions & 0 deletions ...-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantAnnotationCalculatorTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -33,6 +33,7 @@
import org.opencb.cellbase.lib.GenericMongoDBAdaptorTest;
import org.opencb.cellbase.lib.variant.annotation.VariantAnnotationCalculator;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.commons.datastore.core.result.QueryResult;

import java.io.IOException;
import java.nio.file.Path;
Expand Down Expand Up @@ -1957,6 +1958,39 @@ public void testGetAllConsequenceTypesByVariant() throws IOException, QueryExcep
// }
}

@Test
// long variant should have same annotations as short variant + cnvPadding
public void testCNVExtraPadding() throws Exception {

// short variant
Variant shortVariant = new Variant("chr17:43087248-43087249:<CNV>");
// long variant
Variant longVariant = new Variant("chr17:43087248-43098506:<CNV>");

QueryOptions queryOptions = new QueryOptions("useCache", false);
queryOptions.put("include", "consequenceType, reference, alternate ,clinical");
queryOptions.put("normalize", true);
queryOptions.put("skipDecompose", false);
queryOptions.put("checkAminoAcidChange", true);
queryOptions.put("imprecise", true);
queryOptions.put("phased", false);

// long variant
CellBaseDataResult<ConsequenceType> consequenceTypeResult =
variantAnnotationCalculator.getAllConsequenceTypesByVariant(longVariant, queryOptions);
assertEquals(27, consequenceTypeResult.getNumResults());

// short variant
consequenceTypeResult = variantAnnotationCalculator.getAllConsequenceTypesByVariant(shortVariant, queryOptions);
assertEquals(27, consequenceTypeResult.getNumResults());

queryOptions.put("cnvExtraPadding", 10000);

// short variant with padding
consequenceTypeResult = variantAnnotationCalculator.getAllConsequenceTypesByVariant(shortVariant, queryOptions);
assertEquals(27, consequenceTypeResult.getNumResults());
}

private <T> void assertObjectListEquals(String expectedConsequenceTypeJson, List<T> actualList,
Class<T> clazz) throws IOException {
ObjectReader reader = jsonObjectMapper
Expand Down