Examples with MetricsFile htsjdk.samtools.metrics.MetricsFile used on opensource projects

Example 21 with MetricsFile

use of htsjdk.samtools.metrics.MetricsFile in project gatk by broadinstitute.

the class CollectAlignmentSummaryMetricsTest method testMultipleLevelsOfMetrics.

@Test
public void testMultipleLevelsOfMetrics() throws IOException {
    final File input = new File(TEST_DATA_DIR, "summary_alignment_stats_test_multiple.sam");
    final File outfile = BaseTest.createTempFile("alignmentMetrics", ".txt");
    final String[] args = new String[] { "--input", input.getAbsolutePath(), "--output", outfile.getAbsolutePath(), "--METRIC_ACCUMULATION_LEVEL", "ALL_READS", "--METRIC_ACCUMULATION_LEVEL", "SAMPLE", "--METRIC_ACCUMULATION_LEVEL", "LIBRARY", "--METRIC_ACCUMULATION_LEVEL", "READ_GROUP" };
    runCommandLine(args);
    final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<>();
    output.read(new FileReader(outfile));
    for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
        Assert.assertEquals(metrics.MEAN_READ_LENGTH, 101.0);
        if (metrics.SAMPLE == null) {
            switch(metrics.CATEGORY) {
                case FIRST_OF_PAIR:
                    Assert.assertEquals(metrics.TOTAL_READS, 9);
                    Assert.assertEquals(metrics.PF_READS, 7);
                    Assert.assertEquals(metrics.PF_NOISE_READS, 1);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                    Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                    Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                    Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                    Assert.assertEquals(metrics.BAD_CYCLES, 19);
                    break;
                case SECOND_OF_PAIR:
                    Assert.assertEquals(metrics.TOTAL_READS, 9);
                    Assert.assertEquals(metrics.PF_READS, 9);
                    Assert.assertEquals(metrics.PF_NOISE_READS, 1);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                    Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                    Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                    Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                    Assert.assertEquals(metrics.BAD_CYCLES, 3);
                    break;
                case PAIR:
                    Assert.assertEquals(metrics.TOTAL_READS, 18);
                    Assert.assertEquals(metrics.PF_READS, 16);
                    Assert.assertEquals(metrics.PF_NOISE_READS, 2);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                    Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                    Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                    Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                    Assert.assertEquals(metrics.BAD_CYCLES, 22);
                    break;
                case UNPAIRED:
                default:
                    Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
            }
        } else if (metrics.SAMPLE.equals("Ma")) {
            // every level should be identical
            switch(metrics.CATEGORY) {
                case FIRST_OF_PAIR:
                    Assert.assertEquals(metrics.TOTAL_READS, 5);
                    Assert.assertEquals(metrics.PF_READS, 3);
                    Assert.assertEquals(metrics.PF_NOISE_READS, 1);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                    Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                    Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                    Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                    Assert.assertEquals(metrics.BAD_CYCLES, 24);
                    break;
                case SECOND_OF_PAIR:
                    Assert.assertEquals(metrics.TOTAL_READS, 5);
                    Assert.assertEquals(metrics.PF_READS, 5);
                    Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                    Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                    Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                    Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                    Assert.assertEquals(metrics.BAD_CYCLES, 3);
                    break;
                case PAIR:
                    Assert.assertEquals(metrics.TOTAL_READS, 10);
                    Assert.assertEquals(metrics.PF_READS, 8);
                    Assert.assertEquals(metrics.PF_NOISE_READS, 1);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                    Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                    Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                    Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                    Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                    Assert.assertEquals(metrics.BAD_CYCLES, 27);
                    break;
                case UNPAIRED:
                default:
                    Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
            }
        } else if (metrics.SAMPLE.equals("Pa")) {
            // Two libraries and three read groups for this sample
            if (metrics.LIBRARY == null) {
                switch(metrics.CATEGORY) {
                    case FIRST_OF_PAIR:
                        Assert.assertEquals(metrics.TOTAL_READS, 4);
                        Assert.assertEquals(metrics.PF_READS, 4);
                        Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                        Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                        Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                        Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                        Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                        Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                        Assert.assertEquals(metrics.BAD_CYCLES, 19);
                        break;
                    case SECOND_OF_PAIR:
                        Assert.assertEquals(metrics.TOTAL_READS, 4);
                        Assert.assertEquals(metrics.PF_READS, 4);
                        Assert.assertEquals(metrics.PF_NOISE_READS, 1);
