Package org.broadinstitute.gatk.engine.datasources.rmd

Examples of org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource

992
993
994
995
996
997
998
999
1000
1001
1002
                                                            getArguments().disableAutoIndexCreationAndLockingWhenReadingRods,
                                                            sampleRenameMap);

        final List<ReferenceOrderedDataSource> dataSources = new ArrayList<ReferenceOrderedDataSource>();
        for (RMDTriplet fileDescriptor : referenceMetaDataFiles)
            dataSources.add(new ReferenceOrderedDataSource(fileDescriptor,
                                                           builder,
                                                           sequenceDictionary,
                                                           genomeLocParser,
                                                           flashbackData()));
View Full Code Here
106
107
108
109
110
111
112
113
114
115
116
     */
    @Test
    public void testSingleBinding() {
        String fileName = privateTestDir + "TabularDataTest.dat";
        RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
        ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);

        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));

        LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.singletonList(dataSource));
        ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
View Full Code Here
129
130
131
132
133
134
135
136
137
138
139
140
141
142
    @Test
    public void testMultipleBinding() {
        File file = new File(privateTestDir + "TabularDataTest.dat");

        RMDTriplet testTriplet1 = new RMDTriplet("tableTest1","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
        ReferenceOrderedDataSource dataSource1 = new ReferenceOrderedDataSource(testTriplet1,builder,seq.getSequenceDictionary(),genomeLocParser,false);

        RMDTriplet testTriplet2 = new RMDTriplet("tableTest2","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
        ReferenceOrderedDataSource dataSource2 = new ReferenceOrderedDataSource(testTriplet2,builder,seq.getSequenceDictionary(),genomeLocParser,false);

        Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));

        LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Arrays.asList(dataSource1,dataSource2));
        ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
View Full Code Here
TOP

Related Classes of org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource

  • org.broadinstitute.gatk.engine.datasources.providers.ReferenceOrderedViewUnitTest
  • org.broadinstitute.gatk.engine.GenomeAnalysisEngine
  • java.io.File
    • 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.