private boolean sameVariant(Variant variant, Variant other) { return variant.getChromosome().equals(other.getChromosome()) && variant.getStart().equals(other.getStart()) && variant.getReference().equals(other.getReference()) && variant.getAlternate().equals(other.getAlternate()); }
private boolean potentialCodingSNVOverlap(Variant variant1, Variant variant2) { return Math.abs(variant1.getStart() - variant2.getStart()) < 3 && variant1.getChromosome().equals(variant2.getChromosome()) && variant1.getType().equals(VariantType.SNV) && variant2.getType().equals(VariantType.SNV) && samePhase(variant1, variant2); }
private boolean potentialCodingSNVOverlap(Variant variant1, Variant variant2) { return Math.abs(variant1.getStart() - variant2.getStart()) < 3 && variant1.getChromosome().equals(variant2.getChromosome()) && variant1.getType().equals(VariantType.SNV) && variant2.getType().equals(VariantType.SNV) && samePhase(variant1, variant2); }
public static boolean isSameVariant(Variant a, AlternateCoordinate b){ return StringUtils.equals(a.getChromosome(), b.getChromosome()) && a.getStart().equals(b.getStart()) && a.getEnd().equals(b.getEnd()) && StringUtils.equals(a.getReference(), b.getReference()) && StringUtils.equals(a.getAlternate(), b.getAlternate()); }
private void addVariant(Variant variant) { String chromosome = variant.getChromosome(); // Remap studyId and fileId StudyEntry studyEntry = variant.getStudies().get(0); studyEntry.setStudyId(studyId); studyEntry.getFiles().get(0).setFileId(fileId); long[] coveredSlicePositions = getCoveredSlicePositions(variant); for (long slicePos : coveredSlicePositions) { addVariant(variant, chromosome, slicePos); } }
private void addVariant(Variant var) { String chromosome = var.getChromosome(); long[] coveredSlicePositions = getCoveredSlicePositions(var); for (long slicePos : coveredSlicePositions) { String blockKey = keyFactory.generateBlockId(helper.getFileId(), chromosome, slicePos); addVariant(blockKey, var); } }
private Put buildSampleIndexPut(Variant variant, Put put, Integer sampleId, String gt) { Put sampleIndexPut = new Put( SampleIndexConverter.toRowKey(sampleId, variant.getChromosome(), variant.getStart()), put.getTimeStamp()); sampleIndexPut.addColumn(helper.getColumnFamily(), SampleIndexConverter.toPendingColumn(variant, gt), null); return sampleIndexPut; }
public VariantStatsWrapper(Variant variant, Map<String, VariantStats> cohortStats) { this.chromosome = variant.getChromosome(); this.start = variant.getStart(); this.end = variant.getEnd(); this.reference = variant.getReference(); this.alternate = variant.getAlternate(); this.sv = variant.getSv(); this.cohortStats = cohortStats; }
@Test public void testAnnotateRegion() throws Exception { annotate(new Query(VariantQueryParam.REGION.key(), "22"), new QueryOptions()); checkAnnotation(v -> v.getChromosome().equals("22")); annotate(new Query(VariantQueryParam.REGION.key(), "1"), new QueryOptions()); checkAnnotation(v -> v.getChromosome().equals("22") || v.getChromosome().equals("1")); }
public void writeVariant(MongoDBVariantStageConverterTask converterTask, MongoDBVariantStageLoader loader, String variantStr) { Variant variant = new Variant(variantStr); variant.setNames(Collections.emptyList()); StudyEntry studyEntry = new StudyEntry("1", "1"); studyEntry.setFormat(Collections.emptyList()); variant.addStudyEntry(studyEntry); variantMap.put(variant.getChromosome(), variant); loader.write(converterTask.apply(Collections.singletonList(variant))); }
private Region startBreakpointToRegion(Variant variant) { if (imprecise && variant.getSv() != null) { return new Region(variant.getChromosome(), variant.getSv().getCiStartLeft() != null ? variant.getSv().getCiStartLeft() - svExtraPadding : variant.getStart(), variant.getSv().getCiStartRight() != null ? variant.getSv().getCiStartRight() + svExtraPadding : variant.getStart()); } else { return new Region(variant.getChromosome(), variant.getStart(), variant.getStart()); } }
