Examples of SAMSequenceRecord

Examples of htsjdk.samtools.SAMSequenceRecord

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    private SAMFileHeader samFileHeader;

    @BeforeClass
    public void init() {
        SAMSequenceDictionary sequenceDictionary = new SAMSequenceDictionary();
        sequenceDictionary.addSequence(new SAMSequenceRecord("1",500));
        sequenceDictionary.addSequence(new SAMSequenceRecord("2",500));

        samFileHeader = new SAMFileHeader();
        samFileHeader.setSequenceDictionary(sequenceDictionary);
    }
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Examples of htsjdk.samtools.SAMSequenceRecord

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            // Write the ann and amb for this reference sequence.
            annFile = File.createTempFile("bwt",".ann");
            ambFile = File.createTempFile("bwt",".amb");

            SAMSequenceDictionary dictionary = new SAMSequenceDictionary();
            dictionary.addSequence(new SAMSequenceRecord("autogenerated",normalizedReferenceSequence.length));

            ANNWriter annWriter = new ANNWriter(annFile);
            annWriter.write(dictionary);
            annWriter.close();
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Examples of htsjdk.samtools.SAMSequenceRecord

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        return getReferenceBases(genomeLocParser.createGenomeLoc(read));

    }

    protected byte[] getReferenceBases( GenomeLoc genomeLoc ) {
        SAMSequenceRecord sequenceInfo = reference.getSequenceDictionary().getSequence(genomeLoc.getContig());

        long start = genomeLoc.getStart();
        long stop = Math.min( genomeLoc.getStop(), sequenceInfo.getSequenceLength() );

        // Read with no aligned bases?  Return an empty array.
        if(stop - start + 1 == 0)
            return new byte[0];
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Examples of htsjdk.samtools.SAMSequenceRecord

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    private static Logger logger = Logger.getLogger(SequenceDictionaryUtilsUnitTest.class);


    @DataProvider( name = "SequenceDictionaryDataProvider" )
    public Object[][] generateSequenceDictionaryTestData() {
        final SAMSequenceRecord CHRM_HG19 = new SAMSequenceRecord("chrM", 16571);
        final SAMSequenceRecord CHR_NONSTANDARD1 = new SAMSequenceRecord("NonStandard1", 8675309);
        final SAMSequenceRecord CHR_NONSTANDARD2 = new SAMSequenceRecord("NonStandard2", 8675308);

        final Class NO_COMMON_CONTIGS_EXCEPTION = UserException.IncompatibleSequenceDictionaries.class;
        final Class UNEQUAL_COMMON_CONTIGS_EXCEPTION = UserException.IncompatibleSequenceDictionaries.class;
        final Class NON_CANONICAL_HUMAN_ORDER_EXCEPTION = UserException.LexicographicallySortedSequenceDictionary.class;
        final Class OUT_OF_ORDER_EXCEPTION = UserException.IncompatibleSequenceDictionaries.class;
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Examples of htsjdk.samtools.SAMSequenceRecord

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    @Test(dataProvider = "fastas", enabled = true && ! DEBUG)
    public void testCachingIndexedFastaReaderSequential1(File fasta, int cacheSize, int querySize) throws FileNotFoundException {
        final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false);

        SAMSequenceRecord contig = caching.getSequenceDictionary().getSequence(0);
        logger.warn(String.format("Checking contig %s length %d with cache size %d and query size %d",
                contig.getSequenceName(), contig.getSequenceLength(), cacheSize, querySize));
        testSequential(caching, fasta, querySize);
    }
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Examples of htsjdk.samtools.SAMSequenceRecord

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    private void testSequential(final CachingIndexedFastaSequenceFile caching, final File fasta, final int querySize) throws FileNotFoundException {
        Assert.assertTrue(caching.isPreservingCase(), "testSequential only works for case preserving CachingIndexedFastaSequenceFile readers");

        final IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta);

        SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);
        for ( int i = 0; i < contig.getSequenceLength(); i += STEP_SIZE ) {
            int start = i;
            int stop = start + querySize;
            if ( stop <= contig.getSequenceLength() ) {
                ReferenceSequence cachedVal = caching.getSubsequenceAt(contig.getSequenceName(), start, stop);
                ReferenceSequence uncachedVal = uncached.getSubsequenceAt(contig.getSequenceName(), start, stop);

                Assert.assertEquals(cachedVal.getName(), uncachedVal.getName());
                Assert.assertEquals(cachedVal.getContigIndex(), uncachedVal.getContigIndex());
                Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases());
            }
        }

