Java Code Examples for htsjdk.variant.variantcontext.VariantContext#getStart()
The following examples show how to use
htsjdk.variant.variantcontext.VariantContext#getStart() .
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Example 1
| Source File: SegmentedCpxVariantSimpleVariantExtractor.java From gatk with BSD 3-Clause "New" or "Revised" License | 6 votes |
|
@VisibleForTesting
static boolean deletionConsistencyCheck(final VariantContext simple, final Set<SimpleInterval> missingSegments) {
if (missingSegments.isEmpty()) return false;
final SimpleInterval deletedRange = new SimpleInterval(simple.getContig(), simple.getStart() + 1, simple.getEnd());
// dummy number for chr to be used in constructing SVInterval, since 2 input AI's both map to the same chr by this point
final int dummyChr = 0;
final SVInterval intervalOne = new SVInterval(dummyChr, deletedRange.getStart() - 1, deletedRange.getEnd());
for (final SimpleInterval missing : missingSegments) {
if ( ! missing.overlaps(deletedRange) )
return false;
final SVInterval intervalTwo = new SVInterval(dummyChr, missing.getStart() - 1, missing.getEnd());
// allow 1-base fuzziness from either end
if ( Math.abs(missing.size() - deletedRange.size()) > 2 )
return false;
if( 2 >= Math.abs( Math.min(missing.size(), deletedRange.size()) - intervalTwo.overlapLen(intervalOne) ) ){
return true;
}
}
return false;
}
Example 2
| Source File: KataegisQueue.java From hmftools with GNU General Public License v3.0 | 6 votes |
|
@NotNull
private KataegisWindow longestViableWindow(@NotNull final VariantContext first) {
KataegisWindow result = new KataegisWindow(first);
final KataegisWindow window = new KataegisWindow(first);
for (VariantContext context : buffer) {
if (context.getStart() - window.end() > MAX_ABS_DISTANCE) {
return result;
}
if (candidate.test(context)) {
window.add(context);
}
if (window.isViable(MIN_COUNT, MAX_AVG_DISTANCE)) {
result = new KataegisWindow(window);
}
}
return result;
}
Example 3
| Source File: KataegisQueue.java From hmftools with GNU General Public License v3.0 | 5 votes |
|
private void processFirstContext() {
if (!buffer.isEmpty()) {
final VariantContext first = buffer.peekFirst();
if (!candidate.test(first)) {
consumer.accept(buffer.pollFirst());
} else {
final KataegisWindow window = longestViableWindow(first);
final boolean isWindowViable = window.isViable(MIN_COUNT, MAX_AVG_DISTANCE);
if (isWindowViable) {
identifier++;
}
while (!buffer.isEmpty()) {
final VariantContext peek = buffer.peekFirst();
if (peek.getStart() > window.end()) {
return;
}
if (isWindowViable && candidate.test(peek)) {
peek.getCommonInfo().putAttribute(KATAEGIS_FLAG, idPrefix + "_" + identifier, true);
}
consumer.accept(buffer.pollFirst());
}
}
}
}
Example 4
| Source File: SegmentedCpxVariantSimpleVariantExtractor.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
private AnnotatedInterval(final VariantContext vc) {
sourceVC = vc;
interval = new SimpleInterval( vc.getContig(), vc.getStart(), vc.getEnd());
id = vc.getID();
type = vc.getAttributeAsString(SVTYPE, "");
svlen = vc.getAttributeAsInt(SVLEN, 0);
alleles = vc.getAlleles();
}
Example 5
| Source File: StrelkaPostProcess.java From hmftools with GNU General Public License v3.0 | 5 votes |
|
@VisibleForTesting
static GenomePosition variantGenomePosition(@NotNull final VariantContext variant) {
return new GenomePosition() {
@Override
@NotNull
public String chromosome() {
return variant.getContig();
}
@Override
public long position() {
return variant.getStart();
}
};
}
Example 6
| Source File: ArHetvarFilter.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
private boolean variantContextsMatch(VariantContext v1, VariantContext v2) {
return v1.getContig().equals(v2.getContig())
&& v1.getStart() == v2.getStart()
&& v1.getEnd() == v2.getEnd()
&& v1.getReference() == v2.getReference()
&& v1.getAlternateAlleles().size() == v2.getAlternateAlleles().size()
&& v1.getAlternateAlleles().containsAll(v2.getAlternateAlleles());
}
Example 7
