Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContext

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        final GenomeLoc loc = data.getActiveRegion().getExtendedLoc();
        final List<Boolean> seenBP = new ArrayList<>(Collections.nCopies(data.getActiveRegion().getLocation().size(), false));

        for ( int i = 0; i < loc.size(); i++ ) {
            final GenomeLoc curPos = parser.createGenomeLoc(loc.getContig(), loc.getStart() + i);
            final VariantContext call = model.getOverlappingVariantContext(curPos, calls);
            final VariantContext refModel = model.getOverlappingVariantContext(curPos, contexts);

            if ( ! data.getActiveRegion().getLocation().containsP(curPos) ) {
                // part of the extended interval, but not the full interval
                Assert.assertNull(refModel);
                continue;
            }

            if ( call != null ) {
                if (call.isVariant() && refModel.getType() ==  VariantContext.Type.SYMBOLIC ) {
                    //Assert.assertEquals(refModel, call, "Should have found call " + call + " but found " + refModel + " instead");
                    Assert.assertTrue(call.getReference().length() > 1); // must be a deletion.
                    Assert.assertTrue(call.getStart() < refModel.getStart()); // the deletion must not start at the same position
                    Assert.assertEquals(call.getReference().getBaseString().substring(refModel.getStart() - call.getStart(),
                                refModel.getStart() - call.getStart() + 1), refModel.getReference().getBaseString(), "" + data.getRefHap()); // the reference must be the same.
                    Assert.assertTrue(refModel.getGenotype(0).getGQ() <= 0); // No confidence in the reference hom-ref call across the deletion
                    Assert.assertEquals(refModel.getAlleles().size(),2); // the reference and the lonelly <NON_REF>
                    Assert.assertEquals(refModel.getAlleles().get(1),GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
                } else {
                    Assert.assertEquals(refModel, call, "Should have found call " + call + " but found " + refModel + " instead");
                }

            } else {
                final int expectedDP = expectedDPs.get(curPos.getStart() - data.getActiveRegion().getLocation().getStart());
                Assert.assertEquals(refModel.getStart(), loc.getStart() + i);
                Assert.assertEquals(refModel.getEnd(), loc.getStart() + i);
                Assert.assertFalse(refModel.hasLog10PError());
                Assert.assertEquals(refModel.getAlternateAlleles().size(), 1);
                Assert.assertEquals(refModel.getAlternateAllele(0), GATKVariantContextUtils.NON_REF_SYMBOLIC_ALLELE);
                Assert.assertTrue(refModel.hasGenotype(sample));

                final Genotype g = refModel.getGenotype(sample);
                Assert.assertTrue(g.hasAD());
                Assert.assertTrue(g.hasDP());
                Assert.assertEquals(g.getDP(), expectedDP);
                Assert.assertTrue(g.hasGQ());
                Assert.assertTrue(g.hasPL());
            }

            final VariantContext vc = call == null ? refModel : call;
            if ( curPos.getStart() == vc.getStart() ) {
                for ( int pos = vc.getStart(); pos <= vc.getEnd(); pos++ ) {
                    final int j = pos - data.getActiveRegion().getLocation().getStart();
                    Assert.assertFalse(seenBP.get(j));
                    seenBP.set(j, true);
                }
            }
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        for( final VariantContext vc : VCs ) {

            if( VariantDataManager.checkVariationClass( vc, MODE ) && (IGNORE_ALL_FILTERS || vc.isNotFiltered() || ignoreInputFilterSet.containsAll(vc.getFilters())) ) {

                final VariantContext recalDatum = getMatchingRecalVC(vc, recals);
                if( recalDatum == null ) {
                    throw new UserException("Encountered input variant which isn't found in the input recal file. Please make sure VariantRecalibrator and ApplyRecalibration were run on the same set of input variants. First seen at: " + vc );
                }

                final String lodString = recalDatum.getAttributeAsString(VariantRecalibrator.VQS_LOD_KEY, null);
                if( lodString == null ) {
                    throw new UserException("Encountered a malformed record in the input recal file. There is no lod for the record at: " + vc );
                }
                final double lod;
                try {
                    lod = Double.valueOf(lodString);
                } catch (NumberFormatException e) {
                    throw new UserException("Encountered a malformed record in the input recal file. The lod is unreadable for the record at: " + vc );
                }

                VariantContextBuilder builder = new VariantContextBuilder(vc);

