Examples with SamReader htsjdk.samtools.SamReader used on opensource projects

Example 46 with SamReader

use of htsjdk.samtools.SamReader in project gatk by broadinstitute.

the class MultiLevelCollectorTest method multilevelCollectorTest.

@Test(dataProvider = "variedAccumulationLevels")
public void multilevelCollectorTest(final Set<MetricAccumulationLevel> accumulationLevels) {
    final SamReader in = SamReaderFactory.makeDefault().open(TESTFILE);
    final RecordCountMultiLevelCollector collector = new RecordCountMultiLevelCollector(accumulationLevels, in.getFileHeader().getReadGroups());
    for (final SAMRecord rec : in) {
        collector.acceptRecord(rec, null);
    }
    collector.finish();
    int totalProcessed = 0;
    int totalMetrics = 0;
    for (final MetricAccumulationLevel level : accumulationLevels) {
        final Map<String, Integer> keyToMetrics = accumulationLevelToPerUnitReads.get(level);
        for (final Map.Entry<String, Integer> entry : keyToMetrics.entrySet()) {
            final TotalNumberMetric metric = collector.getUnitsToMetrics().get(entry.getKey());
            Assert.assertEquals(entry.getValue(), metric.TALLY);
            Assert.assertTrue(metric.FINISHED);
            totalProcessed += metric.TALLY;
            totalMetrics += 1;
        }
    }
    Assert.assertEquals(collector.getUnitsToMetrics().size(), totalMetrics);
    Assert.assertEquals(totalProcessed, collector.getNumProcessed());
    CloserUtil.close(in);
}

Example 47 with SamReader

use of htsjdk.samtools.SamReader in project gatk by broadinstitute.

the class MultiLevelReducibleCollectorUnitTest method multilevelCollectorTest.

@Test(dataProvider = "variedAccumulationLevels")
public void multilevelCollectorTest(final Set<MetricAccumulationLevel> accumulationLevels) {
    final SamReader in = SamReaderFactory.makeDefault().open(TESTFILE);
    final RecordCountMultiLevelCollector collector1 = new RecordCountMultiLevelCollector(accumulationLevels, in.getFileHeader().getReadGroups());
    final RecordCountMultiLevelCollector collector2 = new RecordCountMultiLevelCollector(accumulationLevels, in.getFileHeader().getReadGroups());
    //distribute the reads across the two collectors
    int count = 1;
    for (final SAMRecord rec : in) {
        if (count % 2 == 0) {
            collector1.acceptRecord(rec, null);
        } else {
            collector2.acceptRecord(rec, null);
        }
        count++;
    }
    collector1.finish();
    collector2.finish();
    // combine the results into collector1
    collector1.combine(collector2);
    int totalProcessed = 0;
    int totalMetrics = 0;
    for (final MetricAccumulationLevel level : accumulationLevels) {
        final Map<String, Integer> keyToMetrics = accumulationLevelToPerUnitReads.get(level);
        for (final Map.Entry<String, Integer> entry : keyToMetrics.entrySet()) {
            final TotalNumberMetric metric = collector1.getUnitsToMetrics().get(entry.getKey());
            Assert.assertEquals(entry.getValue(), metric.TALLY);
            Assert.assertTrue(metric.FINISHED);
            totalProcessed += metric.TALLY;
            totalMetrics += 1;
        }
    }
    Assert.assertEquals(collector1.getUnitsToMetrics().size(), totalMetrics);
    Assert.assertEquals(totalProcessed, collector1.getNumProcessed());
    CloserUtil.close(in);
}

Example 48 with SamReader

use of htsjdk.samtools.SamReader in project gatk-protected by broadinstitute.

the class GetBayesianHetCoverageIntegrationTest method initHeaders.

@BeforeClass
public void initHeaders() throws IOException {
    try (final SamReader normalBamReader = SamReaderFactory.makeDefault().open(NORMAL_BAM_FILE);
        final SamReader tumorBamReader = SamReaderFactory.makeDefault().open(TUMOR_BAM_FILE)) {
        normalHeader = normalBamReader.getFileHeader();
        tumorHeader = tumorBamReader.getFileHeader();
    }
}

Example 49 with SamReader

use of htsjdk.samtools.SamReader in project gatk by broadinstitute.

the class FilterReadsIntegrationTest method getReadCounts.

private int getReadCounts(final String resultFileName, final String referenceFileName) {
    final File path = new File(resultFileName);
    IOUtil.assertFileIsReadable(path);
    final File refFile = null == referenceFileName ? null : new File(TEST_DATA_DIR, referenceFileName);
    final SamReader in = SamReaderFactory.makeDefault().referenceSequence(refFile).open(path);
    int count = 0;
    for (@SuppressWarnings("unused") final SAMRecord rec : in) {
        count++;
    }
    CloserUtil.close(in);
    return count;
}