Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader

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    // -----------------------------------------------------------------------------------------------

    @DataProvider(name = "BadReadsTest")
    public Object[][] makeBadReadsTest() {
        List<Object[]> tests = new ArrayList<Object[]>();
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        tests.add(new Object[]{
                ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, 10),
                ArtificialSAMUtils.createArtificialRead(header, "read2", 0, 9, 10)});
        tests.add(new Object[]{
                ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, 10),
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    @BeforeClass
    public void init() {
        File hg18Ref = new File(BaseTest.hg18Reference);
        try {
            ReferenceDataSource referenceDataSource = new ReferenceDataSource(hg18Ref);
            hg18Header = new SAMFileHeader();
            hg18Header.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary());
            ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg18Ref);
            hg18GenomeLocParser = new GenomeLocParser(seq);
            hg18ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()).toList()) ;
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(hg18Ref,ex);
        }

        File hg19Ref = new File(BaseTest.hg19Reference);
        try {
            ReferenceDataSource referenceDataSource = new ReferenceDataSource(hg19Ref);
            hg19Header = new SAMFileHeader();
            hg19Header.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary());
            ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(hg19Ref);
            hg19GenomeLocParser = new GenomeLocParser(seq);
            hg19ReferenceLocs = Collections.unmodifiableList(GenomeLocSortedSet.createSetFromSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()).toList()) ;
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    @Test(dataProvider="invalidIntervalTestData")
    public void testInvalidPicardIntervalHandling(GATKArgumentCollection argCollection, GenomeLocParser genomeLocParser,
                                                  String contig, int intervalStart, int intervalEnd ) throws Exception {

        SAMFileHeader picardFileHeader = new SAMFileHeader();
        picardFileHeader.addSequence(genomeLocParser.getContigInfo("chr1"));
        IntervalList picardIntervals = new IntervalList(picardFileHeader);
        picardIntervals.add(new Interval(contig, intervalStart, intervalEnd, true, "dummyname"));

        File picardIntervalFile = createTempFile("testInvalidPicardIntervalHandling", ".intervals");
        picardIntervals.write(picardIntervalFile);
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    @Test (enabled = true)
    public void testReadWithNsRefIndexInDeletion() throws FileNotFoundException {

        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final int readLength = 76;

        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
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    @Test (enabled = true)
    public void testReadWithNsRefAfterDeletion() throws FileNotFoundException {

        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final int readLength = 76;

        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
        read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
        read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
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    @DataProvider(name = "HasWellDefinedFragmentSizeData")
    public Object[][] makeHasWellDefinedFragmentSizeData() throws Exception {
        final List<Object[]> tests = new LinkedList<Object[]>();

        // setup a basic read that will work
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader();
        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 10, 10);
        read.setReadPairedFlag(true);
        read.setProperPairFlag(true);
        read.setReadUnmappedFlag(false);
        read.setMateUnmappedFlag(false);
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    final static String BASES = "ACTG";
    final static String QUALS = "!+5?";

    @BeforeClass
    public void init() {
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
        read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, BASES.length());
        read.setReadUnmappedFlag(true);
        read.setReadBases(new String(BASES).getBytes());
        read.setBaseQualityString(new String(QUALS));
    }
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    /**
     * A unit test that creates an artificial read for testing some code that uses reads
     */
    @Test()
    public void testWithARead() {
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
        Assert.assertEquals(read.getReadLength(), 10);
        // TODO -- add some tests here using read
    }
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     * Note that effective creation of RBPs isn't so good.  If you need pileups of specific properties, you shoud
     * look into building them yourself as in the example below
     */
    @Test()
    public void testWithAPileup() {
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final GenomeLoc myLocation = genomeLocParser.createGenomeLoc("1", 10);
        final ReadBackedPileup pileup = ArtificialSAMUtils.createReadBackedPileup(header, myLocation, 10, 400, 10);
        Assert.assertFalse(pileup.isEmpty());
        // TODO -- add some tests here using pileup
    }
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     *
     * Builds the pileup from scratch to have specific properties
     */
    @Test()
    public void testBuildingAPileupWithSpecificProperties() {
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
        final GenomeLoc myLocation = genomeLocParser.createGenomeLoc("1", 10);

        final int pileupSize = 100;
        final int readLength = 10;
        final List<GATKSAMRecord> reads = new LinkedList<GATKSAMRecord>();
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Related Classes of htsjdk.samtools.SAMFileHeader

  • org.broad.igv.sam.PicardAlignment
  • org.broad.igv.sam.reader.BAMFileReader
  • org.broad.igv.sam.reader.BAMHttpQueryReaderTest
  • org.broad.igv.sam.reader.BAMHttpReader
  • org.broad.igv.sam.reader.MergedAlignmentReader
  • org.broad.igv.sam.reader.SAMFileGroup
  • org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancerUnitTest
  • org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtilsUnitTest
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIteratorUnitTest
  • org.broadinstitute.gatk.engine.downsampling.FractionalDownsamplerUnitTest$FractionalDownsamplerTest
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