| Source File: PileupSummary.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
public PileupSummary(final VariantContext vc, final ReadPileup pileup) {
contig = vc.getContig();
position = vc.getStart();
alleleFrequency = vc.getAttributeAsDouble(VCFConstants.ALLELE_FREQUENCY_KEY, 0);
final byte altBase = vc.getAlternateAllele(0).getBases()[0];
final byte refBase = vc.getReference().getBases()[0];
final int[] baseCounts = pileup.getBaseCounts();
altCount = baseCounts[BaseUtils.simpleBaseToBaseIndex(altBase)];
refCount = baseCounts[BaseUtils.simpleBaseToBaseIndex(refBase)];
totalCount = (int) MathUtils.sum(baseCounts);
otherAltsCount = totalCount - altCount - refCount;
}
Example 8
| Source File: SVVCFReader.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
|
public static SVIntervalTree<String> readBreakpointsFromTruthVCF(final String truthVCF,
final SAMSequenceDictionary dictionary,
final int padding ) {
SVIntervalTree<String> breakpoints = new SVIntervalTree<>();
try ( final FeatureDataSource<VariantContext> dataSource =
new FeatureDataSource<>(truthVCF, null, 0, VariantContext.class) ) {
for ( final VariantContext vc : dataSource ) {
final StructuralVariantType svType = vc.getStructuralVariantType();
if ( svType == null ) continue;
final String eventName = vc.getID();
final int contigID = dictionary.getSequenceIndex(vc.getContig());
if ( contigID < 0 ) {
throw new UserException("VCF contig " + vc.getContig() + " does not appear in dictionary.");
}
final int start = vc.getStart();
switch ( svType ) {
case DEL:
case INV:
case CNV:
final int end = vc.getEnd();
breakpoints.put(new SVInterval(contigID,start-padding, end+padding), eventName);
break;
case INS:
case DUP:
case BND:
breakpoints.put(new SVInterval(contigID,start-padding, start+padding), eventName);
break;
}
}
}
return breakpoints;
}
Example 9
| Source File: LiftoverVcfTest.java From picard with MIT License | 5 votes |
|
@Test(dataProvider = "indelFlipData")
public void testFlipIndel(final VariantContext source, final ReferenceSequence reference, final VariantContext result) {
final LiftOver liftOver = new LiftOver(CHAIN_FILE);
final Interval originalLocus = new Interval(source.getContig(), source.getStart(), source.getEnd());
final Interval target = liftOver.liftOver(originalLocus);
if (target != null && !target.isNegativeStrand()) {
throw new RuntimeException("not reversed");
}
final VariantContext flipped = LiftoverUtils.liftVariant(source, target, reference, false, false);
VcfTestUtils.assertEquals(flipped, result);
}
Example 10
| Source File: KataegisWindow.java From hmftools with GNU General Public License v3.0 | 4 votes |
|
KataegisWindow(final VariantContext context) {
this.contig = context.getContig();
this.start = context.getStart();
this.end = this.start;
this.count = 0;
}
Example 11
| Source File: FuncotatorEngineUnitTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
@Test(dataProvider = "provideGt")
public void testGetFuncotationFactoriesAndCreateFuncotationMapForVariant(final File vcfFile,
final List<String> correspondingGeneName,
final boolean[] hasClinvarHit) {
final Pair<VCFHeader, List<VariantContext>> entireVcf = VariantContextTestUtils.readEntireVCFIntoMemory(vcfFile.getAbsolutePath());
final Map<Path, Properties> configData = DataSourceUtils.getAndValidateDataSourcesFromPaths("hg19", Collections.singletonList(DS_PIK3CA_DIR));
final Pair<VCFHeader, List<VariantContext>> vcfFileContents = VariantContextTestUtils.readEntireVCFIntoMemory(vcfFile.getAbsolutePath());
// Set up our arguments:
final FuncotatorVariantArgumentCollection funcotatorArguments = new FuncotatorVariantArgumentCollection();
funcotatorArguments.referenceVersion = BaseFuncotatorArgumentCollection.FuncotatorReferenceVersionHg19;
funcotatorArguments.transcriptSelectionMode = TranscriptSelectionMode.CANONICAL;
funcotatorArguments.lookaheadFeatureCachingInBp = FuncotatorArgumentDefinitions.LOOKAHEAD_CACHE_IN_BP_DEFAULT_VALUE;
// Create the metadata directly from the input.