                        Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                        Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                        Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                        Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                        Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                        Assert.assertEquals(metrics.BAD_CYCLES, 3);
                        break;
                    case PAIR:
                        Assert.assertEquals(metrics.TOTAL_READS, 8);
                        Assert.assertEquals(metrics.PF_READS, 8);
                        Assert.assertEquals(metrics.PF_NOISE_READS, 1);
                        Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
                        Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
                        Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
                        Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
                        Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
                        Assert.assertEquals(metrics.BAD_CYCLES, 22);
                        break;
                    case UNPAIRED:
                    default:
                        Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
                }
            } else if (metrics.LIBRARY.equals("lib1")) {
                // Only one read group in this library so library and RG metrics should be identical
                switch(metrics.CATEGORY) {
                    case FIRST_OF_PAIR:
                        Assert.assertEquals(metrics.TOTAL_READS, 2);
                        Assert.assertEquals(metrics.PF_READS, 2);
                        Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                        Assert.assertEquals(metrics.BAD_CYCLES, 19);
                        break;
                    case SECOND_OF_PAIR:
                        Assert.assertEquals(metrics.TOTAL_READS, 2);
                        Assert.assertEquals(metrics.PF_READS, 2);
                        Assert.assertEquals(metrics.PF_NOISE_READS, 1);
                        Assert.assertEquals(metrics.BAD_CYCLES, 3);
                        break;
                    case PAIR:
                        Assert.assertEquals(metrics.TOTAL_READS, 4);
                        Assert.assertEquals(metrics.PF_READS, 4);
                        Assert.assertEquals(metrics.PF_NOISE_READS, 1);
                        Assert.assertEquals(metrics.BAD_CYCLES, 22);
                        break;
                    case UNPAIRED:
                    default:
                        Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
                }
            } else if (metrics.LIBRARY.equals("lib2")) {
                if (metrics.READ_GROUP == null) {
                    switch(metrics.CATEGORY) {
                        case FIRST_OF_PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 2);
                            Assert.assertEquals(metrics.PF_READS, 2);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 19);
                            break;
                        case SECOND_OF_PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 2);
                            Assert.assertEquals(metrics.PF_READS, 2);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 3);
                            break;
                        case PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 4);
                            Assert.assertEquals(metrics.PF_READS, 4);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 22);
                            break;
                        case UNPAIRED:
                        default:
                            Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
                    }
                } else if (metrics.READ_GROUP.equals("i")) {
                    switch(metrics.CATEGORY) {
                        case FIRST_OF_PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 1);
                            Assert.assertEquals(metrics.PF_READS, 1);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 19);
                            break;
                        case SECOND_OF_PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 1);
                            Assert.assertEquals(metrics.PF_READS, 1);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 3);
                            break;
                        case PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 2);
                            Assert.assertEquals(metrics.PF_READS, 2);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 22);
                            break;
                        case UNPAIRED:
                        default:
                            Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
                    }
                } else if (metrics.READ_GROUP.equals("i2")) {
                    switch(metrics.CATEGORY) {
                        case FIRST_OF_PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 1);
                            Assert.assertEquals(metrics.PF_READS, 1);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 27);
                            break;
                        case SECOND_OF_PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 1);
                            Assert.assertEquals(metrics.PF_READS, 1);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 3);
                            break;
                        case PAIR:
                            Assert.assertEquals(metrics.TOTAL_READS, 2);
                            Assert.assertEquals(metrics.PF_READS, 2);
                            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
                            Assert.assertEquals(metrics.BAD_CYCLES, 30);
                            break;
                        case UNPAIRED:
                        default:
                            Assert.fail("Data does not contain this category: " + metrics.CATEGORY);
                    }
                } else {
                    Assert.fail("Data does not contain this read group: " + metrics.READ_GROUP);
                }
            } else {
                Assert.fail("Data does not contain this library: " + metrics.LIBRARY);
            }
        } else {
            Assert.fail("Data does not contain this sample: " + metrics.SAMPLE);
        }
    }
}

Example 22 with MetricsFile

use of htsjdk.samtools.metrics.MetricsFile in project gatk by broadinstitute.

the class ExampleMultiMetricsCollector method saveMetrics.

