Package htsjdk.samtools

Examples of htsjdk.samtools.SAMSequenceDictionary

41
42
43
44
45
46
47
48
49
50
51
    String inpath = TestUtils.DATA_DIR + "vcf/SRP32_v4.sorted.0.vcf";
    File outFile = new File(TestUtils.TMP_OUTPUT_DIR, "testwriterout.vcf");

    private VariantContextWriter getWriter() {
        SAMSequenceDictionary seqDict = new SAMSequenceDictionary();
        EnumSet<Options> options = VariantContextWriterFactory.DEFAULT_OPTIONS;
        options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
        VariantContextWriter writer = VariantContextWriterFactory.create(outFile, seqDict, options);
        return writer;
    }
View Full Code Here
42
43
44
45
46
47
48
49
50
51
52
    }

    @Override
    public Map<String, Object> encodeAll(OutputStream outputStream, Iterator<? extends VCFVariant> features) throws IOException {

        SAMSequenceDictionary seqDict = new SAMSequenceDictionary();
        EnumSet<Options> options = VariantContextWriterFactory.DEFAULT_OPTIONS;
        options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
        options.remove(Options.INDEX_ON_THE_FLY);
        VariantContextWriter writer = VariantContextWriterFactory.create(outputStream, seqDict, options);
View Full Code Here
135
136
137
138
139
140
141
142
143
144
145
            return chromoName;
        }
    }

    private GenomeLocParser createGenomeLocParser() {
        SAMSequenceDictionary dict = new SAMSequenceDictionary();
        for (Chromosome chr : GenomeManager.getInstance().getCurrentGenome().getChromosomes()) {
            dict.addSequence(new SAMSequenceRecord(chromoNameToStandard(chr.getName()), chr.getLength()));
        }
        return new GenomeLocParser(dict);
    }
View Full Code Here
215
216
217
218
219
220
221
        return haplotypeList;
    }


    protected SAMSequenceDictionary artificialSAMSequenceDictionary() {
        return new SAMSequenceDictionary(Collections.singletonList(new SAMSequenceRecord("00",reference.length())));
    }
View Full Code Here
81
82
83
84
85
86
87
88
89
90
91
92
93
94
        List<Object[]> tests = new ArrayList<Object[]>();

        for ( final String ref : Arrays.asList(b37KGReference, hg18Reference) ) {
            final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(ref));
            final GenomeLocParser genomeLocParser = new GenomeLocParser(seq);
            final SAMSequenceDictionary dict = genomeLocParser.getContigs();

            for ( final SAMSequenceRecord rec1 : dict.getSequences() ) {
                for ( final SAMSequenceRecord rec2 : dict.getSequences() ) {
                    final int expected = Integer.valueOf(rec1.getSequenceIndex()).compareTo(rec2.getSequenceIndex());
                    tests.add(new Object[]{dict, rec1.getSequenceName(), rec2.getSequenceName(), expected});
                }
            }
        }
View Full Code Here
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
                                                                        String name,
                                                                        File inputFile,
                                                                        RMDStorageType storageType) {
        // Feature source and sequence dictionary to use as the ultimate reference
        AbstractFeatureReader featureSource = null;
        SAMSequenceDictionary sequenceDictionary = null;

        // Detect whether or not this source should be indexed.
        boolean canBeIndexed = (storageType == RMDStorageType.FILE);

        if(canBeIndexed) {
            try {
                Index index = loadIndex(inputFile, createCodec(descriptor, name, inputFile));
                try { logger.info(String.format("  Index for %s has size in bytes %d", inputFile, Sizeof.getObjectGraphSize(index))); }
                catch (ReviewedGATKException e) { }

                sequenceDictionary = IndexDictionaryUtils.getSequenceDictionaryFromProperties(index);

                // if we don't have a dictionary in the Tribble file, and we've set a dictionary for this builder, set it in the file if they match
                if (sequenceDictionary.size() == 0 && dict != null) {
                    validateAndUpdateIndexSequenceDictionary(inputFile, index, dict);

                    if ( ! disableAutoIndexCreation ) {
                        File indexFile = Tribble.indexFile(inputFile);
                        try { // re-write the index
View Full Code Here
413
414
415
416
417
418
419
420
421
422
423
     */
    public void validateAndUpdateIndexSequenceDictionary(final File inputFile, final Index index, final SAMSequenceDictionary dict) {
        if (dict == null) throw new ReviewedGATKException("BUG: dict cannot be null");

        // check that every contig in the RMD contig list is at least in the sequence dictionary we're being asked to set
        final SAMSequenceDictionary currentDict = IndexDictionaryUtils.createSequenceDictionaryFromContigList(index, new SAMSequenceDictionary());
        validateTrackSequenceDictionary(inputFile.getAbsolutePath(), currentDict, dict);

        // actually update the dictionary in the index
        IndexDictionaryUtils.setIndexSequenceDictionary(index, dict);
    }
View Full Code Here
54
55
56
57
58
59
60
61
62
63
64
65
66
     * get the sequence dictionary from the track, if available.  If not, make it from the contig list that is always in the index
     * @param index the index file to use
     * @return a SAMSequenceDictionary if available, null if unavailable
     */
    public static SAMSequenceDictionary getSequenceDictionaryFromProperties(Index index) {
        SAMSequenceDictionary dict = new SAMSequenceDictionary();
        for (Map.Entry<String,String> entry : index.getProperties().entrySet()) {
            if (entry.getKey().startsWith(SequenceDictionaryPropertyPredicate))
                dict.addSequence(new SAMSequenceRecord(entry.getKey().substring(SequenceDictionaryPropertyPredicate.length() , entry.getKey().length()),
                        Integer.valueOf(entry.getValue())));
        }
        return dict;
    }
View Full Code Here
48
49
50
51
52
53
54
55
56
57
58
59
public class VerifyingSamIteratorUnitTest {
    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);
    }
View Full Code Here
63
64
65
66
67
68
69
70
            index = loadIndex(inputFile, codec);
            featureReader = new TestFeatureReader(inputFile.getAbsolutePath(), codec);
        } catch (IOException e) {
            throw new RuntimeException(e);
        }
        SAMSequenceDictionary sequenceDictionary = IndexDictionaryUtils.getSequenceDictionaryFromProperties(index);
        return new RMDTrack(descriptor.getCodecClass(), name, inputFile, featureReader, sequenceDictionary, genomeLocParser, codec);
    }
View Full Code Here
TOP

Related Classes of htsjdk.samtools.SAMSequenceDictionary

  • org.broad.igv.cli_plugin.VCFEncoder
  • org.broad.igv.plugin.mongovariant.VariantReviewSource
  • org.broad.igv.variant.vcf.VCFWriterTest
  • org.broadinstitute.gatk.engine.alignment.bwa.BWTFiles
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.BWTSupplementaryFileGenerator
  • org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndexUnitTest
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngine
  • org.broadinstitute.gatk.engine.iterators.VerifyingSamIteratorUnitTest
  • org.broadinstitute.gatk.engine.refdata.tracks.IndexDictionaryUtils
  • org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.