Package htsjdk.samtools.util

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

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                        out.println(interval.getSequence() + "\t" +
                                    interval.getStart() + "\t" +
                                    interval.getEnd() + "\t" +
                                    interval.length() + "\t" +
                                    interval.getName() + "\t" +
                                    fmt.format(gcDouble) + "\t" +
                                    fmt.format(coverage) + "\t" +
                                    fmt.format(coverage / this.metrics.MEAN_TARGET_COVERAGE)
                        );
                    }
                }
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                                    interval.getStart() + "\t" +
                                    interval.getEnd() + "\t" +
                                    interval.length() + "\t" +
                                    interval.getName() + "\t" +
                                    fmt.format(gcDouble) + "\t" +
                                    fmt.format(coverage) + "\t" +
                                    fmt.format(coverage / this.metrics.MEAN_TARGET_COVERAGE)
                        );
                    }
                }
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                                    interval.getEnd() + "\t" +
                                    interval.length() + "\t" +
                                    interval.getName() + "\t" +
                                    fmt.format(gcDouble) + "\t" +
                                    fmt.format(coverage) + "\t" +
                                    fmt.format(coverage / this.metrics.MEAN_TARGET_COVERAGE)
                        );
                    }
                }

                if (out != null) out.close();
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        expectedMetrics.READ_PAIR_DUPLICATES = expectedMetrics.READ_PAIR_DUPLICATES / 2;
        expectedMetrics.READ_PAIRS_EXAMINED = expectedMetrics.READ_PAIRS_EXAMINED / 2;
        expectedMetrics.calculateDerivedMetrics();

        // Have to run this Double value through the same format/parsing operations as during a file write/read
        expectedMetrics.PERCENT_DUPLICATION = formatter.parseDouble(formatter.format(expectedMetrics.PERCENT_DUPLICATION));
    }

    public void setExpectedOpticalDuplicate(final int expectedOpticalDuplicatePairs) {
        expectedMetrics.READ_PAIR_OPTICAL_DUPLICATES = expectedOpticalDuplicatePairs;
    }
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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)), "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)), "?");
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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)), "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");
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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)), "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");
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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)), "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");
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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)), "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");
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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)), "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
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