/**
     * Finish the metrics collection and save any results to the metrics file.
     * @param metricsFile a metricsFile where the collected metrics should be stored. May not be null.
     * @param authHolder Authentication info for this context.
     */
public void saveMetrics(final MetricsFile<ExampleMultiMetrics, Integer> metricsFile, final AuthHolder authHolder) {
    Utils.nonNull(metricsFile);
    finish();
    addAllLevelsToFile(metricsFile);
    if (null != authHolder) {
        MetricsUtils.saveMetrics(metricsFile, inputArgs.output, authHolder);
    } else {
        metricsFile.write(new File(inputArgs.output));
    }
}

Example 23 with MetricsFile

use of htsjdk.samtools.metrics.MetricsFile in project gatk by broadinstitute.

the class MetricsUtilsTest method testSaveMetrics.

@Test(dataProvider = "metricsPaths", groups = "cloud")
public void testSaveMetrics(String destinationPrefix) throws IOException {
    final String outputPath = BucketUtils.getTempFilePath(destinationPrefix, ".txt");
    TestMetric testMetric = new TestMetric();
    testMetric.value1 = 10;
    testMetric.value2 = 5;
    final MetricsFile<TestMetric, ?> metrics = new MetricsFile<>();
    metrics.addMetric(testMetric);
    MetricsUtils.saveMetrics(metrics, outputPath, getAuthentication());
    Assert.assertTrue(BucketUtils.fileExists(outputPath));
    File localCopy = copyFileToLocalTmpFile(outputPath);
    final File expectedMetrics = createTempFile("expectedMetrics", ".txt");
    metrics.write(expectedMetrics);
    Assert.assertTrue(MetricsFile.areMetricsEqual(localCopy, expectedMetrics));
}

Example 24 with MetricsFile

use of htsjdk.samtools.metrics.MetricsFile in project gatk by broadinstitute.

the class PairedVariantSubContextIterator method doWork.

