+ breakend.getMate().getChromosome() + ':' + breakend.getMate().getPosition() + braket; break; + breakend.getMate().getChromosome() + ':' + breakend.getMate().getPosition() + braket + (StringUtils.isEmpty(breakend.getInsSeq()) ? "." : breakend.getInsSeq());
private static StructuralVariation getMateStructuralVariation(Variant variant) { StructuralVariation structuralVariation = new StructuralVariation(); // Check whether mate has CIPOS if (variant.getSv().getBreakend().getMate().getCiPositionLeft() != null && variant.getSv().getBreakend().getMate().getCiPositionRight() != null) { structuralVariation.setCiStartLeft(variant.getSv().getBreakend().getMate().getCiPositionLeft()); structuralVariation.setCiStartRight(variant.getSv().getBreakend().getMate().getCiPositionRight()); } Breakend breakend = new Breakend(new BreakendMate(variant.getChromosome(), variant.getStart(), variant.getSv().getCiStartLeft() != null ? variant.getSv().getCiStartLeft() : null, variant.getSv().getCiStartRight() != null ? variant.getSv().getCiStartRight() : null), getMateOrientation(variant), null); structuralVariation.setBreakend(breakend); return structuralVariation; }
private Variant parseBreakendPair(VariantContext variantContext, VariantContext variantContext1) { // Get Variant object for the first BND Variant variant = converter.convert(variantContext); // Set mate position variant.getSv().getBreakend().getMate().setChromosome(variantContext1.getContig()); variant.getSv().getBreakend().getMate().setPosition(variantContext1.getStart()); // Check the second BND does have CIPOS List ciposValue = variantContext1.getAttributeAsList(CIPOS); if (!ciposValue.isEmpty()) { // Get CIPOS from second BND String ciposString = StringUtils.join(ciposValue, VCFConstants.INFO_FIELD_ARRAY_SEPARATOR); // Set CIPOS string of the sencond BND as part of the file INFO field in the first BND Map<String, String> attributesMap = variant.getStudies().get(0).getFiles().get(0).getAttributes(); attributesMap.put(MATE_CIPOS, ciposString); // CIPOS of the second breakend List ciposParts = variantContext1.getAttributeAsList(CIPOS); variant.getSv() .getBreakend() .getMate() .setCiPositionLeft(variantContext1.getStart() + Integer.valueOf((String) ciposParts.get(0))); variant.getSv() .getBreakend() .getMate() .setCiPositionRight(variantContext1.getStart() + Integer.valueOf((String) ciposParts.get(1))); // If not, it's a precise call, just position is stored (above) } return variant; }
if (sv.getBreakend().getMate() != null) { Document mongoBndMate = new Document(); putNotNull(mongoBndMate, SV_BND_MATE_CHR, sv.getBreakend().getMate().getChromosome()); putNotNull(mongoBndMate, SV_BND_MATE_POS, sv.getBreakend().getMate().getPosition()); putNotNull(mongoBndMate, SV_BND_MATE_CI_POS_L, sv.getBreakend().getMate().getCiPositionLeft()); putNotNull(mongoBndMate, SV_BND_MATE_CI_POS_R, sv.getBreakend().getMate().getCiPositionRight()); mongoBnd.append(SV_BND_MATE, mongoBndMate);
return new Breakend(new BreakendMate(chromosome, start, null, null), type, insSeq); } else { throw breakendParseException(alternate);
ifNotNull(bnd.getMate().getChromosome(), bndMateBuilder::setChromosome); ifNotNull(bnd.getMate().getPosition(), bndMateBuilder::setPosition); ifNotNull(bnd.getMate().getCiPositionLeft(), bndMateBuilder::setCiPositionLeft); ifNotNull(bnd.getMate().getCiPositionRight(), bndMateBuilder::setCiPositionRight); bndBuilder.setMate(bndMateBuilder);
@Override public BreakendMate build() { try { BreakendMate record = new BreakendMate(); record.chromosome = fieldSetFlags()[0] ? this.chromosome : (java.lang.String) defaultValue(fields()[0]); record.position = fieldSetFlags()[1] ? this.position : (java.lang.Integer) defaultValue(fields()[1]); record.ciPositionLeft = fieldSetFlags()[2] ? this.ciPositionLeft : (java.lang.Integer) defaultValue(fields()[2]); record.ciPositionRight = fieldSetFlags()[3] ? this.ciPositionRight : (java.lang.Integer) defaultValue(fields()[3]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
public static Variant getMateBreakend(Variant variant) { // Check variant does have a mate if (variant.getSv() != null && variant.getSv().getBreakend() != null && variant.getSv().getBreakend().getMate() != null) { Variant mate = new Variant(variant.getSv().getBreakend().getMate().getChromosome(), variant.getSv().getBreakend().getMate().getPosition(), null, null); mate.setType(VariantType.BREAKEND); mate.setSv(getMateStructuralVariation(variant)); return mate; } else { return null; } }
Document mongoBndMate = mongoBnd.get(SV_BND_MATE, Document.class); if (mongoBndMate != null) { BreakendMate mate = new BreakendMate(); mate.setChromosome(mongoBndMate.getString(SV_BND_MATE_CHR)); mate.setPosition(mongoBndMate.getInteger(SV_BND_MATE_POS)); mate.setCiPositionLeft(mongoBndMate.getInteger(SV_BND_MATE_CI_POS_L)); mate.setCiPositionRight(mongoBndMate.getInteger(SV_BND_MATE_CI_POS_R)); bnd.setMate(mate);
if (variant.getSv() != null && variant.getSv().getBreakend() != null && variant.getSv().getBreakend().getMate() != null) { return getRegulatoryRegionOverlaps(variant.getSv().getBreakend().getMate().getChromosome(), Math.max(1, variant.getSv().getBreakend().getMate().getPosition())); } else { return overlapsRegulatoryRegion;
if (variant.getSv() != null && variant.getSv().getBreakend() != null && variant.getSv().getBreakend().getMate() != null) { return getRegulatoryRegionOverlaps(variant.getSv().getBreakend().getMate().getChromosome(), Math.max(1, variant.getSv().getBreakend().getMate().getPosition())); } else { return overlapsRegulatoryRegion;