Breakend bnd = parseBreakend(reference, alternates.get(0)); if (bnd != null) { sv.setBreakend(bnd);
keyFields.getSv().setBreakend(breakend); return keyFields;
bnd.setMate(mate); sv.setBreakend(bnd);
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; }