Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.FormatUtil.format()

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        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.HET_TRUTH_STATES)), "0.769231");
        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES)), "0.766234");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.HOM_VAR_CALL_STATES)), "0.730337");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES)), "?");
        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES)), "0.734807");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.VAR_CALL_STATES)), "0.707447");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES)), "0.769231");
    }

    private void assertNonZeroCountsAgree(final GenotypeConcordanceCounts counter, final Map<TruthAndCallStates, Integer> expectedCountMap) {
        for (final TruthState truthState : TruthState.values()) {
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        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES)), "0.766234");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.HOM_VAR_CALL_STATES)), "0.730337");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.HOM_VAR_TRUTH_STATES)), "?");
        Assert.assertEquals(fmt.format(concordanceCounts.getSensitivity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES)), "0.734807");
        Assert.assertEquals(fmt.format(concordanceCounts.Ppv(scheme, GenotypeConcordanceCounts.VAR_CALL_STATES)), "0.707447");
        Assert.assertEquals(fmt.format(concordanceCounts.getSpecificity(scheme, GenotypeConcordanceCounts.VAR_TRUTH_STATES)), "0.769231");
    }

    private void assertNonZeroCountsAgree(final GenotypeConcordanceCounts counter, final Map<TruthAndCallStates, Integer> expectedCountMap) {
        for (final TruthState truthState : TruthState.values()) {
            for (final CallState callState : CallState.values()) {
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        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)), "?");
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        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");
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        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");
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        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");
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        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");
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        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
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        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;
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        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";
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