final FuncotatorEngine funcotatorEngine =
new FuncotatorEngine(
funcotatorArguments,
vcfFileContents.getLeft().getSequenceDictionary(),
VcfFuncotationMetadata.create(new ArrayList<>(entireVcf.getLeft().getInfoHeaderLines())),
DataSourceUtils.createDataSourceFuncotationFactoriesForDataSources(
configData,
new LinkedHashMap<>(),
TranscriptSelectionMode.CANONICAL,
new HashSet<>(),
new DummyPlaceholderGatkTool(),
FuncotatorArgumentDefinitions.LOOKAHEAD_CACHE_IN_BP_DEFAULT_VALUE,
new FlankSettings(0, 0),
false,
FuncotatorUtils.DEFAULT_MIN_NUM_BASES_FOR_VALID_SEGMENT)
);
for (int i = 0; i < entireVcf.getRight().size(); i++) {
final VariantContext vc = entireVcf.getRight().get(i);
final SimpleInterval variantInterval = new SimpleInterval(vc.getContig(), vc.getStart(), vc.getEnd());
final ReferenceContext referenceContext = new ReferenceContext(ReferenceDataSource.of(Paths.get(FuncotatorReferenceTestUtils.retrieveHg19Chr3Ref())), variantInterval);
final FeatureContext featureContext = FuncotatorTestUtils.createFeatureContext(funcotatorEngine.getFuncotationFactories(), "TEST", variantInterval,
0,0,0, null);
final FuncotationMap funcotationMap = funcotatorEngine.createFuncotationMapForVariant(vc, referenceContext, featureContext);
// Check that all of the transcripts at this location have the same gene name as the corresponding gene.
// The ground truth selected has the same gene name for all transcripts.
// Also, input VCF has no multiallelics.
for (final String txId : funcotationMap.getTranscriptList()) {
Assert.assertEquals(funcotationMap.getFieldValue(txId, "Gencode_19_hugoSymbol", vc.getAlternateAllele(0)), correspondingGeneName.get(i));
Assert.assertTrue((funcotationMap.getFieldValue(txId, "dummy_ClinVar_VCF_ALLELEID", vc.getAlternateAllele(0)).isEmpty()) != hasClinvarHit[i]);
}
}
}
Example 12
| Source File: CosmicFuncotationFactory.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
@Override
protected List<Funcotation> createFuncotationsOnVariant(final VariantContext variant, final ReferenceContext referenceContext, final List<Feature> featureList, final List<GencodeFuncotation> gencodeFuncotations) {
final List<Funcotation> outputFuncotations = new ArrayList<>();
// Keep count of each overlapping mutation here:
final Map<String, Integer> proteinChangeCounts = new LinkedHashMap<>();
// If we have gencodeFuncotations we go through them and get the gene name
// Then query our DB for matches on the gene name.
// Then grab Genome position / Protein position and see if we overlap.
