this.CREATE_INDEX = true;
}
@Override
protected int doWork() {
final ProgressLogger progress = new ProgressLogger(log, 10000);
final List<String> sampleList = new ArrayList<String>();
final Collection<CloseableIterator<VariantContext>> iteratorCollection = new ArrayList<CloseableIterator<VariantContext>>(INPUT.size());
final Collection<VCFHeader> headers = new HashSet<VCFHeader>(INPUT.size());
VariantContextComparator variantContextComparator = null;
SAMSequenceDictionary sequenceDictionary = null;
if (SEQUENCE_DICTIONARY != null) sequenceDictionary = SAMFileReader.getSequenceDictionary(SEQUENCE_DICTIONARY);
for (final File file : INPUT) {
IOUtil.assertFileIsReadable(file);
final VCFFileReader fileReader = new VCFFileReader(file, false);
final VCFHeader fileHeader = fileReader.getFileHeader();
if (variantContextComparator == null) {
variantContextComparator = fileHeader.getVCFRecordComparator();
} else {
if ( ! variantContextComparator.isCompatible(fileHeader.getContigLines())) {
throw new IllegalArgumentException(
"The contig entries in input file " + file.getAbsolutePath() + " are not compatible with the others.");
}
}
if (sequenceDictionary == null) sequenceDictionary = fileHeader.getSequenceDictionary();
if (sampleList.isEmpty()) {
sampleList.addAll(fileHeader.getSampleNamesInOrder());
} else {
if ( ! sampleList.equals(fileHeader.getSampleNamesInOrder())) {
throw new IllegalArgumentException("Input file " + file.getAbsolutePath() + " has sample entries that don't match the other files.");
}
}
headers.add(fileHeader);
iteratorCollection.add(fileReader.iterator());
}
if (CREATE_INDEX && sequenceDictionary == null) {
throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
}
final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
.setOutputFile(OUTPUT)
.setReferenceDictionary(sequenceDictionary)
.clearOptions();
if (CREATE_INDEX)
builder.setOption(Options.INDEX_ON_THE_FLY);
final VariantContextWriter writer = builder.build();
writer.writeHeader(new VCFHeader(VCFUtils.smartMergeHeaders(headers, false), sampleList));
final MergingIterator<VariantContext> mergingIterator = new MergingIterator<VariantContext>(variantContextComparator, iteratorCollection);
while (mergingIterator.hasNext()) {
final VariantContext context = mergingIterator.next();
writer.add(context);
progress.record(context.getChr(), context.getStart());
}
CloserUtil.close(mergingIterator);
writer.close();
return 0;