Package org.broadinstitute.gatk.tools.walkers.na12878kb.core

Examples of org.broadinstitute.gatk.tools.walkers.na12878kb.core.NA12878DBArgumentCollection

143
144
145
146
147
148
149
150
151
152
153
    private Iterator<VCFVariant> getFeature() throws IOException {
        return source.getFeatures(chr, start, end);
    }

    private int resetDB() throws Exception {
        NA12878DBArgumentCollection args = new NA12878DBArgumentCollection(dbSpecPath);
        NA12878KnowledgeBase kb = new NA12878KnowledgeBase(null, args);

        List<WriteResult> writeResults = kb.removeCall(mvc);
        kb.close();
        int errCount = 0;
View Full Code Here
58
59
60
61
62
63
64
65
66
67
68
                log.error("VariantReviewPlugin requires Java 7 or higher. This plugin will be disabled");
                return;
            }
            //Test that we can load this class, plugin loader will catch the exception and
            //not load plugin if it can't be loaded
            NA12878DBArgumentCollection col = new NA12878DBArgumentCollection();
            initMenuItems();

            TrackLoader.registerHandler(VARIANT_DB_EXT, new TrackLoadHandler());
        }
    }
View Full Code Here
136
137
138
139
140
141
142
143
144
145
146
     * @param mvc
     * @return
     */
    static String addCall(String dbSpecPath, MongoVariantContext mvc) {

        NA12878DBArgumentCollection args = new NA12878DBArgumentCollection(dbSpecPath);

        String errorMessage = null;
        NA12878KnowledgeBase kb = null;
        try {
            kb = new NA12878KnowledgeBase(null, args);
View Full Code Here
TOP

Related Classes of org.broadinstitute.gatk.tools.walkers.na12878kb.core.NA12878DBArgumentCollection

  • org.broad.igv.plugin.mongovariant.VariantReviewDialog
  • org.broad.igv.plugin.mongovariant.VariantReviewPlugin
  • org.broad.igv.plugin.mongovariant.VariantReviewTest
    • 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.