Package picard.vcf.GenotypeConcordanceStates

Examples of picard.vcf.GenotypeConcordanceStates.TruthAndCallStates

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        genotypeConcordance.OUTPUT = outputBaseFileName;

        Assert.assertEquals(genotypeConcordance.instanceMain(new String[0]), 0);

        final Map<TruthAndCallStates, Integer> nonZeroCounts = new HashMap<TruthAndCallStates, Integer>();
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HET_REF_VAR1, CallState.HET_REF_VAR1), 1);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.VC_FILTERED, CallState.VC_FILTERED), 2);

        GenotypeConcordanceCounts concordanceCounts = genotypeConcordance.getSnpCounter();
        assertNonZeroCountsAgree(concordanceCounts, nonZeroCounts);

        final FormatUtil fmt = new FormatUtil();

        final GenotypeConcordanceScheme scheme = new GenotypeConcordanceScheme();
        concordanceCounts.validateCountsAgainstScheme(scheme);

        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HET_TRUTH_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.HET_CALL_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.HET_TRUTH_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES)), "?");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.HOM_VAR_CALL_STATES)), "?");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES)), "?");
        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.VAR_CALL_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES)), "1");

        // Now run it again with different samples
        genotypeConcordance.TRUTH_VCF = CEU_TRIOS_SNPS_VCF;
        genotypeConcordance.TRUTH_SAMPLE = "NA12878";
        genotypeConcordance.CALL_VCF = CEU_TRIOS_SNPS_VCF;
        genotypeConcordance.CALL_SAMPLE = "NA12891";
        genotypeConcordance.INTERVALS = Collections.singletonList(INTERVALS_FILE);
        Assert.assertEquals(genotypeConcordance.instanceMain(new String[0]), 0);

        nonZeroCounts.clear();
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HOM_REF, CallState.HET_REF_VAR1), 1);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HET_REF_VAR1, CallState.HET_REF_VAR1), 1);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.VC_FILTERED, CallState.VC_FILTERED), 2);

        concordanceCounts = genotypeConcordance.getSnpCounter();
        assertNonZeroCountsAgree(concordanceCounts, nonZeroCounts);

        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HET_TRUTH_STATES)), "1");
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                                                       final int minGq, final int minDp) {
        final GenotypeConcordance genotypeConcordance = new GenotypeConcordance();
        genotypeConcordance.TRUTH_SAMPLE = TRUTH_SAMPLE_NAME;
        genotypeConcordance.CALL_SAMPLE = CALL_SAMPLE_NAME;

        final TruthAndCallStates truthAndCallStates = genotypeConcordance.determineState(truthVariantContext, TRUTH_SAMPLE_NAME,
                callVariantContext, CALL_SAMPLE_NAME, minGq, minDp);
        Assert.assertEquals(truthAndCallStates.truthState, expectedTruthState);
        Assert.assertEquals(truthAndCallStates.callState, expectedCallState);
    }
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        genotypeConcordance.OUTPUT = outputBaseFileName;

        Assert.assertEquals(genotypeConcordance.instanceMain(new String[0]), 0);

        final Map<TruthAndCallStates, Integer> nonZeroCounts = new HashMap<TruthAndCallStates, Integer>();
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HET_REF_VAR1, CallState.HET_REF_VAR1), 104);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HOM_VAR1, CallState.HOM_VAR1), 59);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.VC_FILTERED, CallState.VC_FILTERED), 40);

        GenotypeConcordanceCounts concordanceCounts = genotypeConcordance.getSnpCounter();
        assertNonZeroCountsAgree(concordanceCounts, nonZeroCounts);

        final FormatUtil fmt = new FormatUtil();

        final GenotypeConcordanceScheme scheme = new GenotypeConcordanceScheme();
        concordanceCounts.validateCountsAgainstScheme(scheme);

        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HET_TRUTH_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.HET_CALL_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.HET_TRUTH_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.HOM_VAR_CALL_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES)), "?");
        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.VAR_CALL_STATES)), "1");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES)), "1");

        // Now run it again with different samples
        genotypeConcordance.TRUTH_VCF = CEU_TRIOS_SNPS_VCF;
        genotypeConcordance.TRUTH_SAMPLE = "NA12878";
        genotypeConcordance.CALL_VCF = CEU_TRIOS_SNPS_VCF;
        genotypeConcordance.CALL_SAMPLE = "NA12891";
        Assert.assertEquals(genotypeConcordance.instanceMain(new String[0]), 0);

        nonZeroCounts.clear();
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HOM_REF, CallState.HET_REF_VAR1), 31);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HET_REF_VAR1, CallState.HOM_REF), 30);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HET_REF_VAR1, CallState.HET_REF_VAR1), 50);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HET_REF_VAR1, CallState.HOM_VAR1), 24);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HOM_VAR1, CallState.HET_REF_VAR1), 18);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.HOM_VAR1, CallState.HOM_VAR1), 41);
        nonZeroCounts.put(new TruthAndCallStates(TruthState.VC_FILTERED, CallState.VC_FILTERED), 49);

        concordanceCounts = genotypeConcordance.getSnpCounter();
        assertNonZeroCountsAgree(concordanceCounts, nonZeroCounts);

        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HET_TRUTH_STATES)), "0.711538");
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    }

    private void assertNonZeroCountsAgree(final GenotypeConcordanceCounts counter, final Map<TruthAndCallStates, Integer> expectedCountMap) {
        for (final TruthState truthState : TruthState.values()) {
            for (final CallState callState : CallState.values()) {
                Integer expectedCount = expectedCountMap.get(new TruthAndCallStates(truthState, callState));
                if (expectedCount == null) expectedCount = 0;
                Assert.assertEquals(counter.getCount(truthState, callState), expectedCount.intValue());
            }
        }
    }
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Related Classes of picard.vcf.GenotypeConcordanceStates.TruthAndCallStates

  • picard.vcf.GenotypeConcordanceTest
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