static boolean onSameVariant (Variant a, Variant b){ return a.onSameRegion(b) && StringUtils.equals(a.getReference(), b.getReference()) && StringUtils.equals(a.getAlternate(), b.getAlternate()); }
public static byte[] getArchiveVariantColumn(Variant variant) { return Bytes.toBytes(VARIANT_COLUMN_PREFIX + '_' + variant.getStart() + '_' + variant.getReference() + '_' + variant.getAlternate()); }
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()); }
public static VariantStats calculateHemizygous(Variant variant, int refCount, int altCount, int missingCount) { Map<Genotype, Integer> gtCount = new HashMap<>(4); gtCount.put(new Genotype("0"), refCount); gtCount.put(new Genotype("1"), altCount); gtCount.put(new Genotype("."), missingCount); VariantStats variantStats = new VariantStats(); calculate(gtCount, variantStats, variant.getReference(), variant.getAlternate()); return variantStats; }
public static VariantStats calculate(Variant variant, int homRefCount, int hetCount, int homAltCount, int missingCount) { Map<Genotype, Integer> gtCount = new HashMap<>(4); gtCount.put(new Genotype("0/0"), homRefCount); gtCount.put(new Genotype("0/1"), hetCount); gtCount.put(new Genotype("1/1"), homAltCount); gtCount.put(new Genotype("./."), missingCount); VariantStats variantStats = new VariantStats(); calculate(gtCount, variantStats, variant.getReference(), variant.getAlternate()); return variantStats; }
public static VariantStats calculate(Variant variant, Map<Genotype, Integer> genotypeCount) { VariantStats variantStats = new VariantStats(); calculate(genotypeCount, variantStats, variant.getReference(), variant.getAlternate()); return variantStats; }
public Integer getLengthReference() { return VariantBuilder.getLengthReference(getReference(), getType(), getLength()); }
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()); }
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; }
@Override public Document convertToStorageType(Variant variant) { return new Document(ID_FIELD, idConverter.buildId(variant)) .append(REF_FIELD, variant.getReference()) // Add left and right SvInsSeq to the alternate .append(ALT_FIELD, idConverter.buildSVAlternate(variant.getAlternate(), variant.getSv())) .append(END_FIELD, variant.getEnd()); }
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; }
@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())) ); }
@Test public void testProcessLine() throws Exception { List<Variant> vars = reader.read(); assertEquals("Expect only one Variant inline",1,vars.size()); Variant variant = vars.get(0); assertEquals("Reference wrong", "T", variant.getReference()); assertEquals("Alt wrong", "A", variant.getAlternate()); vars = reader.read(22); assertEquals("Expect only one Variant inline",22,vars.size()); }
@Test public void resolveSameVariantWithSecAlt() throws Exception { Variant a = getVariant("2:10048155:TCTTTTTTTT:AC", "PASS", "220", "1/2"); Variant b = getVariant("2:10048155:TCTTTTTTTT:-", "PASS", "220", "2/1"); a.getStudies().get(0).getSecondaryAlternates().add(new AlternateCoordinate("2", b.getStart(), b.getEnd(), b.getReference(), b.getAlternate(), INDEL)); a.getStudies().get(0).getFiles().get(0).setCall("10048155:TTCTTTTTTTT:TAC,T:0"); b.getStudies().get(0).getSecondaryAlternates().add(new AlternateCoordinate("2", a.getStart(), a.getEnd(), a.getReference(), a.getAlternate(), INDEL)); b.getStudies().get(0).getFiles().get(0).setCall("10048155:TTCTTTTTTTT:TAC,T:1"); Collection<Variant> resolved = new VariantLocalConflictResolver().resolveConflicts(Arrays.asList(a, b)); assertEquals(1, resolved.size()); }
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; }