IOUtils.java 文件源码

public static BigLong2ShortHashMap loadReads(File[] files, int k, int minSeqLen,
                                             int availableProcessors, Logger logger)
        throws ExecutionFailedException {
    BigLong2ShortHashMap hm = new BigLong2ShortHashMap(
            (int) (Math.log(availableProcessors) / Math.log(2)) + 4, 12, true);

    ReadsLoadWorker[] workers = new ReadsLoadWorker[availableProcessors];
    for (int i = 0; i < workers.length; ++i) {
        workers[i] = new ReadsLoadWorker(hm, k, minSeqLen);
    }

    run(files, workers, hm, logger);

    // calculating statistics...
    int totalSeq = 0, goodSeq = 0;
    long totalLen = 0, goodLen = 0;
    for (ReadsLoadWorker worker : workers) {
        totalSeq += worker.totalSeq;
        goodSeq += worker.goodSeq;
        totalLen += worker.totalLen;
        goodLen += worker.goodLen;
    }
    Tool.debug(logger,
            "Good/Total sequences count = " + NumUtils.groupDigits(goodSeq) + "/" + NumUtils.groupDigits(totalSeq)
            + " (" + String.format("%.1f", goodSeq * 100.0 / totalSeq) + "%)");
    Tool.debug(logger,
            "Good/Total sequences length = " + NumUtils.groupDigits(goodLen) + "/" + NumUtils.groupDigits(totalLen)
                    + " (" + String.format("%.1f", goodLen * 100.0 / totalLen) + "%)");
    logger.debug("k-mers HM size = " + NumUtils.groupDigits(hm.size()));

    return hm;
}