// TODO: add optimization if the samples are in the same file
// TODO: add option for auto-detect pairs based on same sample name
// TODO: allow multiple sample-pairs in one pass
@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(TRUTH_VCF);
    IOUtil.assertFileIsReadable(CALL_VCF);
    final File summaryMetricsFile = new File(OUTPUT + SUMMARY_METRICS_FILE_EXTENSION);
    final File detailedMetricsFile = new File(OUTPUT + DETAILED_METRICS_FILE_EXTENSION);
    final File contingencyMetricsFile = new File(OUTPUT + CONTINGENCY_METRICS_FILE_EXTENSION);
    IOUtil.assertFileIsWritable(summaryMetricsFile);
    IOUtil.assertFileIsWritable(detailedMetricsFile);
    IOUtil.assertFileIsWritable(contingencyMetricsFile);
    final boolean usingIntervals = this.INTERVALS != null && !this.INTERVALS.isEmpty();
    IntervalList intervals = null;
    SAMSequenceDictionary intervalsSamSequenceDictionary = null;
    if (usingIntervals) {
        logger.info("Loading up region lists.");
        long genomeBaseCount = 0;
        for (final File f : INTERVALS) {
            IOUtil.assertFileIsReadable(f);
            final IntervalList tmpIntervalList = IntervalList.fromFile(f);
            if (genomeBaseCount == 0) {
                // Don't count the reference length more than once.
                intervalsSamSequenceDictionary = tmpIntervalList.getHeader().getSequenceDictionary();
                genomeBaseCount = intervalsSamSequenceDictionary.getReferenceLength();
            }
            if (intervals == null)
                intervals = tmpIntervalList;
            else if (INTERSECT_INTERVALS)
                intervals = IntervalList.intersection(intervals, tmpIntervalList);
            else
                intervals = IntervalList.union(intervals, tmpIntervalList);
        }
        if (intervals != null) {
            intervals = intervals.uniqued();
        }
        logger.info("Finished loading up region lists.");
    }
    final VCFFileReader truthReader = new VCFFileReader(TRUTH_VCF, USE_VCF_INDEX);
    final VCFFileReader callReader = new VCFFileReader(CALL_VCF, USE_VCF_INDEX);
    // Check that the samples actually exist in the files!
    if (!truthReader.getFileHeader().getGenotypeSamples().contains(TRUTH_SAMPLE)) {
        throw new UserException("File " + TRUTH_VCF.getAbsolutePath() + " does not contain genotypes for sample " + TRUTH_SAMPLE);
    }
    if (!callReader.getFileHeader().getGenotypeSamples().contains(CALL_SAMPLE)) {
        throw new UserException("File " + CALL_VCF.getAbsolutePath() + " does not contain genotypes for sample " + CALL_SAMPLE);
    }
    // Verify that both VCFs have the same Sequence Dictionary
    SequenceUtil.assertSequenceDictionariesEqual(truthReader.getFileHeader().getSequenceDictionary(), callReader.getFileHeader().getSequenceDictionary());
    if (usingIntervals) {
        // If using intervals, verify that the sequence dictionaries agree with those of the VCFs
        SequenceUtil.assertSequenceDictionariesEqual(intervalsSamSequenceDictionary, truthReader.getFileHeader().getSequenceDictionary());
    }
    // Build the pair of iterators over the regions of interest
    final Iterator<VariantContext> truthIterator, callIterator;
    if (usingIntervals) {
        truthIterator = new ByIntervalListVariantContextIterator(truthReader, intervals);
        callIterator = new ByIntervalListVariantContextIterator(callReader, intervals);
    } else {
        truthIterator = truthReader.iterator();
        callIterator = callReader.iterator();
    }
    // Now do the iteration and count things up
    final PairedVariantSubContextIterator pairedIterator = new PairedVariantSubContextIterator(truthIterator, TRUTH_SAMPLE, callIterator, CALL_SAMPLE, truthReader.getFileHeader().getSequenceDictionary());
    snpCounter = new GenotypeConcordanceCounts();
    indelCounter = new GenotypeConcordanceCounts();
    // A map to keep track of the count of Truth/Call States which we could not successfully classify
    final Map<String, Integer> unClassifiedStatesMap = new HashMap<>();
    logger.info("Starting iteration over variants.");
    while (pairedIterator.hasNext()) {
        final VcTuple tuple = pairedIterator.next();
        final VariantContext.Type truthVariantContextType = tuple.truthVariantContext != null ? tuple.truthVariantContext.getType() : NO_VARIATION;
        final VariantContext.Type callVariantContextType = tuple.callVariantContext != null ? tuple.callVariantContext.getType() : NO_VARIATION;
        // A flag to keep track of whether we have been able to successfully classify the Truth/Call States.
        // Unclassified include MIXED/MNP/Symbolic...
        boolean stateClassified = false;
        final TruthAndCallStates truthAndCallStates = determineState(tuple.truthVariantContext, TRUTH_SAMPLE, tuple.callVariantContext, CALL_SAMPLE, MIN_GQ, MIN_DP);
        if (truthVariantContextType == SNP) {
            if ((callVariantContextType == SNP) || (callVariantContextType == MIXED) || (callVariantContextType == NO_VARIATION)) {
                // Note.  If truth is SNP and call is MIXED, the event will be logged in the indelCounter, with row = MIXED
                snpCounter.increment(truthAndCallStates);
                stateClassified = true;
            }
