Package htsjdk.variant.variantcontext

Examples of htsjdk.variant.variantcontext.VariantContextBuilder

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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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        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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        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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        }


        final Allele refAllele = Allele.create( ArrayUtils.subarray(refBases, iii, refBases.length), true );
        final Allele altAllele =  Allele.create( ArrayUtils.subarray(altBases, iii, altBases.length), false );
        return new VariantContextBuilder("merged", thisVC.getChr(), thisVC.getStart() + iii, nextVC.getEnd(), Arrays.asList(refAllele, altAllele)).make();
    }
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public class HomRefBlockUnitTest extends BaseTest {
    VariantContext vc;

    @BeforeMethod
    public void setUp() throws Exception {
        vc = new VariantContextBuilder("foo", "20", 1, 1, Arrays.asList(Allele.create("A", true), Allele.create("C"))).make();
    }
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    }

    @Test(dataProvider = "ContiguousData")
    public void testIsContiguous(final String contig, final int pos, final boolean expected) {
        final HomRefBlock band = new HomRefBlock(vc, 10, 20, HomoSapiensConstants.DEFAULT_PLOIDY);
        final VariantContext testVC = new VariantContextBuilder(vc).chr(contig).start(pos).stop(pos).make();
        Assert.assertEquals(band.isContiguous(testVC), expected);
    }
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        final byte[] ref = "AATTCCGGAATTCCGGAATT".getBytes();
        final GenomeLoc refLoc = genomeLocParser.createGenomeLoc("2", 1700, 1700 + ref.length);

        // SNP + SNP = simple MNP
        VariantContext thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","G").make();
        VariantContext nextVC = new VariantContextBuilder().loc("2", 1704, 1704).alleles("C","G").make();
        VariantContext truthVC = new VariantContextBuilder().loc("2", 1703, 1704).alleles("TC","GG").source("merged").make();
        VariantContext mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // SNP + ref + SNP = MNP with ref base gap
        thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","G").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("C","G").make();
        truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","GCG").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // insertion + SNP
        thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","TAAAAA").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("C","G").make();
        truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","TAAAAACG").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // SNP + insertion
        thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","G").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("C","CAAAAA").make();
        truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","GCCAAAAA").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // deletion + SNP
        thisVC = new VariantContextBuilder().loc("2", 1703, 1704).alleles("TC","T").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("C","G").make();
        truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","TG").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // SNP + deletion
        thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","G").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1706).alleles("CG","C").make();
        truthVC = new VariantContextBuilder().loc("2", 1703, 1706).alleles("TCCG","GCC").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // insertion + deletion = MNP
        thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","TA").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1706).alleles("CG","C").make();
        truthVC = new VariantContextBuilder().loc("2", 1704, 1706).alleles("CCG","ACC").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // insertion + deletion
        thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","TAAAAA").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1706).alleles("CG","C").make();
        truthVC = new VariantContextBuilder().loc("2", 1703, 1706).alleles("TCCG","TAAAAACC").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // insertion + insertion
        thisVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("T","TA").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1705).alleles("C","CA").make();
        truthVC = new VariantContextBuilder().loc("2", 1703, 1705).alleles("TCC","TACCA").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // deletion + deletion
        thisVC = new VariantContextBuilder().loc("2", 1701, 1702).alleles("AT","A").make();
        nextVC = new VariantContextBuilder().loc("2", 1705, 1706).alleles("CG","C").make();
        truthVC = new VariantContextBuilder().loc("2", 1701, 1706).alleles("ATTCCG","ATCC").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // deletion + insertion (abutting)
        thisVC = new VariantContextBuilder().loc("2", 1701, 1702).alleles("AT","A").make();
        nextVC = new VariantContextBuilder().loc("2", 1702, 1702).alleles("T","GCGCGC").make();
        truthVC = new VariantContextBuilder().loc("2", 1701, 1702).alleles("AT","AGCGCGC").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());

        // complex + complex
        thisVC = new VariantContextBuilder().loc("2", 1703, 1704).alleles("TC","AAA").make();
        nextVC = new VariantContextBuilder().loc("2", 1706, 1707).alleles("GG","AC").make();
        truthVC = new VariantContextBuilder().loc("2", 1703, 1707).alleles("TCCGG","AAACAC").source("merged").make();
        mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        logger.warn(truthVC + " == " + mergedVC);
        Assert.assertTrue(truthVC.hasSameAllelesAs(mergedVC));
        Assert.assertEquals(truthVC.getStart(), mergedVC.getStart());
        Assert.assertEquals(truthVC.getEnd(), mergedVC.getEnd());
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    public void testInsertionDeletionBecomingNullAllele() {
        final byte[] ref = "CAAA".getBytes();
        final GenomeLoc refLoc = genomeLocParser.createGenomeLoc("2", 1700, 1700 + ref.length);

        // insertion + deletion results in a null allele, should return false
        final VariantContext thisVC = new VariantContextBuilder().loc("2", 1700, 1701).alleles("CA","C").make();
        final VariantContext nextVC = new VariantContextBuilder().loc("2", 1703, 1703).alleles("A","AA").make();
        final VariantContext mergedVC = merger.createMergedVariantContext(thisVC, nextVC, ref, refLoc);
        Assert.assertNull(mergedVC,  "Insertion deletion becoming a null allele should return a null variant context");
    }
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    @Test(dataProvider = "AssembleIntervalsWithVariantData")
    public void testAssembleRefAndSNP(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse, final int variantSite) {
        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
        final Allele refBase = Allele.create(refBases[variantSite], true);
        final Allele altBase = Allele.create((byte)(refBase.getBases()[0] == 'A' ? 'C' : 'A'), false);
        final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite, Arrays.asList(refBase, altBase));
        testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());
    }
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    public void testAssembleRefAndDeletion(final ReadThreadingAssembler assembler, final GenomeLoc loc, final int nReadsToUse, final int variantSite) {
        final byte[] refBases = seq.getSubsequenceAt(loc.getContig(), loc.getStart(), loc.getStop()).getBases();
        for ( int deletionLength = 1; deletionLength < 10; deletionLength++ ) {
            final Allele refBase = Allele.create(new String(refBases).substring(variantSite, variantSite + deletionLength + 1), true);
            final Allele altBase = Allele.create(refBase.getBases()[0], false);
            final VariantContextBuilder vcb = new VariantContextBuilder("x", loc.getContig(), variantSite, variantSite + deletionLength, Arrays.asList(refBase, altBase));
            testAssemblyWithVariant(assembler, refBases, loc, nReadsToUse, vcb.make());
        }
    }
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