                // Annotate the new record with its VQSLOD and the worst performing annotation
                builder.attribute(VariantRecalibrator.VQS_LOD_KEY, lod);
                builder.attribute(VariantRecalibrator.CULPRIT_KEY, recalDatum.getAttribute(VariantRecalibrator.CULPRIT_KEY));
                if ( recalDatum.hasAttribute(VariantRecalibrator.POSITIVE_LABEL_KEY))
                    builder.attribute(VariantRecalibrator.POSITIVE_LABEL_KEY, true);
                if ( recalDatum.hasAttribute(VariantRecalibrator.NEGATIVE_LABEL_KEY))
                    builder.attribute(VariantRecalibrator.NEGATIVE_LABEL_KEY, true);

                final String filterString = generateFilterString(lod);

                if( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
                    builder.passFilters();
                } else {
                    builder.filters(filterString);
                }

                final VariantContext outputVC = builder.make();
                if( !EXCLUDE_FILTERED || outputVC.isNotFiltered() ) {
                    vcfWriter.add( outputVC );
                }
            } else { // valid VC but not compatible with this mode, so just emit the variant untouched
                vcfWriter.add( vc );
            }
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        }
        final GenomeLoc loc = genomeLocParser.createGenomeLoc(artificialContig,locStart+offset,locStart+offset);
        final ReferenceContext referenceContext = new ReferenceContext(genomeLocParser,loc,window,windowBases.getBytes());

        final VariantContext vc = new VariantContextBuilder("test", artificialContig, locStart+offset, locStart+offset+alleles.get(0).length()-1, alleles).make();
        final Pair<VariantContext,Integer> result = LeftAlignAndTrimVariants.alignAndWrite(vc,referenceContext);
        Assert.assertTrue(result.second == (offset>0?1:0));
        Assert.assertEquals(result.first.getStart(), locStart);

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            alleles.add(Allele.create(prefix+"A", true));
            alleles.add(Allele.create(prefix+Utils.dupString("A",Math.abs(indelSize)+1),false));

        }

        final VariantContext vc = GATKVariantContextUtils.trimAlleles( new VariantContextBuilder("test", artificialContig, locStart + offset, locStart + offset + alleles.get(0).length() - 1, alleles).make(),true,true);
        if (indelSize>0)
            Assert.assertEquals(vc.getReference().length(),1);
        else
            Assert.assertEquals(vc.getReference().length(),Math.abs(indelSize)+1);
    }
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        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);
        final String line = lineIterator.next();
        Assert.assertFalse(line == null);
        final VariantContext vc = codec.decode(line);
        Assert.assertTrue(vc.isBiallelic());
        Assert.assertTrue(vc.getReference().basesMatch("ATGTATG"));
        Assert.assertTrue(vc.getAlternateAllele(0).basesMatch("A"));
    }
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        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        genomeLocParser = new GenomeLocParser(seq);
    }

    private VariantContext makeVC(final String source, final String id, final List<String> alleles) {
        final VariantContext vc = GATKVariantContextUtils.makeFromAlleles(source, "20", 10, alleles);
        return new VariantContextBuilder(vc).id(id).make();
    }
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    @DataProvider(name = "AnnotateRsIDData")
    public Object[][] makeAnnotateRsIDData() {
        List<Object[]> tests = new ArrayList<>();

        // this functionality can be adapted to provide input data for whatever you might want in your data
        final VariantContext callNoIDAC = makeVC("call", VCFConstants.EMPTY_ID_FIELD, Arrays.asList("A", "C"));
        final VariantContext callNoIDAT = makeVC("call", VCFConstants.EMPTY_ID_FIELD, Arrays.asList("A", "T"));
        final VariantContext callIDAC = makeVC("call", "foo", Arrays.asList("A", "C"));
        final VariantContext callExistingIDAC = makeVC("call", "rsID1", Arrays.asList("A", "C"));

        final VariantContext dbSNP_AC = makeVC("DBSNP", "rsID1", Arrays.asList("A", "C"));
        final VariantContext dbSNP_AT = makeVC("DBSNP", "rsID2", Arrays.asList("A", "T"));
        final VariantContext dbSNP_AG = makeVC("DBSNP", "rsID3", Arrays.asList("A", "G"));
        final VariantContext dbSNP_AC_AT = makeVC("DBSNP", "rsID1;rsID2", Arrays.asList("A", "C", "T"));
        final VariantContext dbSNP_AC_AG = makeVC("DBSNP", "rsID1;rsID3", Arrays.asList("A", "C", "G"));

        tests.add(new Object[]{callNoIDAC, Arrays.asList(dbSNP_AC), dbSNP_AC.getID(), true});
        tests.add(new Object[]{callNoIDAC, Arrays.asList(dbSNP_AT), VCFConstants.EMPTY_ID_FIELD, false});
        tests.add(new Object[]{callIDAC, Arrays.asList(dbSNP_AC), "foo" + ";" + dbSNP_AC.getID(), true});
        tests.add(new Object[]{callIDAC, Arrays.asList(dbSNP_AT), "foo", false});
        tests.add(new Object[]{callExistingIDAC, Arrays.asList(dbSNP_AC), "rsID1", true});
        tests.add(new Object[]{callExistingIDAC, Arrays.asList(dbSNP_AT), "rsID1", false});

