Package htsjdk.samtools

Examples of htsjdk.samtools.SAMReadGroupRecord

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                    new File(OUTPUT, IOUtil.makeFileNameSafe(lib) + extension)));
        }

        for (Iterator<SAMRecord> it = reader.iterator(); it.hasNext(); ) {
            SAMRecord sam = it.next();
            SAMReadGroupRecord rg = sam.getReadGroup();
            if (rg != null && rg.getLibrary() != null) {
                libraryToWriter.get(rg.getLibrary()).addAlignment(sam);
            }
            else {
                if (unknown == null) {
                    unknown = factory.makeSAMOrBAMWriter(unknownHeader, true,
                            new File(OUTPUT, "unknown" + extension));
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        Assert.assertEquals(pg.getProgramGroupId(), "0");
        Assert.assertEquals(pg.getProgramVersion(), "1.0");
        Assert.assertEquals(pg.getCommandLine(), "align!");
        Assert.assertEquals(pg.getProgramName(), "myAligner");

        final SAMReadGroupRecord rg = result.getFileHeader().getReadGroups().get(0);
        Assert.assertEquals(rg.getReadGroupId(), "0");
        Assert.assertEquals(rg.getSample(), "Hi,Mom!");

        Assert.assertEquals(result.getFileHeader().getSortOrder(), SAMFileHeader.SortOrder.coordinate);

        for (final SAMRecord sam : result) {
            // This tests that we clip both (a) when the adapter is marked in the unmapped BAM file and
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     */
    public static String getLibraryName(final SAMFileHeader header, final SAMRecord rec) {
        final String readGroupId = (String) rec.getAttribute("RG");

        if (readGroupId != null) {
            final SAMReadGroupRecord rg = header.getReadGroup(readGroupId);
            if (rg != null) {
                final String libraryName = rg.getLibrary();
                if (null != libraryName) return libraryName;
            }
        }

        return "Unknown Library";
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        // 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);
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Related Classes of htsjdk.samtools.SAMReadGroupRecord

  • org.broad.igv.sam.PicardAlignment
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIteratorUnitTest
  • org.broadinstitute.gatk.engine.filters.LibraryReadFilter
  • org.broadinstitute.gatk.engine.filters.PlatformUnitFilter
  • org.broadinstitute.gatk.engine.filters.ReadGroupBlackListFilter
  • org.broadinstitute.gatk.engine.filters.ReadGroupBlackListFilterUnitTest
  • org.broadinstitute.gatk.engine.filters.SampleFilter
  • org.broadinstitute.gatk.engine.filters.SingleReadGroupFilter
  • org.broadinstitute.gatk.tools.walkers.coverage.CoverageUtils
  • org.broadinstitute.gatk.tools.walkers.diagnostics.ReadLengthDistribution
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