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

Example 51 with SAMRecord

use of htsjdk.samtools.SAMRecord 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 52 with SAMRecord

use of htsjdk.samtools.SAMRecord 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;
}

Example 53 with SAMRecord

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

the class CollectRnaSeqMetricsTest method basic.

@Test
public void basic() throws Exception {
    final String sequence = "chr1";
    final String ignoredSequence = "chrM";
    // Create some alignments that hit the ribosomal sequence, various parts of the gene, and intergenic.
    final SAMRecordSetBuilder builder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate);
    // Set seed so that strandedness is consistent among runs.
    builder.setRandomSeed(0);
    final int sequenceIndex = builder.getHeader().getSequenceIndex(sequence);
    builder.addPair("pair1", sequenceIndex, 45, 475);
    builder.addPair("pair2", sequenceIndex, 90, 225);
    builder.addPair("pair3", sequenceIndex, 120, 600);
    builder.addFrag("frag1", sequenceIndex, 150, true);
    builder.addFrag("frag2", sequenceIndex, 450, true);
    builder.addFrag("frag3", sequenceIndex, 225, false);
    builder.addPair("rrnaPair", sequenceIndex, 400, 500);
    builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);
    final File samFile = BaseTest.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
    try (final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile)) {
        for (final SAMRecord rec : builder.getRecords()) samWriter.addAlignment(rec);
    }
    // Create an interval list with one ribosomal interval.
    final Interval rRnaInterval = new Interval(sequence, 300, 520, true, "rRNA");
    final IntervalList rRnaIntervalList = new IntervalList(builder.getHeader());
    rRnaIntervalList.add(rRnaInterval);
    final File rRnaIntervalsFile = BaseTest.createTempFile("tmp.rRna.", ".interval_list");
    rRnaIntervalList.write(rRnaIntervalsFile);
    // Generate the metrics.
    final File metricsFile = BaseTest.createTempFile("tmp.", ".rna_metrics");
    final String[] args = new String[] { "--input", samFile.getAbsolutePath(), "--output", metricsFile.getAbsolutePath(), "--REF_FLAT", getRefFlatFile(sequence).getAbsolutePath(), "--RIBOSOMAL_INTERVALS", rRnaIntervalsFile.getAbsolutePath(), "--STRAND_SPECIFICITY", "SECOND_READ_TRANSCRIPTION_STRAND", "--IGNORE_SEQUENCE", ignoredSequence };
    runCommandLine(args);
    final MetricsFile<RnaSeqMetrics, Comparable<?>> output = new MetricsFile<>();
    output.read(new FileReader(metricsFile));
    final RnaSeqMetrics metrics = output.getMetrics().get(0);
    Assert.assertEquals(metrics.PF_ALIGNED_BASES, 396);
    Assert.assertEquals(metrics.PF_BASES, 432);
    Assert.assertEquals(metrics.RIBOSOMAL_BASES.longValue(), 108L);
    Assert.assertEquals(metrics.CODING_BASES, 136);
    Assert.assertEquals(metrics.UTR_BASES, 51);
    Assert.assertEquals(metrics.INTRONIC_BASES, 50);
    Assert.assertEquals(metrics.INTERGENIC_BASES, 51);
    Assert.assertEquals(metrics.CORRECT_STRAND_READS, 3);
    Assert.assertEquals(metrics.INCORRECT_STRAND_READS, 4);
    Assert.assertEquals(metrics.IGNORED_READS, 1);
}