Examples of org.broadinstitute.gatk.tools.walkers.na12878kb.core.NA12878KnowledgeBase

        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;
        for (WriteResult wr : writeResults) {
            if (wr.getError() != null) {
                System.out.println(wr.getError());
                errCount++;

    static String addCall(String dbSpecPath, MongoVariantContext mvc) {


        NA12878DBArgumentCollection args = new NA12878DBArgumentCollection(dbSpecPath);


        String errorMessage = null;
        NA12878KnowledgeBase kb = null;
        try {
            kb = new NA12878KnowledgeBase(null, args);
            WriteResult wr = kb.addCall(mvc);
            errorMessage = wr.getError();
        } catch (Exception ex) {
            errorMessage = ex.getMessage();
            if (errorMessage == null) errorMessage = "" + ex;
        } finally {
            if (kb != null) kb.close();
        }


        return errorMessage;
    }

Related Classes of org.broadinstitute.gatk.tools.walkers.na12878kb.core.NA12878KnowledgeBase

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.