private Point getAbsoluteEdgeExtremity(
ConnectionNodeEditPart editPart, boolean isStart, Float[] preferPosition) {
if (editPart == null) {
return null;
}
PointList points = editPart.getConnectionFigure().getPoints().getCopy();
if (points.size() == 2
&& new Point(0, 0).equals(points.getFirstPoint())
&& new Point(100, 100).equals(points.getLastPoint())) {
// not display yet.
if (preferPosition != null) {
if (isStart && preferPosition[0] != null) {
return new Point(0, preferPosition[0].intValue());
} else if (!isStart && preferPosition[1] != null) {
return new Point(0, preferPosition[1].intValue());
}
}
return SequenceUtil.getAbsoluteEdgeExtremity(editPart, isStart, false);
}
return SequenceUtil.getAbsoluteEdgeExtremity(editPart, isStart, true);
}
private Rectangle getAbsoluteBounds(IGraphicalEditPart editPart, Float[] preferPosition) {
if (editPart == null) {
return null;
}
Rectangle rect = editPart.getFigure().getBounds().getCopy();
if (rect.isEmpty() && rect.x == 0 && rect.y == 0) { // Not displayed yet.
View view = editPart.getNotationView();
if (view instanceof Node) {
LayoutConstraint constraint = ((Node) view).getLayoutConstraint();
if (constraint instanceof Bounds) {
Bounds bounds = (Bounds) constraint;
if (bounds.getX() > 0) {
rect.x = bounds.getX();
}
if (bounds.getY() > 0) {
rect.y = bounds.getY();
} else if (preferPosition != null
&& preferPosition.length > 0
&& preferPosition[0] != null) {
rect.y = preferPosition[0].intValue();
}
if (bounds.getWidth() != -1) {
rect.width = bounds.getWidth();
}
if (bounds.getHeight() != -1) {
rect.height = bounds.getHeight();
}
}
}
Rectangle parentRect = getAbsoluteBounds((IGraphicalEditPart) editPart.getParent(), null);
rect.x += parentRect.x;
rect.y += parentRect.y;
} else {
rect = SequenceUtil.getAbsoluteBounds(editPart);
}
return rect;
}
@Override
protected Object doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
IOUtil.assertFileIsReadable(CHAIN);
IOUtil.assertFileIsWritable(OUTPUT);
IOUtil.assertFileIsWritable(REJECT);
////////////////////////////////////////////////////////////////////////
// Setup the inputs
////////////////////////////////////////////////////////////////////////
final LiftOver liftOver = new LiftOver(CHAIN);
final VCFFileReader in = new VCFFileReader(INPUT, false);
logger.info("Loading up the target reference genome.");
final ReferenceSequenceFileWalker walker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
final Map<String, byte[]> refSeqs = new HashMap<>();
for (final SAMSequenceRecord rec : walker.getSequenceDictionary().getSequences()) {
refSeqs.put(rec.getSequenceName(), walker.get(rec.getSequenceIndex()).getBases());
}
CloserUtil.close(walker);
////////////////////////////////////////////////////////////////////////
// Setup the outputs
////////////////////////////////////////////////////////////////////////
final VCFHeader inHeader = in.getFileHeader();
final VCFHeader outHeader = new VCFHeader(inHeader);
outHeader.setSequenceDictionary(walker.getSequenceDictionary());
final VariantContextWriter out =
new VariantContextWriterBuilder()
.setOption(Options.INDEX_ON_THE_FLY)
.setOutputFile(OUTPUT)
.setReferenceDictionary(walker.getSequenceDictionary())
.build();
out.writeHeader(outHeader);
final VariantContextWriter rejects =
new VariantContextWriterBuilder()
.setOutputFile(REJECT)
.unsetOption(Options.INDEX_ON_THE_FLY)
.build();
final VCFHeader rejectHeader = new VCFHeader(in.getFileHeader());
for (final VCFFilterHeaderLine line : FILTERS) rejectHeader.addMetaDataLine(line);
rejects.writeHeader(rejectHeader);
////////////////////////////////////////////////////////////////////////
// Read the input VCF, lift the records over and write to the sorting
// collection.
////////////////////////////////////////////////////////////////////////
long failedLiftover = 0, failedAlleleCheck = 0, total = 0;
logger.info("Lifting variants over and sorting.");
final SortingCollection<VariantContext> sorter =
SortingCollection.newInstance(
VariantContext.class,
new VCFRecordCodec(outHeader),
outHeader.getVCFRecordComparator(),
MAX_RECORDS_IN_RAM,
TMP_DIR);
ProgressLogger progress = new ProgressLogger(logger, 1000000, "read");
for (final VariantContext ctx : in) {
++total;
final Interval source =
new Interval(
ctx.getContig(),
ctx.getStart(),
ctx.getEnd(),
false,
ctx.getContig() + ":" + ctx.getStart() + "-" + ctx.getEnd());
final Interval target = liftOver.liftOver(source, 1.0);
if (target == null) {
rejects.add(new VariantContextBuilder(ctx).filter(FILTER_CANNOT_LIFTOVER).make());
failedLiftover++;
} else {
// Fix the alleles if we went from positive to negative strand
final List<Allele> alleles = new ArrayList<>();
for (final Allele oldAllele : ctx.getAlleles()) {
if (target.isPositiveStrand() || oldAllele.isSymbolic()) {
alleles.add(oldAllele);
} else {
alleles.add(
Allele.create(
SequenceUtil.reverseComplement(oldAllele.getBaseString()),
oldAllele.isReference()));
}
}
// Build the new variant context
final VariantContextBuilder builder =
new VariantContextBuilder(
ctx.getSource(), target.getContig(), target.getStart(), target.getEnd(), alleles);
builder.id(ctx.getID());
builder.attributes(ctx.getAttributes());
builder.genotypes(ctx.getGenotypes());
builder.filters(ctx.getFilters());
builder.log10PError(ctx.getLog10PError());
// Check that the reference allele still agrees with the reference sequence
boolean mismatchesReference = false;
for (final Allele allele : builder.getAlleles()) {
if (allele.isReference()) {
final byte[] ref = refSeqs.get(target.getContig());
final String refString =
StringUtil.bytesToString(ref, target.getStart() - 1, target.length());
if (!refString.equalsIgnoreCase(allele.getBaseString())) {
mismatchesReference = true;
}
break;
}
}
if (mismatchesReference) {
rejects.add(new VariantContextBuilder(ctx).filter(FILTER_MISMATCHING_REF_ALLELE).make());
failedAlleleCheck++;
} else {
sorter.add(builder.make());
}
}
progress.record(ctx.getContig(), ctx.getStart());
}
final NumberFormat pfmt = new DecimalFormat("0.0000%");
final String pct = pfmt.format((failedLiftover + failedAlleleCheck) / (double) total);
logger.info("Processed ", total, " variants.");
logger.info(Long.toString(failedLiftover), " variants failed to liftover.");
logger.info(
Long.toString(failedAlleleCheck),
" variants lifted over but had mismatching reference alleles after lift over.");
logger.info(pct, " of variants were not successfully lifted over and written to the output.");
rejects.close();
in.close();
////////////////////////////////////////////////////////////////////////
// Write the sorted outputs to the final output file
////////////////////////////////////////////////////////////////////////
sorter.doneAdding();
progress = new ProgressLogger(logger, 1000000, "written");
logger.info("Writing out sorted records to final VCF.");
for (final VariantContext ctx : sorter) {
out.add(ctx);
progress.record(ctx.getContig(), ctx.getStart());
}
out.close();
sorter.cleanup();
return null;
}