        // asserts for efficiency.  We are going to make contig.length / STEP_SIZE queries
        // at each of range: start -> start + querySize against a cache with size of X.
        // we expect to hit the cache each time range falls within X.  We expect a hit
        // on the cache if range is within X.  Which should happen at least (X - query_size * 2) / STEP_SIZE
        // times.
        final int minExpectedHits = (int)Math.floor((Math.min(caching.getCacheSize(), contig.getSequenceLength()) - querySize * 2.0) / STEP_SIZE);
        caching.printEfficiency(Priority.WARN);
        Assert.assertTrue(caching.getCacheHits() >= minExpectedHits, "Expected at least " + minExpectedHits + " cache hits but only got " + caching.getCacheHits());

    }
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Examples of htsjdk.samtools.SAMSequenceRecord

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    @Test(dataProvider = "fastas", enabled = true && ! DEBUG)
    public void testCachingIndexedFastaReaderTwoStage(File fasta, int cacheSize, int querySize) throws FileNotFoundException {
        final IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta);
        final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false);

        SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);

        int middleStart = (contig.getSequenceLength() - querySize) / 2;
        int middleStop = middleStart + querySize;

        logger.warn(String.format("Checking contig %s length %d with cache size %d and query size %d with intermediate query",
                contig.getSequenceName(), contig.getSequenceLength(), cacheSize, querySize));

        for ( int i = 0; i < contig.getSequenceLength(); i += 10 ) {
            int start = i;
            int stop = start + querySize;
            if ( stop <= contig.getSequenceLength() ) {
                ReferenceSequence grabMiddle = caching.getSubsequenceAt(contig.getSequenceName(), middleStart, middleStop);
                ReferenceSequence cachedVal = caching.getSubsequenceAt(contig.getSequenceName(), start, stop);
                ReferenceSequence uncachedVal = uncached.getSubsequenceAt(contig.getSequenceName(), start, stop);

                Assert.assertEquals(cachedVal.getName(), uncachedVal.getName());
                Assert.assertEquals(cachedVal.getContigIndex(), uncachedVal.getContigIndex());
                Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases());
            }
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Examples of htsjdk.samtools.SAMSequenceRecord

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    @Test
    public void testContigHasColon() {
        SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(htsjdk.samtools.SAMFileHeader.SortOrder.coordinate);
        SAMSequenceDictionary dict = new SAMSequenceDictionary();
        SAMSequenceRecord rec = new SAMSequenceRecord("c:h:r1", 10);
        rec.setSequenceLength(10);
        dict.addSequence(rec);
        header.setSequenceDictionary(dict);

        final GenomeLocParser myGenomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
        GenomeLoc loc = myGenomeLocParser.parseGenomeLoc("c:h:r1:4-5");
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Examples of htsjdk.samtools.SAMSequenceRecord

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        GenomeLoc cur = context.getLocation();

        if ( verbose && showSkipped ) {
            for(long i = context.getSkippedBases(); i >= 0; i--) {
                SAMSequenceDictionary dictionary = getToolkit().getReferenceDataSource().getReference().getSequenceDictionary();
                SAMSequenceRecord contig = dictionary.getSequence(cur.getContig());
                if(cur.getStop() < contig.getSequenceLength())
                    cur = getToolkit().getGenomeLocParser().incPos(cur,1);
                else
                    cur = getToolkit().getGenomeLocParser().createGenomeLoc(dictionary.getSequence(contig.getSequenceIndex()+1).getSequenceName(),1,1);
                out.printf("%s: skipped%n", cur);

            }
        }
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Examples of htsjdk.samtools.SAMSequenceRecord

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    @BeforeClass
    public void init() {
        header = ArtificialSAMUtils.createArtificialSamHeader(3, 1, ArtificialSAMUtils.DEFAULT_READ_LENGTH * 2);
        GenomeLocParser genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
        SAMSequenceRecord record;

        record = header.getSequence(0);
        firstContig = genomeLocParser.createGenomeLoc(record.getSequenceName(), 1, record.getSequenceLength());
        record = header.getSequence(1);
        secondContig = genomeLocParser.createGenomeLoc(record.getSequenceName(), 1, record.getSequenceLength());

        readMapped = createMappedRead("mapped", 1);

        readUnmappedFlag = createMappedRead("unmappedFlagged", 2);
        readUnmappedFlag.setReadUnmappedFlag(true);
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