Package htsjdk.samtools

Examples of htsjdk.samtools.SAMSequenceDictionary

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        try {
            // 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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        catch(IllegalArgumentException ex) {
            usage("Invalid output type: " + args[2]);
        }

        ReferenceSequenceFile sequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(fastaFile);
        SAMSequenceDictionary dictionary = sequenceFile.getSequenceDictionary();

        switch(outputType) {
            case ANN:
                ANNWriter annWriter = new ANNWriter(outputFile);
                annWriter.write(dictionary);
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    private void validateDataSourcesAgainstReference(SAMDataSource reads, ReferenceSequenceFile reference, Collection<ReferenceOrderedDataSource> rods) {
        if ((reads.isEmpty() && (rods == null || rods.isEmpty())) || reference == null )
            return;

        // Compile a set of sequence names that exist in the reference file.
        SAMSequenceDictionary referenceDictionary = reference.getSequenceDictionary();

        if (!reads.isEmpty()) {
            // Compile a set of sequence names that exist in the BAM files.
            SAMSequenceDictionary readsDictionary = reads.getHeader().getSequenceDictionary();

            if (readsDictionary.size() == 0) {
                logger.info("Reads file is unmapped.  Skipping validation against reference.");
                return;
            }

            // compare the reads to the reference
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        final Class NON_CANONICAL_HUMAN_ORDER_EXCEPTION = UserException.LexicographicallySortedSequenceDictionary.class;
        final Class OUT_OF_ORDER_EXCEPTION = UserException.IncompatibleSequenceDictionaries.class;
        final Class DIFFERENT_INDICES_EXCEPTION = UserException.IncompatibleSequenceDictionaries.class;

        final List<SAMSequenceRecord> hg19Sequences = Arrays.asList(CHRM_HG19, CHR1_HG19, CHR2_HG19, CHR10_HG19);
        final GenomeLocParser hg19GenomeLocParser = new GenomeLocParser(new SAMSequenceDictionary(hg19Sequences));
        final List<GenomeLoc> hg19AllContigsIntervals = Arrays.asList(hg19GenomeLocParser.createGenomeLoc("chrM", 0, 1),
                                                                      hg19GenomeLocParser.createGenomeLoc("chr1", 0, 1),
                                                                      hg19GenomeLocParser.createGenomeLoc("chr2", 0, 1),
                                                                      hg19GenomeLocParser.createGenomeLoc("chr10", 0, 1));
        final List<GenomeLoc> hg19PartialContigsIntervals = Arrays.asList(hg19GenomeLocParser.createGenomeLoc("chrM", 0, 1),
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                                                  final SequenceDictionaryUtils.SequenceDictionaryCompatibility dictionaryCompatibility,
                                                  final Class expectedExceptionUponValidation,
                                                  final boolean isReadsToReferenceComparison,
                                                  final GenomeLocSortedSet intervals ) {

        final SAMSequenceDictionary firstDictionary = createSequenceDictionary(firstDictionaryContigs);
        final SAMSequenceDictionary secondDictionary = createSequenceDictionary(secondDictionaryContigs);
        final String testDescription = String.format("First dictionary: %s  Second dictionary: %s  Validation exclusions: %s",
                                                     SequenceDictionaryUtils.getDictionaryAsString(firstDictionary),
                                                     SequenceDictionaryUtils.getDictionaryAsString(secondDictionary),
                                                     validationExclusions);
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                                                  final SequenceDictionaryUtils.SequenceDictionaryCompatibility dictionaryCompatibility,
                                                  final Class expectedExceptionUponValidation,
                                                  final boolean isReadsToReferenceComparison,
                                                  final GenomeLocSortedSet intervals ) {

        final SAMSequenceDictionary firstDictionary = createSequenceDictionary(firstDictionaryContigs);
        final SAMSequenceDictionary secondDictionary = createSequenceDictionary(secondDictionaryContigs);
        final String testDescription = String.format("First dictionary: %s  Second dictionary: %s",
                                                     SequenceDictionaryUtils.getDictionaryAsString(firstDictionary),
                                                     SequenceDictionaryUtils.getDictionaryAsString(secondDictionary));

        final SequenceDictionaryUtils.SequenceDictionaryCompatibility reportedCompatibility =
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        // across multiple dictionaries in tests
        for ( SAMSequenceRecord contig : contigs ) {
            clonedContigs.add(contig.clone());
        }

        return new SAMSequenceDictionary(clonedContigs);
    }
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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");
        assertEquals(0, loc.getContigIndex());
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    }

    @Test
    public void testcreateGenomeLocOnContig() throws FileNotFoundException {
        final CachingIndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final SAMSequenceDictionary dict = seq.getSequenceDictionary();
        final GenomeLocParser genomeLocParser = new GenomeLocParser(dict);

        for ( final SAMSequenceRecord rec : dict.getSequences() ) {
            final GenomeLoc loc = genomeLocParser.createOverEntireContig(rec.getSequenceName());
            Assert.assertEquals(loc.getContig(), rec.getSequenceName());
            Assert.assertEquals(loc.getStart(), 1);
            Assert.assertEquals(loc.getStop(), rec.getSequenceLength());
        }
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    public Datum map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        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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