Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader

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     * @param preSorted           whether or not the writer can assume reads are going to be added are already sorted
     * @param walker              the walker object (so we can extract the command line)
     * @param PROGRAM_RECORD_NAME the name for the PG tag
     */
    public static void setupWriter(GATKSAMFileWriter writer, GenomeAnalysisEngine toolkit, SAMFileHeader originalHeader, boolean preSorted, Object walker, String PROGRAM_RECORD_NAME) {
        SAMFileHeader header = setupWriter(toolkit, originalHeader, walker, PROGRAM_RECORD_NAME);
        writer.writeHeader(header);
        writer.setPresorted(preSorted);
    }
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        if (!( walker instanceof ReadWalker ))
            throw new IllegalArgumentException("Walker isn't a read walker!");

        ReadWalker<M, T> readWalker = (ReadWalker<M, T>) walker;
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readsPerChr + DEFAULT_READ_LENGTH);
        iter = new ArtificialPatternedSAMIterator(this.startingChr,
                this.endingChr,
                this.readsPerChr,
                this.unMappedReads,
                header,
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    int insertSize; // set automatically by framework

    @Override protected void setUp() {
        final int nPileupsToGenerate = 100;
        pileups = new ArrayList<ReadBackedPileup>(nPileupsToGenerate);
        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
        GenomeLocParser genomeLocParser;
        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
        GenomeLoc loc = genomeLocParser.createGenomeLoc("chr1", 50);
        final int readLen = 100;

        for ( int pileupN = 0; pileupN < nPileupsToGenerate; pileupN++ ) {
            ReadBackedPileup rbp = ArtificialSAMUtils.createReadBackedPileup(header, loc, readLen, insertSize, pileupSize);
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    }

    @Test(dataProvider = "MergeFragmentsOffContig")
    public void testMergeFragmentsOffContig(final int pre1, final int post1, final int pre2, final int post2) {
        final int contigSize = 10;
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 0, contigSize);

        final GATKSAMRecord read1 = createReadOffContig(header, false, pre1, post1);
        final GATKSAMRecord read2 = createReadOffContig(header, true, pre2, post2);

        final GATKSAMRecord merged = FragmentUtils.mergeOverlappingPairedFragments(read1, read2);
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    }

    /** tes that we get the read we put into the map function */
    @Test
    public void testReturnRead() {
        SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
        GATKSAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
        SAMRecord ret = walker.map(bases, rec, null);
        assertTrue(ret == rec);
        assertTrue(ret.getReadName().equals(rec.getReadName()));
    }
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    protected MalformedReadFilter buildMalformedReadFiter(boolean filterRNO, final ValidationExclusion.TYPE... excl) {
        final ValidationExclusion ve = new ValidationExclusion(Arrays.asList(excl));

        final MalformedReadFilter filter = new MalformedReadFilter();

        final SAMFileHeader h = getHeader();
        final SAMDataSource ds =  getDataSource();

        final GenomeAnalysisEngine gae = new GenomeAnalysisEngine() {
            @Override
            public SAMFileHeader getSAMFileHeader() {
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    @Test
    public void testSimplePositionalDownsamplerSignalNoMoreReadsBefore() {
        ReadsDownsampler<SAMRecord> downsampler = new SimplePositionalDownsampler<SAMRecord>(1000);

        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);

        Collection<SAMRecord> readStack = new ArrayList<SAMRecord>();
        readStack.addAll(ArtificialSAMUtils.createStackOfIdenticalArtificialReads(50, header, "foo", 0, 1, 100));
        downsampler.submit(readStack);
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    @Test
    public void testBasicUnmappedReadsSupport() {
        ReadsDownsampler<SAMRecord> downsampler = new SimplePositionalDownsampler<SAMRecord>(100);

        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);

        Collection<SAMRecord> readStack = new ArrayList<SAMRecord>();
        readStack.addAll(ArtificialSAMUtils.createStackOfIdenticalArtificialReads(200, header, "foo", SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX,
                                                                                  SAMRecord.NO_ALIGNMENT_START, 100));
        for ( SAMRecord read : readStack ) {
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    @Test
    public void testMixedMappedAndUnmappedReadsSupport() {
        ReadsDownsampler<SAMRecord> downsampler = new SimplePositionalDownsampler<SAMRecord>(100);

        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);

        Collection<SAMRecord> mappedReadStack = new ArrayList<SAMRecord>();
        mappedReadStack.addAll(ArtificialSAMUtils.createStackOfIdenticalArtificialReads(200, header, "foo", 0, 1, 100));
        for ( SAMRecord read : mappedReadStack ) {
            Assert.assertFalse(read.getReadUnmappedFlag());
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    @Test
    public void testGATKSAMRecordSupport() {
        ReadsDownsampler<GATKSAMRecord> downsampler = new SimplePositionalDownsampler<GATKSAMRecord>(1000);

        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000000);

        List<GATKSAMRecord> reads = new ArrayList<GATKSAMRecord>();
        for ( int i = 0; i < 10; i++ ) {
            reads.add(ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 10, 20 * i + 10));
        }
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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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