public PositionComparator(final SAMSequenceDictionary dict){ comp = new VariantContextComparator(dict); }
public VariantContextComparator getVCFRecordComparator() { return new VariantContextComparator(this.getContigLines()); }
public VariantContextComparator getVCFRecordComparator() { return new VariantContextComparator(this.getContigLines()); }
public VariantContextComparator getVCFRecordComparator() { return new VariantContextComparator(this.getContigLines()); }
public PairedVariantSubContextIterator(final Iterator<VariantContext> leftIterator, final String leftSample, final Iterator<VariantContext> rightIterator, final String rightSample, final SAMSequenceDictionary dict) { this.leftIterator = new PeekableIterator<>(leftIterator); this.leftSample = leftSample; this.rightIterator = new PeekableIterator<>(rightIterator); this.rightSample = rightSample; this.comparator = new VariantContextComparator(dict); }
public PairedVariantSubContextIterator(final Iterator<VariantContext> leftIterator, final String leftSample, final Iterator<VariantContext> rightIterator, final String rightSample, final SAMSequenceDictionary dict) { this.leftIterator = new PeekableIterator<>(leftIterator); this.leftSample = leftSample; this.rightIterator = new PeekableIterator<>(rightIterator); this.rightSample = rightSample; this.comparator = new VariantContextComparator(dict); }
@Test(expectedExceptions = IllegalArgumentException.class) public void testThrowsOnDuplicateContig() { final List<String> contigs = new ArrayList<String>(3); contigs.add("one"); contigs.add("two"); contigs.add("one"); new VariantContextComparator(contigs); } }
@Test public void testContigs() { final VariantContext contextOne = buildVariantContext("source", "one", 100); final VariantContext contextTwo = buildVariantContext("source", "two", 100); final List<String> contigs = getOrderedContigList(contextOne, contextTwo); Assert.assertTrue(new VariantContextComparator(contigs).compare(contextOne, contextTwo) < 0); Assert.assertTrue(new VariantContextComparator(contigs).compare(contextTwo, contextOne) > 0); }
@Test public void testCombinationOne() { final VariantContext contextOne = buildVariantContext("source", "one", 100); final VariantContext contextTwo = buildVariantContext("source", "two", 150); final List<String> contigs = getOrderedContigList(contextOne, contextTwo); Assert.assertTrue(new VariantContextComparator(contigs).compare(contextOne, contextTwo) < 0); Assert.assertTrue(new VariantContextComparator(contigs).compare(contextTwo, contextOne) > 0); }
@Test public void testCombinationTwo() { final VariantContext contextOne = buildVariantContext("source", "one", 150); final VariantContext contextTwo = buildVariantContext("source", "two", 100); final List<String> contigs = getOrderedContigList(contextOne, contextTwo); Assert.assertTrue(new VariantContextComparator(contigs).compare(contextOne, contextTwo) < 0); Assert.assertTrue(new VariantContextComparator(contigs).compare(contextTwo, contextOne) > 0); }
@Test public void testPositions() { final VariantContext contextOne = buildVariantContext("source", "one", 100); final VariantContext contextTwo = buildVariantContext("source", "one", 150); final List<String> contigs = getOrderedContigList(contextOne, contextTwo); Assert.assertTrue(new VariantContextComparator(contigs).compare(contextOne, contextTwo) < 0); Assert.assertTrue(new VariantContextComparator(contigs).compare(contextTwo, contextOne) > 0); }
@Test public void testIdentical() { final VariantContext contextOne = buildVariantContext("source", "one", 100); final List<String> contigs = getOrderedContigList(contextOne); Assert.assertEquals(0, new VariantContextComparator(contigs).compare(contextOne, contextOne)); }
final VCFHeader header = new VCFFileReader(inputFiles.get(0), false).getFileHeader(); final SAMSequenceDictionary dict = header.getSequenceDictionary(); final VariantContextComparator comparator = new VariantContextComparator(header.getSequenceDictionary()); final List<String> samples = header.getGenotypeSamples();
