Package htsjdk.samtools

Examples of htsjdk.samtools.SAMRecordSetBuilder

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    private boolean deleteOnExit = true;
    private final ArrayList<String> args = new ArrayList<String>();

    public SamFileTester(final int readLength, final boolean deleteOnExit, final int defaultChromosomeLength, final ScoringStrategy duplicateScoringStrategy) {
        this.deleteOnExit = deleteOnExit;
        this.samRecordSetBuilder = new SAMRecordSetBuilder(true, SAMFileHeader.SortOrder.coordinate, true, defaultChromosomeLength, duplicateScoringStrategy);
        samRecordSetBuilder.setReadLength(readLength);
        setOutputDir();
    }
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    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 = File.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile);
        for (final SAMRecord rec: builder.getRecords()) samWriter.addAlignment(rec);
        samWriter.close();

        // 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 = File.createTempFile("tmp.rRna.", ".interval_list");
        rRnaIntervalsFile.deleteOnExit();
        rRnaIntervalList.write(rRnaIntervalsFile);
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    public void testMultiLevel() 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, false);
        // Set seed so that strandedness is consistent among runs.
        builder.setRandomSeed(0);
        final int sequenceIndex = builder.getHeader().getSequenceIndex(sequence);
        final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("2");
        rg1.setSample("Sample");
        rg1.setLibrary("foo");
        builder.setReadGroup(rg1);
        builder.addPair("pair1", sequenceIndex, 45, 475);
        builder.addPair("pair2", sequenceIndex, 90, 225);
        builder.addFrag("frag1", sequenceIndex, 150, true);
        builder.addFrag("frag2", sequenceIndex, 450, true);

        final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("3");
        rg2.setSample("Sample");
        rg2.setLibrary("bar");
        builder.setReadGroup(rg2);
        builder.addPair("pair3", sequenceIndex, 120, 600);
        builder.addFrag("frag3", sequenceIndex, 225, false);
        builder.addPair("rrnaPair", sequenceIndex, 400, 500);

        builder.addFrag("ignoredFrag", builder.getHeader().getSequenceIndex(ignoredSequence), 1, false);

        final File samFile = File.createTempFile("tmp.collectRnaSeqMetrics.", ".sam");
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(builder.getHeader(), false, samFile);
        for (final SAMRecord rec: builder.getRecords()) samWriter.addAlignment(rec);
        samWriter.close();

        // 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 = File.createTempFile("tmp.rRna.", ".interval_list");
        rRnaIntervalsFile.deleteOnExit();
        rRnaIntervalList.write(rRnaIntervalsFile);
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Related Classes of htsjdk.samtools.SAMRecordSetBuilder

  • picard.analysis.CollectRnaSeqMetricsTest
  • picard.sam.testers.SamFileTester
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