        final VariantContext callNoIDACT = makeVC("call", VCFConstants.EMPTY_ID_FIELD, Arrays.asList("A", "C", "T"));
        tests.add(new Object[]{callNoIDACT, Arrays.asList(dbSNP_AC), dbSNP_AC.getID(), true});
        tests.add(new Object[]{callNoIDACT, Arrays.asList(dbSNP_AT), dbSNP_AT.getID(), true});
        tests.add(new Object[]{callNoIDACT, Arrays.asList(dbSNP_AG), VCFConstants.EMPTY_ID_FIELD, false});
        tests.add(new Object[]{callNoIDACT, Arrays.asList(dbSNP_AC_AT), dbSNP_AC_AT.getID(), true});
        tests.add(new Object[]{callNoIDACT, Arrays.asList(dbSNP_AC_AG), dbSNP_AC_AG.getID(), true});

        // multiple options
        tests.add(new Object[]{callNoIDAC, Arrays.asList(dbSNP_AC, dbSNP_AT), "rsID1", true});
        tests.add(new Object[]{callNoIDAC, Arrays.asList(dbSNP_AT, dbSNP_AC), "rsID1", true});
        tests.add(new Object[]{callNoIDAC, Arrays.asList(dbSNP_AC_AT), "rsID1;rsID2", true});
        tests.add(new Object[]{callNoIDAT, Arrays.asList(dbSNP_AC_AT), "rsID1;rsID2", true});
        tests.add(new Object[]{callNoIDAC, Arrays.asList(dbSNP_AC_AG), "rsID1;rsID3", true});
        tests.add(new Object[]{callNoIDAT, Arrays.asList(dbSNP_AC_AG), VCFConstants.EMPTY_ID_FIELD, false});

        final VariantContext dbSNP_AC_FAIL = new VariantContextBuilder(makeVC("DBSNP", "rsID1", Arrays.asList("A", "C"))).filter("FAIL").make();
        tests.add(new Object[]{callNoIDAC, Arrays.asList(dbSNP_AC_FAIL), VCFConstants.EMPTY_ID_FIELD, false});


        return tests.toArray(new Object[][]{});
    }
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    }

    @Test(dataProvider = "AnnotateRsIDData")
    public void testAnnotateRsID(final VariantContext toAnnotate, final List<VariantContext> dbSNPRecords, final String expectedID, final boolean expectOverlap) throws Exception {
        final VariantOverlapAnnotator annotator = makeAnnotator("dbnsp");
        final VariantContext annotated = annotator.annotateRsID(dbSNPRecords, toAnnotate);
        Assert.assertNotNull(annotated);
        Assert.assertEquals(annotated.getID(), expectedID);
    }
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    @Test(dataProvider = "AnnotateRsIDData")
    public void testAnnotateOverlaps(final VariantContext toAnnotate, final List<VariantContext> records, final String expectedID, final boolean expectOverlap) throws Exception {
        final String name = "binding";
        final VariantOverlapAnnotator annotator = makeAnnotator(null, name);
        final VariantContext annotated = annotator.annotateOverlap(records, name, toAnnotate);
        Assert.assertNotNull(annotated);
        Assert.assertEquals(annotated.getID(), toAnnotate.getID(), "Shouldn't modify annotation");
        Assert.assertEquals(annotated.hasAttribute(name), expectOverlap);
        if ( expectOverlap ) {
            Assert.assertEquals(annotated.getAttribute(name), true);
        }
    }
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                    logger.info("-- " + toMerge.firstVC);
                    logger.info("-- " + toMerge.secondVC);
                }

                if( pPhased > MERGE_EVENTS_PROB_PHASED_THRESHOLD) {
                    final VariantContext mergedVC = createMergedVariantContext(toMerge.firstVC, toMerge.secondVC, ref, refLoc);
                    // if for some reason the merging resulting in a bad allele, mergedVC will be null, and we will just remove first and second
                    replaceVariantContextsInMap(haplotypes, startPosKeySet, mergedVC, toMerge.firstVC, toMerge.secondVC);
                    return true; // break out of tree set iteration since it was just updated, start over from the beginning and keep merging events
                }
            }
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Related Classes of htsjdk.variant.variantcontext.VariantContext

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  • org.broadinstitute.gatk.engine.EngineFeaturesIntegrationTest
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