Package org.broadinstitute.gatk.utils.fasta

Examples of org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile

79
80
81
82
83
84
85
86
    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
        genomeLocParser = new GenomeLocParser(seq);
    }
View Full Code Here
98
99
100
101
102
103
104
105
106
107
108
    public MergeSegregatingAlternateAllelesVCFWriter(VariantContextWriter innerWriter, GenomeLocParser genomeLocParser, File referenceFile, VariantContextMergeRule vcMergeRule, PhasingUtils.AlleleMergeRule alleleMergeRule, String singleSample, boolean emitOnlyMergedRecords, Logger logger, boolean takeOwnershipOfInner, boolean trackAltAlleleStats) {
        this.innerWriter = innerWriter;
        this.genomeLocParser = genomeLocParser;
        try {
            this.referenceFileForMNPmerging = new CachingIndexedFastaSequenceFile(referenceFile);
        }
        catch(FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
        }       
        this.vcMergeRule = vcMergeRule;
View Full Code Here
92
93
94
95
96
97
98
        ATCATC = Allele.create("ATCATC");
        ATCATCT = Allele.create("ATCATCT");
        ATref = Allele.create("AT",true);
        Anoref = Allele.create("A",false);
        GT = Allele.create("GT",false);
        genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(hg18Reference)));
    }
View Full Code Here
69
70
71
72
73
74
75
76
77
    SAMSequenceDictionary dictForFails;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        // sequence
        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        final GenomeLocParser genomeLocParser = new GenomeLocParser(seq);
        dictForFails = genomeLocParser.getContigs();
    }
View Full Code Here
79
80
81
82
83
84
85
86
87
88
89
    @DataProvider(name = "MyDataProvider")
    public Object[][] makeMyDataProvider() throws Exception {
        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() ) {
View Full Code Here
158
159
160
161
162
163
164
165
166
167
168
            // we don't want to assume that reads will be written in order by the manager because in deep, deep pileups it won't work
            Utils.setupWriter(writer, toolkit, toolkit.getSAMFileHeader(), false, this, PROGRAM_RECORD_NAME);
        }

        try {
            final CachingIndexedFastaSequenceFile referenceReader = new CachingIndexedFastaSequenceFile(toolkit.getArguments().referenceFile);
            overhangManager = new OverhangFixingManager(writer, toolkit.getGenomeLocParser(), referenceReader, MAX_RECORDS_IN_MEMORY, MAX_MISMATCHES_IN_OVERHANG, MAX_BASES_TO_CLIP, doNotFixOverhangs);
        }
        catch (FileNotFoundException ex) {
            throw new UserException.CouldNotReadInputFile(toolkit.getArguments().referenceFile, ex);
        }
View Full Code Here
68
69
70
71
72
73
74
75
    private SAMFileHeader header;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
    }
View Full Code Here
74
75
76
77
78
79
80
81
    private SAMFileHeader header;

    @BeforeClass
    public void setup() throws FileNotFoundException {
        final IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
    }
View Full Code Here
52
53
54
55
56
57
58
public class ProgressMeterDaemonUnitTest extends BaseTest {
    private GenomeLocParser genomeLocParser;

    @BeforeClass
    public void init() throws FileNotFoundException {
        genomeLocParser = new GenomeLocParser(new CachingIndexedFastaSequenceFile(new File(b37KGReference)));
    }
View Full Code Here
92
93
94
95
96
97
98
99
100
101
102
    private static final int numReadsPerContig = 250000;
    private static final List<String> contigs = Arrays.asList("1", "2", "3");

    @BeforeClass
    private void init() throws IOException {
        reference = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        dictionary = reference.getSequenceDictionary();
        genomeLocParser = new GenomeLocParser(dictionary);
        header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test");
        header.setSequenceDictionary(dictionary);
        header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
View Full Code Here
TOP

Related Classes of org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile

  • htsjdk.samtools.reference.ReferenceSequence
  • htsjdk.samtools.SAMSequenceRecord
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceViewTemplate
  • org.broadinstitute.gatk.engine.datasources.reads.FilePointerUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSourceUnitTest
  • org.broadinstitute.gatk.engine.datasources.reference.ReferenceDataSource
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataPoolUnitTest
  • org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPoolUnitTest
  • org.broadinstitute.gatk.engine.ReadMetricsUnitTest
    • 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.