Examples with GridssConfiguration au.edu.wehi.idsv.configuration.GridssConfiguration used on opensource projects

Example 6 with GridssConfiguration

use of au.edu.wehi.idsv.configuration.GridssConfiguration in project gridss by PapenfussLab.

the class MultipleSamFileCommandLineProgram method getContext.

public ProcessingContext getContext() {
    if (processContext == null) {
        GridssConfiguration config;
        try {
            config = new GridssConfiguration(CONFIGURATION_FILE, WORKING_DIR);
        } catch (ConfigurationException e) {
            throw new RuntimeException(e);
        }
        processContext = new ProcessingContext(getFileSystemContext(), REFERENCE_SEQUENCE, null, getDefaultHeaders(), config);
        processContext.setCommandLineProgram(this);
        processContext.setFilterDuplicates(IGNORE_DUPLICATES);
        processContext.setWorkerThreadCount(WORKER_THREADS);
        if (BLACKLIST != null) {
            try {
                processContext.setBlacklist(BLACKLIST);
            } catch (IOException e) {
                log.error(e, "Error loading BED blacklist. ", BLACKLIST);
                throw new RuntimeException(e);
            }
        }
    }
    return processContext;
}