// If any do, we create our CosmicFuncotation
for ( final GencodeFuncotation gencodeFuncotation : gencodeFuncotations ) {
final String geneName = gencodeFuncotation.getHugoSymbol();
final SimpleInterval genomePosition = new SimpleInterval(variant.getContig(), variant.getStart(), variant.getEnd());
final SimpleInterval proteinPosition;
if ( gencodeFuncotation.getProteinChange() != null ) {
proteinPosition = parseProteinString(gencodeFuncotation.getProteinChange());
}
else {
proteinPosition = null;
}
try {
try ( final Statement statement = dbConnection.createStatement() ) {
try ( final ResultSet resultSet = statement.executeQuery(RESULT_QUERY_TEMPLATE + "\"" + geneName + "\";") ) {
// iterate through our results:
while ( resultSet.next() ) {
// Get the genome position:
final SimpleInterval cosmicGenomePosition = getGenomePositionFromResults(resultSet);
// Try to match on genome position first:
if ( cosmicGenomePosition != null ) {
if ( genomePosition.overlaps(cosmicGenomePosition) ) {
// If we overlap the records, we get the protein change and add it to the map:
updateProteinChangeCountMap(proteinChangeCounts, resultSet);
continue;
}
}
// Get the protein position:
final SimpleInterval cosmicProteinPosition = getProteinPositionFromResults(resultSet);
// Now try to match on protein position:
if ( proteinPosition != null ) {
// If we overlap the records, we update the counter:
if ( proteinPosition.overlaps(cosmicProteinPosition) ) {
updateProteinChangeCountMap(proteinChangeCounts, resultSet);
}
}
// NOTE: We can't annotate if the protein position is null.
}
}
}
}
catch (final SQLException ex) {
throw new GATKException("Unable to query the database for geneName: " + geneName, ex);
}
}
// Add our counts to all alternate alleles in this variant:
for ( final Allele altAllele : variant.getAlternateAlleles() ) {
outputFuncotations.add(
TableFuncotation.create(
new ArrayList<>(supportedFields),
Collections.singletonList(proteinChangeCounts.entrySet().stream()
.map(entry -> entry.getKey() + '('+ entry.getValue() + ')')
.collect(Collectors.joining("|"))),
altAllele,
name, null
)
);
}
return outputFuncotations;
}
Example 13
| Source File: CreateSnpIntervalFromVcf.java From Drop-seq with MIT License | 4 votes |
|
public IntervalList processData(final File vcfFile, final File sdFile, final Set<String> sample, int GQThreshold, final boolean hetSNPsOnly) {
final VCFFileReader reader = new VCFFileReader(vcfFile, false);
if (!VCFUtils.GQInHeader(reader)) {
GQThreshold=-1;
log.info("Genotype Quality [GQ] not found in header. Disabling GQ_THRESHOLD parameter");
}
final VCFHeader inputVcfHeader = new VCFHeader(reader.getFileHeader().getMetaDataInInputOrder());
SAMSequenceDictionary sequenceDictionary = inputVcfHeader.getSequenceDictionary();
Set<String> sampleListFinal = sample;
if (sample==null || sample.isEmpty()) {
ArrayList<String> s = reader.getFileHeader().getSampleNamesInOrder();
sampleListFinal=new TreeSet<String>(s);
}
if (sdFile != null)
sequenceDictionary = getSequenceDictionary(sdFile);
final ProgressLogger progress = new ProgressLogger(this.log, 500000);
final SAMFileHeader samHeader = new SAMFileHeader();
samHeader.setSequenceDictionary(sequenceDictionary);
IntervalList result = new IntervalList(samHeader);
// Go through the input, find sites we want to keep.
final PeekableIterator<VariantContext> iterator = new PeekableIterator<>(reader.iterator());
validateRequestedSamples (iterator, sampleListFinal);
while (iterator.hasNext()) {
final VariantContext site = iterator.next();
progress.record(site.getContig(), site.getStart());
// for now drop any filtered site.
if (site.isFiltered())
continue;
// move onto the next record if the site is not a SNP or the samples aren't all heterozygous.