public static Variant asVariant(Variant v) { Variant variant = new Variant(v.getChromosome(), v.getStart(), v.getEnd(), v.getReference(), v.getAlternate(), v.getStrand()); variant.setType(v.getType()); return variant; }
private Region startBreakpointToRegion(Variant variant) { if (imprecise && variant.getSv() != null) { return new Region(variant.getChromosome(), variant.getSv().getCiStartLeft() != null ? variant.getSv().getCiStartLeft() - svExtraPadding : variant.getStart(), variant.getSv().getCiStartRight() != null ? variant.getSv().getCiStartRight() + svExtraPadding : variant.getStart()); } else { return new Region(variant.getChromosome(), variant.getStart(), variant.getStart()); } }
@Override protected void assertValidStats(Variant variant, VariantStats variantStats) { assertNotEquals("Stats seem with no valid values, for instance (chr=" + variant.getChromosome() + ", start=" + variant.getStart() + ", ref=" + variant.getReference() + ", alt=" + variant.getAlternate() + "), gtc=" + variantStats.getGenotypeCount().toString(), 0, variantStats.getGenotypeCount().size()); } }
public static Matcher<VariantAnnotation> at(final String variant) { Variant v = new Variant(variant); return allOf(with("chromosome", VariantAnnotation::getChromosome, is(v.getChromosome())), with("position", VariantAnnotation::getStart, is(v.getStart())), with("reference", VariantAnnotation::getReference, is(v.getReference())), with("alternate", VariantAnnotation::getAlternate, is(v.getAlternate())) ); }
protected static VariantAnnotation newVariantAnnotation(Variant variant) { VariantAnnotation va; va = new VariantAnnotation(); va.setChromosome(variant.getChromosome()); va.setReference(variant.getReference()); va.setAlternate(variant.getAlternate()); va.setStart(variant.getStart()); va.setEnd(variant.getEnd()); return va; }
protected void assertValidStats(Variant variant, VariantStats variantStats) { assertNotEquals("Stats seem with no valid values, for instance (chr=" + variant.getChromosome() + ", start=" + variant.getStart() + ", ref=" + variant.getReference() + ", alt=" + variant.getAlternate() + "), maf=" + variantStats.getMaf(), -1, variantStats.getMaf(), 0.001); } }
private Variant createVariantSecAlt(String varString, String secAlt) { Variant secAltVar = new Variant(secAlt); Variant variant = new Variant(varString); StudyEntry se = new StudyEntry("1"); AlternateCoordinate ac = new AlternateCoordinate( secAltVar.getChromosome(), secAltVar.getStart(), secAltVar.getEnd(), secAltVar.getReference(), secAltVar.getAlternate(), secAltVar.getType()); se.setSecondaryAlternates(Collections.singletonList(ac)); variant.setStudies(Collections.singletonList(se)); return variant; }
private Variant convert(org.opencb.biodata.models.variant.Variant var) { Variant build = Variant.newBuilder() .setChromosome(var.getChromosome()) .setStart(var.getStart()) .setEnd(var.getEnd()) .setLength(var.getLength()) .setReference(var.getReference()) .setAlternate(var.getAlternate()) .addAllIds(var.getIds()) .build(); return build; }
private static AlternateCoordinate copyAlt(Variant var, AlternateCoordinate orig) { AlternateCoordinate copy = new AlternateCoordinate(); copy.setChromosome(orig.getChromosome() == null ? var.getChromosome() : orig.getChromosome()); copy.setStart(orig.getStart() == null ? var.getStart() : orig.getStart()); copy.setEnd(orig.getEnd() == null ? var.getEnd() : orig.getEnd()); copy.setReference(orig.getReference() == null ? var.getReference() : orig.getReference()); copy.setAlternate(orig.getAlternate() == null ? var.getAlternate() : orig.getAlternate()); copy.setType(orig.getType() == null ? var.getType() : orig.getType()); return copy; }