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EVA-3829 update variant vcf factory to handle non variant in case of mulitple alternates #109

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Merged
nitin-ebi merged 1 commit into from
Jun 23, 2025
Merged

EVA-3829 update variant vcf factory to handle non variant in case of mulitple alternates #109

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6 changes: 5 additions & 1 deletion ...ons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -108,6 +108,10 @@ public List<Variant> create(String fileId, String studyId, String line)
}
}

if (variants.isEmpty()) {
throw new NonVariantException("No valid variants could be found");
}

return variants;
}

Expand Down Expand Up @@ -211,7 +215,7 @@ protected void setOtherFields(Variant variant, String fileId, String studyId, Se
}
if (quality > -1) {
variant.getSourceEntry(fileId, studyId)
.addAttribute("QUAL", String.valueOf(quality));
.addAttribute("QUAL", String.valueOf(quality));
}
if (!filter.isEmpty()) {
variant.getSourceEntry(fileId, studyId).addAttribute("FILTER", filter);
Expand Down
13 changes: 7 additions & 6 deletions ...est/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactoryTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
import org.junit.rules.ExpectedException;
import uk.ac.ebi.eva.commons.core.models.VariantStatistics;
import uk.ac.ebi.eva.commons.core.models.factories.exception.IncompleteInformationException;
import uk.ac.ebi.eva.commons.core.models.factories.exception.NonVariantException;
import uk.ac.ebi.eva.commons.core.models.genotype.Genotype;
import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;

Expand Down Expand Up @@ -136,8 +137,8 @@ public void getGenotype() {
public void variantWithAlleleFrequencyZero() {
String line = "1\t10040\trs123\tT\tC\t.\t.\tAF=0";

List<Variant> variantList = factory.create(FILE_ID, STUDY_ID, line);
assertTrue(variantList.isEmpty());
thrown.expect(NonVariantException.class);
factory.create(FILE_ID, STUDY_ID, line);
}

@Test
Expand All @@ -154,8 +155,8 @@ public void multiallelicWithAlleleFrequencyZero() {
public void variantWithAlleleCountZero() {
String line = "1\t10040\trs123\tT\tC\t.\t.\tAN=5;AC=0";

List<Variant> variantList = factory.create(FILE_ID, STUDY_ID, line);
assertTrue(variantList.isEmpty());
thrown.expect(NonVariantException.class);
factory.create(FILE_ID, STUDY_ID, line);
}

@Test
Expand All @@ -172,8 +173,8 @@ public void multiAlleleWithOneAlleleCountZero() {
public void variantWithAlleleTotalNumberZero() {
String line = "1\t10040\trs123\tT\tC\t.\t.\tAN=0;AC=5";

List<Variant> variantList = factory.create(FILE_ID, STUDY_ID, line);
assertTrue(variantList.isEmpty());
thrown.expect(NonVariantException.class);
factory.create(FILE_ID, STUDY_ID, line);
}

@Test
Expand Down
21 changes: 11 additions & 10 deletions ...test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactoryTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.ExpectedException;
import uk.ac.ebi.eva.commons.core.models.factories.exception.NonVariantException;
import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
import uk.ac.ebi.eva.commons.core.models.pipeline.VariantSourceEntry;

Expand Down Expand Up @@ -432,40 +433,40 @@ public void testMultiallelicVariantWitnNoSampleInformation() {
public void variantWithNoAltGenotypes() {
String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t0/0\t0|0\t./.\t0|0\t./.";

List<Variant> variantList = factory.create(FILE_ID, STUDY_ID, line);
assertTrue(variantList.isEmpty());
thrown.expect(NonVariantException.class);
factory.create(FILE_ID, STUDY_ID, line);
}

@Test
public void haploidVariantWithNoAltGenotypes() {
String line = "Y\t10040\trs123\tT\tC\t.\t.\t.\tGT\t.\t0\t0\t.";

List<Variant> variantList = factory.create(FILE_ID, STUDY_ID, line);
assertTrue(variantList.isEmpty());
thrown.expect(NonVariantException.class);
factory.create(FILE_ID, STUDY_ID, line);
}

@Test
public void triploidVariantWithNoAltGenotypes() {
String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t0/0/0\t0|0|0\t././.\t0|0|0\t././.";

List<Variant> variantList = factory.create(FILE_ID, STUDY_ID, line);
assertTrue(variantList.isEmpty());
thrown.expect(NonVariantException.class);
factory.create(FILE_ID, STUDY_ID, line);
}

@Test
public void variantWhereAllGenotypesAreMissingValues() {
String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t./.\t./.\t./.\t./.\t./.";

List<Variant> variantList = factory.create(FILE_ID, STUDY_ID, line);
assertTrue(variantList.isEmpty());
thrown.expect(NonVariantException.class);
factory.create(FILE_ID, STUDY_ID, line);
}

@Test
public void variantWhereAllGenotypesAreReference() {
String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t0/0\t0|0\t0/0\t0|0\t0/0";

List<Variant> variantList = factory.create(FILE_ID, STUDY_ID, line);
assertTrue(variantList.isEmpty());
thrown.expect(NonVariantException.class);
factory.create(FILE_ID, STUDY_ID, line);
}

@Test
Expand Down
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