private void writeAllViolations(final MendelianViolationDetector.Result result) { if (VCF_DIR != null) { LOG.info(String.format("Writing family violation VCFs to %s/", VCF_DIR.getAbsolutePath())); final VariantContextComparator vcComparator = new VariantContextComparator(inputHeader.get().getContigLines()); final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>(inputHeader.get().getMetaDataInInputOrder()); headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.MENDELIAN_VIOLATION_KEY, 1, VCFHeaderLineType.String, "Type of mendelian violation.")); headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AC, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Original AC")); headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AF, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Original AF")); headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AN, 1, VCFHeaderLineType.Integer, "Original AN")); for (final PedFile.PedTrio trio : pedFile.get().values()) { final File outputFile = new File(VCF_DIR, IOUtil.makeFileNameSafe(trio.getFamilyId() + IOUtil.VCF_FILE_EXTENSION)); LOG.info(String.format("Writing %s violation VCF to %s", trio.getFamilyId(), outputFile.getAbsolutePath())); final VariantContextWriter out = new VariantContextWriterBuilder() .setOutputFile(outputFile) .unsetOption(INDEX_ON_THE_FLY) .build(); final VCFHeader newHeader = new VCFHeader(headerLines, CollectionUtil.makeList(trio.getMaternalId(), trio.getPaternalId(), trio.getIndividualId())); final TreeSet<VariantContext> orderedViolations = new TreeSet<>(vcComparator); orderedViolations.addAll(result.violations().get(trio.getFamilyId())); out.writeHeader(newHeader); orderedViolations.forEach(out::add); out.close(); } } }
final VCFHeader header = new VCFFileReader(inputFiles.get(0), false).getFileHeader(); final SAMSequenceDictionary dict = header.getSequenceDictionary(); final VariantContextComparator comparator = new VariantContextComparator(header.getSequenceDictionary()); final List<String> samples = header.getGenotypeSamples();
private void writeAllViolations(final MendelianViolationDetector.Result result) { if (VCF_DIR != null) { LOG.info(String.format("Writing family violation VCFs to %s/", VCF_DIR.getAbsolutePath())); final VariantContextComparator vcComparator = new VariantContextComparator(inputHeader.get().getContigLines()); final Set<VCFHeaderLine> headerLines = new LinkedHashSet<>(inputHeader.get().getMetaDataInInputOrder()); headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.MENDELIAN_VIOLATION_KEY, 1, VCFHeaderLineType.String, "Type of mendelian violation.")); headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AC, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Original AC")); headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AF, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Original AF")); headerLines.add(new VCFInfoHeaderLine(MendelianViolationDetector.ORIGINAL_AN, 1, VCFHeaderLineType.Integer, "Original AN")); for (final PedFile.PedTrio trio : pedFile.get().values()) { final File outputFile = new File(VCF_DIR, IOUtil.makeFileNameSafe(trio.getFamilyId() + IOUtil.VCF_FILE_EXTENSION)); LOG.info(String.format("Writing %s violation VCF to %s", trio.getFamilyId(), outputFile.getAbsolutePath())); final VariantContextWriter out = new VariantContextWriterBuilder() .setOutputFile(outputFile) .unsetOption(INDEX_ON_THE_FLY) .build(); final VCFHeader newHeader = new VCFHeader(headerLines, CollectionUtil.makeList(trio.getMaternalId(), trio.getPaternalId(), trio.getIndividualId())); final TreeSet<VariantContext> orderedViolations = new TreeSet<>(vcComparator); orderedViolations.addAll(result.violations().get(trio.getFamilyId())); out.writeHeader(newHeader); orderedViolations.forEach(out::add); out.close(); } } }
firstHeader = header; out.writeHeader(firstHeader); comparator = new VariantContextComparator(firstHeader.getContigLines());
firstHeader = header; out.writeHeader(firstHeader); comparator = new VariantContextComparator(firstHeader.getContigLines());