Examples of org.broadinstitute.gatk.utils.UnvalidatingGenomeLoc

org.broadinstitute.gatk.utils.UnvalidatingGenomeLoc
GenomeLocs are very useful objects to keep track of genomic locations and perform set operations with them. However, GenomeLocs are bound to strict validation through the GenomeLocParser and cannot be created easily for small tasks that do not require the rigors of the GenomeLocParser validation UnvalidatingGenomeLoc is a simple utility to create GenomeLocs without going through the parser. WARNING: SHOULD BE USED ONLY BY EXPERT USERS WHO KNOW WHAT THEY ARE DOING! User: carneiro Date: 10/16/12 Time: 2:07 PM

        final Metrics noData = new Metrics(0.5, 0.0, 0.0, 0, 20);
        final Metrics unknown = new Metrics(0.5, 30.0, 120000.0, 2500, 20);


        final Metrics[] array = {unmappable, highGC, lowGC, unsequenceable, noData, unknown};


        final GenomeLoc testInterval = new UnvalidatingGenomeLoc("chr1", 0, 10000, 20000);
        final GenomeLoc smallInterval = new UnvalidatingGenomeLoc("chr1", 0, 1, 4);




        Assert.assertNotEquals(tool.checkMappability(unmappable), "");
        Assert.assertNotEquals(tool.checkGCContent(highGC), "");
        Assert.assertNotEquals(tool.checkGCContent(lowGC), "");

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            Assert.assertEquals(tool.interpret(m, smallInterval), QualifyMissingIntervals.Interpretation.SMALL_INTERVAL.toString());
    }


    @Test(enabled = true)
    void testGetPositionInTarget () {
        final UnvalidatingGenomeLoc target = new UnvalidatingGenomeLoc("a", 0, 30, 50);
        final List<GenomeLoc> targets = new ObjectArrayList<>(1);
        targets.add(target);


        // left overlap
        UnvalidatingGenomeLoc interval = new UnvalidatingGenomeLoc("a", 0, 10, 50);
        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -20);


        // right overlap
        interval = new UnvalidatingGenomeLoc("a", 0, 40, 60);
        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -10);


        // interval > target with short right tail
        interval = new UnvalidatingGenomeLoc("a", 0, 10, 60);
        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -10);


        // interval > target with short left tail
        interval = new UnvalidatingGenomeLoc("a", 0, 10, 80);
        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -30);


        // interval < target with short right tail
        interval = new UnvalidatingGenomeLoc("a", 0, 32, 40);
        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), 2);


        // interval < target with short left tail
        interval = new UnvalidatingGenomeLoc("a", 0, 40, 42);
        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), 8);


        // no overlap
        interval = new UnvalidatingGenomeLoc("a", 0, 40, 42);
        Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, new ObjectArrayList<GenomeLoc>()), Integer.MIN_VALUE);
    }

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    @Test
    public void trimHaplotypesToNullAlleleTest() {
        // we need a case where start and stop > haplotype coordinates
        final int start = 100, stop = 100;
  final Haplotype h = new Haplotype(new byte[]{(byte)'A'}, new UnvalidatingGenomeLoc("1", 0, 10, 10));
  final Map<Allele, Haplotype> input = new HashMap<Allele, Haplotype>(1);
  input.put(Allele.create("A"), h);


  final Map<Allele, Haplotype> output = PairHMMIndelErrorModel.trimHaplotypes(input, start, stop, null);
        Assert.assertTrue(output.isEmpty());

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     * Example testng test using MyDataProvider
     */
    @Test(dataProvider = "BlockSubstitutionsData")
    public void testBlockSubstitutionsData(final String refBases, final String haplotypeBases, final String cigar, final VariantContext expectedBlock) {
        final Haplotype hap = new Haplotype(haplotypeBases.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
        final GenomeLoc loc = new UnvalidatingGenomeLoc(CHR, 0, 1, refBases.length());
        final EventMap ee = new EventMap(hap, refBases.getBytes(), loc, NAME);
        ee.replaceClumpedEventsWithBlockSubstitutions();
        Assert.assertEquals(ee.getNumberOfEvents(), 1);
        final VariantContext actual = ee.getVariantContexts().iterator().next();
        Assert.assertTrue(GATKVariantContextUtils.equalSites(actual, expectedBlock), "Failed with " + actual);

