Examples with SplitReadRealigner au.edu.wehi.idsv.SplitReadRealigner used on opensource projects

Example 1 with SplitReadRealigner

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

the class SoftClipsToSplitReads method doWork.

@Override
protected int doWork() {
    log.debug("Setting language-neutral locale");
    java.util.Locale.setDefault(Locale.ROOT);
    validateParameters();
    GenomicProcessingContext pc = new GenomicProcessingContext(getFileSystemContext(), REFERENCE_SEQUENCE, getReference());
    pc.setCommandLineProgram(this);
    pc.setFilterDuplicates(IGNORE_DUPLICATES);
    SplitReadRealigner realigner = new SplitReadRealigner(pc);
    realigner.setMinSoftClipLength(MIN_CLIP_LENGTH);
    realigner.setMinSoftClipQuality(MIN_CLIP_QUAL);
    realigner.setProcessSecondaryAlignments(PROCESS_SECONDARY_ALIGNMENTS);
    realigner.setWorkerThreads(WORKER_THREADS);
    try {
        SamReaderFactory readerFactory = SamReaderFactory.make();
        SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
        if (ALIGNER_STREAMING) {
            ExternalProcessStreamingAligner aligner = new ExternalProcessStreamingAligner(readerFactory, ALIGNER_COMMAND_LINE, REFERENCE_SEQUENCE, WORKER_THREADS);
            realigner.createSupplementaryAlignments(aligner, INPUT, OUTPUT);
        } else {
            ExternalProcessFastqAligner aligner = new ExternalProcessFastqAligner(readerFactory, writerFactory, ALIGNER_COMMAND_LINE);
            realigner.createSupplementaryAlignments(aligner, INPUT, OUTPUT);
        }
    } catch (IOException e) {
        log.error(e);
        return -1;
    }
    return 0;
}