if (!site.isSNP())
continue;
if (!sitePassesFilters(site, sampleListFinal, GQThreshold, hetSNPsOnly))
continue;
Interval varInt = new Interval(site.getContig(), site.getStart(),
site.getEnd(), true, site.getID());
// final Interval site = findHeterozygousSites(full, SAMPLE);
result.add(varInt);
}
CloserUtil.close(iterator);
CloserUtil.close(reader);
return (result);
}
Example 14
| Source File: HotspotEnrichment.java From hmftools with GNU General Public License v3.0 | 4 votes |
|
private static boolean exactMatch(@NotNull final VariantHotspot hotspot, @NotNull final VariantContext variant) {
return hotspot.position() == variant.getStart() && hotspot.ref().equals(variant.getReference().getBaseString())
&& variant.getAlternateAlleles().stream().map(Allele::getBaseString).collect(Collectors.toList()).contains(hotspot.alt());
}
Example 15
| Source File: ReadPosRankSumTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
@Override
public boolean isUsableRead(final GATKRead read, final VariantContext vc) {
Utils.nonNull(read);
// we use vc.getEnd() + 1 in case of a leading indel -- if this isn't relevant getReadPosition will return empty
return super.isUsableRead(read, vc) && read.getSoftStart() <= vc.getEnd() + 1 && read.getSoftEnd() >= vc.getStart();
}
Example 16
| Source File: CombineGVCFsIntegrationTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
@Test
public void testCombineSomaticGvcfs() throws Exception {
final File output = createTempFile("combinegvcfs", ".vcf");
final ArgumentsBuilder args = new ArgumentsBuilder();
args.addReference(new File(b37Reference)).addOutput(output)
.addVCF(getTestFile("NA12878.MT.filtered.g.vcf"))
.addVCF(getTestFile("NA19240.MT.filtered.g.vcf"))
.add(CombineGVCFs.SOMATIC_INPUT_LONG_NAME, true);
runCommandLine(args);
final List<VariantContext> actualVC = getVariantContexts(output);
for (final VariantContext vc : actualVC) {
if (vc.getAlternateAlleles().size() > 1) { //if there's a real ALT
Assert.assertTrue(vc.filtersWereApplied()); //filtering should happen during combine
}
else {
Assert.assertFalse(vc.filtersWereApplied());
}
//MT:302 has an alphabet soup of alleles in the GVCF
if (vc.getStart() == 302) {
Assert.assertEquals(vc.getNAlleles(), 9);
}
//make sure phasing is retained
if (vc.getStart() == 317 || vc.getStart() == 320) {
VariantContextTestUtils.assertGenotypeIsPhasedWithAttributes(vc.getGenotype(1));
}
//MT:4769 in combined GVCF has uncalled alleles, but we should keep them around
if (vc.getStart() == 4769) {
Assert.assertEquals(vc.getNAlleles(), 4);
Assert.assertTrue(vc.getAlternateAlleles().contains(Allele.create("G", false)));
Assert.assertTrue(vc.getAlternateAlleles().contains(Allele.create("T", false)));
Assert.assertTrue(vc.getAlternateAlleles().contains(Allele.NON_REF_ALLELE));
}
//check genotype filtering
if (vc.getStart() == 14872) {
Assert.assertTrue(!vc.isFiltered());
Assert.assertTrue(!vc.getGenotype(0).isFiltered());
}
}
final List<VariantContext> expectedVC = getVariantContexts(getTestFile("twoSamples.MT.g.vcf"));
final VCFHeader header = getHeaderFromFile(output);
assertForEachElementInLists(actualVC, expectedVC, (a, e) -> VariantContextTestUtils.assertVariantContextsAreEqualAlleleOrderIndependent(a, e, Arrays.asList(), Collections.emptyList(), header));
}
Example 17
| Source File: CustomMafFuncotationCreatorUnitTest.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
/**
* As a side effect, this also tests (https://github.com/broadinstitute/gatk/issues/4972)
*/
@Test(dataProvider = "provideDbSnpVariants")
public void testCreateDbSnpCustomFields(final VariantContext variant, final int gtNumHits, final String gtDbSnpValStatusField) {
final Path sourceFilePath = IOUtils.getPath(FuncotatorTestConstants.DBSNP_HG19_SNIPPET_FILE_PATH);
final DataSourceFuncotationFactory vcfFuncotationFactory =
new VcfFuncotationFactory(DBSNP_DS_NAME,
"snippetTest",
sourceFilePath,
new LinkedHashMap<>(),
new FeatureInput<VariantContext>(sourceFilePath.toString(), DBSNP_DS_NAME, new HashMap<>())
);
/* dbSNP records of relevance.