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     * Example testng test using MyDataProvider
     */
    @Test(dataProvider = "AdjacentSNPIndelTest")
    public void testAdjacentSNPIndelTest(final String refBases, final String haplotypeBases, final String cigar, final List<List<String>> expectedAlleles) {
        final Haplotype hap = new Haplotype(haplotypeBases.getBytes(), false, 0, TextCigarCodec.getSingleton().decode(cigar));
        final GenomeLoc loc = new UnvalidatingGenomeLoc(CHR, 0, 1, refBases.length());
        final EventMap ee = new EventMap(hap, refBases.getBytes(), loc, NAME);
        ee.replaceClumpedEventsWithBlockSubstitutions();
        Assert.assertEquals(ee.getNumberOfEvents(), expectedAlleles.size());
        final List<VariantContext> actuals = new ArrayList<VariantContext>(ee.getVariantContexts());
        for ( int i = 0; i < ee.getNumberOfEvents(); i++ ) {

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    @DataProvider(name = "TrimmingData")
    public Object[][] makeTrimmingData() {
        List<Object[]> tests = new ArrayList<Object[]>();


        // this functionality can be adapted to provide input data for whatever you might want in your data
        final GenomeLoc loc = new UnvalidatingGenomeLoc("20", 0, 10, 20);
        final String fullBases = "ACGTAACCGGT";
        for ( int trimStart = loc.getStart(); trimStart < loc.getStop(); trimStart++ ) {
            for ( int trimStop = trimStart; trimStop <= loc.getStop(); trimStop++ ) {
                final int start = trimStart - loc.getStart();
                final int stop = start + (trimStop - trimStart) + 1;
                final GenomeLoc trimmedLoc = new UnvalidatingGenomeLoc("20", 0, start + loc.getStart(), stop + loc.getStart() - 1);
                final String expectedBases = fullBases.substring(start, stop);
                final Haplotype full = new Haplotype(fullBases.getBytes(), loc);
                final Haplotype trimmed = new Haplotype(expectedBases.getBytes(), trimmedLoc);


                final int hapStart = 10;
                full.setAlignmentStartHapwrtRef(hapStart);
                full.setCigar(TextCigarCodec.getSingleton().decode(full.length() + "M"));


                trimmed.setAlignmentStartHapwrtRef(hapStart + start);
                trimmed.setCigar(TextCigarCodec.getSingleton().decode(trimmed.length() + "M"));


                tests.add(new Object[]{full, trimmedLoc, trimmed});
            }
        }


        final Haplotype full = new Haplotype("ACT".getBytes(), new UnvalidatingGenomeLoc("20", 0, 10, 14));
        full.setAlignmentStartHapwrtRef(10);
        full.setCigar(TextCigarCodec.getSingleton().decode("1M2D2M"));
        tests.add(new Object[]{full, new UnvalidatingGenomeLoc("20", 0, 11, 12), null});
        tests.add(new Object[]{full, new UnvalidatingGenomeLoc("20", 0, 10, 12), null});
        tests.add(new Object[]{full, new UnvalidatingGenomeLoc("20", 0, 11, 13), null});


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

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        }
    }


    @Test(expectedExceptions = IllegalArgumentException.class)
    public void testBadTrimLoc() {
        final GenomeLoc loc = new UnvalidatingGenomeLoc("20", 0, 10, 20);
        final Haplotype hap = new Haplotype("ACGTAACCGGT".getBytes(), loc);
        hap.trim(new UnvalidatingGenomeLoc("20", 0, 1, 20));
    }

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    }


    @Test(expectedExceptions = IllegalStateException.class)
    public void testBadTrimNoLoc() {
        final Haplotype hap = new Haplotype("ACGTAACCGGT".getBytes());
        hap.trim(new UnvalidatingGenomeLoc("20", 0, 1, 20));
    }

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Related Classes of org.broadinstitute.gatk.utils.UnvalidatingGenomeLoc

org.broadinstitute.gatk.tools.walkers.diagnostics.missing.QualifyMissingIntervalsUnitTest

org.broadinstitute.gatk.tools.walkers.indels.PairHMMIndelErrorModelUnitTest

org.broadinstitute.gatk.utils.haplotype.EventMapUnitTest

org.broadinstitute.gatk.utils.haplotype.HaplotypeUnitTest

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