private static BreakendOrientation getMateOrientation(Variant variant) { switch (variant.getSv().getBreakend().getOrientation()) { case ES: return BreakendOrientation.SE; case SE: return BreakendOrientation.ES; default: return variant.getSv().getBreakend().getOrientation(); } }
int indexOfDifference; char braket = '['; switch (breakend.getOrientation()) { case SS: braket = ']'; break; default: throw new IllegalStateException("Unknown breakend orientation " + breakend.getOrientation());
putNotNull(mongoBnd, SV_BND_ORIENTATION, sv.getBreakend().getOrientation().toString()); putNotNull(mongoBnd, SV_BND_INS_SEQ, sv.getBreakend().getInsSeq()); if (sv.getBreakend().getMate() != null) {
bndBuilder.setMate(bndMateBuilder); ifNotNull(bnd.getOrientation(), type -> bndBuilder.setOrientation(VariantProto.BreakendOrientation.valueOf(type.toString())));