1 10177 rs367896724 A AC . . RS=367896724;RSPOS=10177;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050000020005170026000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP;VLD;G5A;G5;KGPhase3;CAF=0.5747,0.4253;COMMON=1
1 10352 rs555500075 T TA . . RS=555500075;RSPOS=10352;dbSNPBuildID=142;SSR=0;SAO=0;VP=0x050000020005170026000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP;VLD;G5A;G5;KGPhase3;CAF=0.5625,0.4375;COMMON=1
1 10352 rs145072688 T TA . . RS=145072688;RSPOS=10353;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000020005000002000200;GENEINFO=DDX11L1:100287102;WGT=1;VC=DIV;R5;ASP;CAF=0.5625,0.4375;COMMON=1
*/
// Create features from the file:
final List<Feature> vcfFeatures;
try (final VCFFileReader vcfReader = new VCFFileReader(IOUtils.getPath(FuncotatorTestConstants.DBSNP_HG19_SNIPPET_FILE_PATH))) {
vcfFeatures = vcfReader.query(variant.getContig(), variant.getStart(), variant.getEnd()).stream().collect(Collectors.toList());
}
Assert.assertEquals(vcfFeatures.size(), gtNumHits);
final Map<String, List<Feature>> vcfFuncotationSourceMap = ImmutableMap.of(DBSNP_DS_NAME, vcfFeatures);
final ReferenceContext referenceContext = new ReferenceContext(ReferenceDataSource.of(Paths.get(HG19_CHR1_1M_FASTA)),
new SimpleInterval(variant.getContig(),
variant.getStart(), variant.getEnd()));
final FeatureContext featureContext = FuncotatorTestUtils.createFeatureContext(Collections.singletonList(vcfFuncotationFactory),
"TEST_CREATE_DB_SNP_CUSTOM_FIELDS",
new SimpleInterval(variant.getContig(), variant.getStart(), variant.getEnd()),
0, 0, 0, null);
final List<Funcotation> funcotations = vcfFuncotationFactory.createFuncotations(variant, referenceContext, featureContext);
Assert.assertTrue(funcotations.size() > 0);
for (final Funcotation f : funcotations) {
Assert.assertEquals(StringUtils.split(f.getField(DBSNP_DS_NAME + "_VLD"), "|").length, vcfFuncotationSourceMap.get(DBSNP_DS_NAME).size());
}
final List<Funcotation> customDbSnpFuncotations = CustomMafFuncotationCreator.createCustomMafDbSnpFields(funcotations);
Assert.assertEquals(customDbSnpFuncotations.stream().map(f -> f.getField(MAF_DBSNP_VAL_STATUS_FIELD)).collect(Collectors.toList()),
Collections.singletonList(gtDbSnpValStatusField));
// Now add some dummy (non-DbSNP) funcotations and make sure that we are not getting any additional custom dbsnp maf fields.
final List<String> dummyFieldNames = Arrays.asList("foo_field", "bar_field");
final Funcotation dummyFuncotation = TableFuncotation.create(dummyFieldNames, Arrays.asList("1", "2"), Allele.create("AA"), "DUMMY", FuncotationMetadataUtils.createWithUnknownAttributes(dummyFieldNames));
funcotations.add(dummyFuncotation);
final List<Funcotation> customDbSnpFuncotationsWithoutDummies = CustomMafFuncotationCreator.createCustomMafDbSnpFields(funcotations);
Assert.assertEquals(customDbSnpFuncotationsWithoutDummies, customDbSnpFuncotations);
}
Example 18
| Source File: MNVRegionValidator.java From hmftools with GNU General Public License v3.0 | 4 votes |
|
private boolean containsAllMNVPositions(@NotNull final SAMRecord record) {
final VariantContext lastVariant = region().variants().get(region().variants().size() - 1);
return record.getAlignmentStart() <= region().start()
&& record.getAlignmentEnd() >= lastVariant.getStart() + lastVariant.getReference().length() - 1;
}
Example 19
| Source File: TandemRepeat.java From gatk with BSD 3-Clause "New" or "Revised" License | 4 votes |
|
public static Pair<List<Integer>, byte[]> getNumTandemRepeatUnits(final ReferenceContext ref, final VariantContext vc) {
final byte[] refBases = ref.getBases();
final int startIndex = vc.getStart() + 1 - ref.getWindow().getStart(); // +1 to exclude leading match base common to VC's ref and alt alleles
return GATKVariantContextUtils.getNumTandemRepeatUnits(vc, Arrays.copyOfRange(refBases, startIndex, refBases.length));
}