        } else if (truthVariantContextType == INDEL) {
            // Note.  If truth is Indel and call is MIXED, the event will be logged in the indelCounter, with row = MIXED
            if ((callVariantContextType == INDEL) || (callVariantContextType == MIXED) || (callVariantContextType == NO_VARIATION)) {
                indelCounter.increment(truthAndCallStates);
                stateClassified = true;
            }
        } else if (truthVariantContextType == MIXED) {
            // Note.  If truth is MIXED and call is SNP, the event will be logged in the snpCounter, with column = MIXED
            if (callVariantContextType == SNP) {
                snpCounter.increment(truthAndCallStates);
                stateClassified = true;
            } else // Note.  If truth is MIXED and call is INDEL, the event will be logged in the snpCounter, with column = MIXED
            if (callVariantContextType == INDEL) {
                indelCounter.increment(truthAndCallStates);
                stateClassified = true;
            }
        } else if (truthVariantContextType == NO_VARIATION) {
            if (callVariantContextType == SNP) {
                snpCounter.increment(truthAndCallStates);
                stateClassified = true;
            } else if (callVariantContextType == INDEL) {
                indelCounter.increment(truthAndCallStates);
                stateClassified = true;
            }
        }
        if (!stateClassified) {
            final String condition = truthVariantContextType + " " + callVariantContextType;
            Integer count = unClassifiedStatesMap.get(condition);
            if (count == null)
                count = 0;
            unClassifiedStatesMap.put(condition, ++count);
        }
        final VariantContext variantContextForLogging = tuple.truthVariantContext != null ? tuple.truthVariantContext : tuple.callVariantContext;
        progress.record(variantContextForLogging.getContig(), variantContextForLogging.getStart());
    }
    // Calculate and store the summary-level metrics
    final MetricsFile<GenotypeConcordanceSummaryMetrics, ?> genotypeConcordanceSummaryMetricsFile = getMetricsFile();
    GenotypeConcordanceSummaryMetrics summaryMetrics = new GenotypeConcordanceSummaryMetrics(SNP, snpCounter, TRUTH_SAMPLE, CALL_SAMPLE);
    genotypeConcordanceSummaryMetricsFile.addMetric(summaryMetrics);
    summaryMetrics = new GenotypeConcordanceSummaryMetrics(INDEL, indelCounter, TRUTH_SAMPLE, CALL_SAMPLE);
    genotypeConcordanceSummaryMetricsFile.addMetric(summaryMetrics);
    genotypeConcordanceSummaryMetricsFile.write(summaryMetricsFile);
    // Calculate and store the detailed metrics for both SNP and indels
    final MetricsFile<GenotypeConcordanceDetailMetrics, ?> genotypeConcordanceDetailMetrics = getMetricsFile();
    outputDetailMetricsFile(SNP, genotypeConcordanceDetailMetrics, snpCounter, TRUTH_SAMPLE, CALL_SAMPLE);
    outputDetailMetricsFile(INDEL, genotypeConcordanceDetailMetrics, indelCounter, TRUTH_SAMPLE, CALL_SAMPLE);
    genotypeConcordanceDetailMetrics.write(detailedMetricsFile);
    // Calculate and score the contingency metrics
    final MetricsFile<GenotypeConcordanceContingencyMetrics, ?> genotypeConcordanceContingencyMetricsFile = getMetricsFile();
    GenotypeConcordanceContingencyMetrics contingencyMetrics = new GenotypeConcordanceContingencyMetrics(SNP, snpCounter, TRUTH_SAMPLE, CALL_SAMPLE);
    genotypeConcordanceContingencyMetricsFile.addMetric(contingencyMetrics);
    contingencyMetrics = new GenotypeConcordanceContingencyMetrics(INDEL, indelCounter, TRUTH_SAMPLE, CALL_SAMPLE);
    genotypeConcordanceContingencyMetricsFile.addMetric(contingencyMetrics);
    genotypeConcordanceContingencyMetricsFile.write(contingencyMetricsFile);
    for (final String condition : unClassifiedStatesMap.keySet()) {
        logger.info("Uncovered truth/call Variant Context Type Counts: " + condition + " " + unClassifiedStatesMap.get(condition));
    }
    return null;
}

Example 25 with MetricsFile

use of htsjdk.samtools.metrics.MetricsFile in project gatk by broadinstitute.

the class PreAdapterOrientationScorerUnitTest method testBasicScoring.

/**
     * Note that (due to raw data), this test includes collapsing over libraries (not just the contexts).
     * @throws IOException
     */
@Test
public void testBasicScoring() throws IOException {
    final MetricsFile<SequencingArtifactMetrics.PreAdapterDetailMetrics, Comparable<?>> mf = new MetricsFile<>();
    mf.read(new FileReader(testPreAdapterDetailsMetrics));
    final Map<Transition, Double> scoreMap = PreAdapterOrientationScorer.scoreOrientationBiasMetricsOverContext(mf.getMetrics());
    Assert.assertNotNull(scoreMap);
    Assert.assertEquals(scoreMap.keySet().size(), 12);
    // Ground truth values painstakingly derived manually
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'C')), 100.0, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'G')), 50.5788416297570, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('A', 'T')), 100.0, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'A')), 100.0, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'G')), 100.0, 1e-6);
    Assert.assertEquals(scoreMap.get(Transition.transitionOf('C', 'T')), 58.0641821538479, 1e-6);
}