@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;
}
@Override
protected void doWork(VcfIterator r, VariantContextWriter w) throws IOException {
AbstractVCFCodec codeIn3 = VCFUtils.createDefaultVCFCodec();
String line;
StringWriter sw = new StringWriter();
LOG.info("opening tabix file: " + this.TABIX);
TabixReader tabix = new TabixReader(this.TABIX);
while ((line = tabix.readLine()) != null) {
if (!line.startsWith(VCFHeader.HEADER_INDICATOR)) {
break;
}
sw.append(line).append("\n");
}
VCFHeader header3 =
(VCFHeader)
codeIn3.readActualHeader(
new LineIteratorImpl(
LineReaderUtil.fromBufferedStream(
new ByteArrayInputStream(sw.toString().getBytes()))));
VCFHeader header1 = r.getHeader();
VCFHeader h2 =
new VCFHeader(header1.getMetaDataInInputOrder(), header1.getSampleNamesInOrder());
for (String infoId : this.INFO_IDS) {
VCFInfoHeaderLine vihl = header3.getInfoHeaderLine(infoId);
if (vihl == null) {
LOG.warn("Not INFO=" + infoId + " in " + TABIX);
continue;
}
if (h2.getInfoHeaderLine(infoId) != null) {
LOG.warn("Input already contains INFO=" + vihl);
}
h2.addMetaDataLine(vihl);
}
if (ALT_CONFLICT_FLAG != null) {
h2.addMetaDataLine(
new VCFInfoHeaderLine(
ALT_CONFLICT_FLAG,
1,
VCFHeaderLineType.Flag,
"conflict ALT allele with " + this.TABIX));
}
w.writeHeader(h2);
while (r.hasNext()) {
VariantContext ctx1 = r.next();
VariantContextBuilder vcb = new VariantContextBuilder(ctx1);
String line2;
String BEST_ID = null;
boolean best_id_match_alt = false;
List<VariantContext> variantsList = new ArrayList<VariantContext>();
int[] array = tabix.parseReg(ctx1.getChr() + ":" + (ctx1.getStart()) + "-" + (ctx1.getEnd()));
TabixReader.Iterator iter = null;
if (array != null && array.length == 3 && array[0] != -1 && array[1] >= 0 && array[2] >= 0) {
iter = tabix.query(array[0], array[1], array[2]);
} else {
LOG.info("Cannot get " + ctx1.getChr() + ":" + (ctx1.getStart()) + "-" + (ctx1.getEnd()));
}
while (iter != null && (line2 = iter.next()) != null) {
VariantContext ctx3 = codeIn3.decode(line2);
if (ctx3.getStart() != ctx1.getStart()) continue;
if (ctx3.getEnd() != ctx1.getEnd()) continue;
if (ctx1.getReference().equals(ctx3.getReference())
&& ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles())) {
variantsList.clear();
variantsList.add(ctx3);
break;
} else {
variantsList.add(ctx3);
}
}
for (VariantContext ctx3 : variantsList) {
if (this.REF_ALLELE_MATTERS && !ctx1.getReference().equals(ctx3.getReference())) {
continue;
}
if (this.ALT_ALLELES_MATTERS
&& !ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles())) {
continue;
}
if (ctx3.getID() != null && this.REPLACE_ID) {
if (BEST_ID != null && best_id_match_alt) {
// nothing
} else {
BEST_ID = ctx3.getID();
best_id_match_alt = ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles());
}
}
for (String id : this.INFO_IDS) {
Object info3 = ctx3.getAttribute(id);
if (info3 == null) {
continue;
}
Object info1 = ctx1.getAttribute(id);
if (info1 != null && !this.REPLACE_INFO_FIELD) {
continue;
}
vcb.attribute(id, info3);
}
if (ALT_CONFLICT_FLAG != null
&& !ctx1.getAlternateAlleles().equals(ctx3.getAlternateAlleles())) {
vcb.attribute(ALT_CONFLICT_FLAG, true);
}
}
if (BEST_ID != null) {
vcb.id(BEST_ID);
}
w.add(vcb.make());
}
tabix.close();
}
