return new Breakend(new BreakendMate(chromosome, start, null, null), type, insSeq); } else { throw breakendParseException(alternate);
@Override public Breakend build() { try { Breakend record = new Breakend(); record.mate = fieldSetFlags()[0] ? this.mate : (org.opencb.biodata.models.variant.avro.BreakendMate) defaultValue(fields()[0]); record.orientation = fieldSetFlags()[1] ? this.orientation : (org.opencb.biodata.models.variant.avro.BreakendOrientation) defaultValue(fields()[1]); record.insSeq = fieldSetFlags()[2] ? this.insSeq : (java.lang.String) defaultValue(fields()[2]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
Breakend bnd = new Breakend(); bnd.setOrientation(BreakendOrientation.valueOf(mongoBnd.getString(SV_BND_ORIENTATION))); bnd.setInsSeq(mongoBnd.getString(SV_BND_INS_SEQ));
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; }