Package org.broadinstitute.gatk.utils

Examples of org.broadinstitute.gatk.utils.GenomeLocParser

60
61
62
63
64
65
66
67
68
69
70

    @BeforeMethod
    public void doBefore() {
        header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
        genomeLocParser =new GenomeLocParser(header.getSequenceDictionary());

        engine = new GenomeAnalysisEngine();
        engine.setReferenceDataSource(refFile);
        engine.setGenomeLocParser(genomeLocParser);
       
View Full Code Here
99
100
101
102
103
104
105
106
107
108
109
            ref = new CachingIndexedFastaSequenceFile(refFile);
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(refFile,ex);
        }
        genomeLocParser = new GenomeLocParser(ref);

        engine = new GenomeAnalysisEngine();
        engine.setReferenceDataSource(refFile);
        engine.setGenomeLocParser(genomeLocParser);
    }
View Full Code Here
66
67
68
69
70
71
72
    protected GenomeLocParser genomeLocParser = null;

    @BeforeClass
    public void setupGenomeLoc() throws FileNotFoundException {
        sequenceSourceFile = fakeReferenceSequenceFile();
        genomeLocParser = new GenomeLocParser(sequenceSourceFile);
    }
View Full Code Here
52
53
54
55
56
57
58
    protected GenomeLocParser genomeLocParser;

    @BeforeClass
    public void beforeClass() {
        header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
    }
View Full Code Here
91
92
93
94
95
96
97
98
99
100
101
    @BeforeClass
    private void init() throws IOException {
        //reference = new CachingIndexedFastaSequenceFile(new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta")); // hg19Reference));
        reference = new CachingIndexedFastaSequenceFile(new File(hg19Reference));
        dictionary = reference.getSequenceDictionary();
        genomeLocParser = new GenomeLocParser(dictionary);

        // TODO: reads with indels
        // TODO: reads which span many regions
        // TODO: reads which are partially between intervals (in/outside extension)
        // TODO: duplicate reads
View Full Code Here
53
54
55
56
57
58
59
60
61
62
63
    @Param({"101M", "50M10I40M", "50M10D40M"})
    String cigar; // set automatically by framework

    @Override protected void setUp() {
        header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());

        for ( int j = 0; j < nReads; j++ ) {
            GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, locus, readLength);
            read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
            final byte[] quals = new byte[readLength];
View Full Code Here
47
48
49
50
51
52
53
54
    @BeforeClass
    public void setup() throws FileNotFoundException {
        // sequence
        final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(10, 0, 10000);
        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
        readsDataSource = null;
    }
View Full Code Here
61
62
63
64
65
66
67
68
69
    @BeforeClass
    public void beforeClass() {
        header = ArtificialSAMUtils.createArtificialSamHeader((endingChr - startingChr) + 1, startingChr, readCount + DEFAULT_READ_LENGTH);
        contig = header.getSequence(0).getSequenceName();
        genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());

        initializeTests();
    }
View Full Code Here
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
    private List<SAMRecord> testReads;

    @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);
View Full Code Here
68
69
70
71
72
73
74
     * Initialize the fasta.
     */
    @BeforeClass
    public void initialize() throws FileNotFoundException {
        sequenceFile = new CachingIndexedFastaSequenceFile( new File(hg18Reference) );
        genomeLocParser = new GenomeLocParser(sequenceFile);
    }
View Full Code Here
TOP

Related Classes of org.broadinstitute.gatk.utils.GenomeLocParser

  • htsjdk.samtools.SAMSequenceRecord
  • org.broad.igv.plugin.mongovariant.VariantReviewSource
  • org.broadinstitute.gatk.engine.datasources.providers.IntervalReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.LocusViewTemplate
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceViewTemplate
  • org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancerUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.FilePointerUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIteratorUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.ReadShardBalancerUnitTest$ReadShardBalancerTest
    • 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.