Examples with Interval htsjdk.samtools.util.Interval used on opensource projects

Example 21 with Interval

use of htsjdk.samtools.util.Interval in project gatk by broadinstitute.

the class IntervalUtilsUnitTest method testLoadIntervalsInvalidPicardIntervalHandling.

@Test(expectedExceptions = UserException.MalformedFile.class, dataProvider = "invalidIntervalTestData")
public void testLoadIntervalsInvalidPicardIntervalHandling(GenomeLocParser genomeLocParser, String contig, int intervalStart, int intervalEnd) throws Exception {
    SAMFileHeader picardFileHeader = new SAMFileHeader();
    picardFileHeader.addSequence(genomeLocParser.getContigInfo("1"));
    // Intentionally add an extra contig not in our genomeLocParser's sequence dictionary
    // so that we can add intervals to the Picard interval file for contigs not in our dictionary
    picardFileHeader.addSequence(new SAMSequenceRecord("2", 100000));
    IntervalList picardIntervals = new IntervalList(picardFileHeader);
    picardIntervals.add(new Interval(contig, intervalStart, intervalEnd, true, "dummyname"));
    File picardIntervalFile = createTempFile("testLoadIntervalsInvalidPicardIntervalHandling", ".intervals");
    picardIntervals.write(picardIntervalFile);
    List<String> intervalArgs = new ArrayList<>(1);
    intervalArgs.add(picardIntervalFile.getAbsolutePath());
    // loadIntervals() will validate all intervals against the sequence dictionary in our genomeLocParser,
    // and should throw for all intervals in our invalidIntervalTestData set
    IntervalUtils.loadIntervals(intervalArgs, IntervalSetRule.UNION, IntervalMergingRule.ALL, 0, genomeLocParser);
}

Example 22 with Interval

use of htsjdk.samtools.util.Interval in project gatk by broadinstitute.

the class IntervalUtilsUnitTest method testIntervalFileToListInvalidPicardIntervalHandling.

@Test(expectedExceptions = UserException.CouldNotReadInputFile.class, dataProvider = "invalidIntervalTestData")
public void testIntervalFileToListInvalidPicardIntervalHandling(GenomeLocParser genomeLocParser, String contig, int intervalStart, int intervalEnd) throws Exception {
    final SAMFileHeader picardFileHeader = new SAMFileHeader();
    picardFileHeader.addSequence(genomeLocParser.getContigInfo("1"));
    picardFileHeader.addSequence(new SAMSequenceRecord("2", 100000));
    final IntervalList picardIntervals = new IntervalList(picardFileHeader);
    picardIntervals.add(new Interval(contig, intervalStart, intervalEnd, true, "dummyname"));
    final File picardIntervalFile = createTempFile("testIntervalFileToListInvalidPicardIntervalHandling", ".intervals");
    picardIntervals.write(picardIntervalFile);
    // loadIntervals() will validate all intervals against the sequence dictionary in our genomeLocParser,
    // and should throw for all intervals in our invalidIntervalTestData set
    IntervalUtils.intervalFileToList(genomeLocParser, picardIntervalFile.getAbsolutePath());
}

Example 23 with Interval

use of htsjdk.samtools.util.Interval 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);
}

Example 24 with Interval

use of htsjdk.samtools.util.Interval in project gatk by broadinstitute.

the class IntervalListScattererTest method composeIntervalList.

private static IntervalList composeIntervalList(final IntervalList source, final String chromosome, final int... segmentsByPair) {
    final IntervalList intervals = new IntervalList(source.getHeader());
    for (int i = 0; i < segmentsByPair.length; i += 2) {
        final Interval parentInterval = lookupIntervalContainingLocus(source, chromosome, segmentsByPair[i]);
        intervals.add(new Interval("1", segmentsByPair[i], segmentsByPair[i + 1], parentInterval.isNegativeStrand(), parentInterval.getName()));
    }
    return intervals;
}