__init__.py 文件源码

def calculate_memory_for_sort():
    """Calculate available memory for ``samtools sort`` function.
    If there is enough memory, no temp files are created. **Enough**
    is defined as at least 1G per CPU.

    Returns
    -------
    sort_memory: str or None
        String to use directly with *-m* option in sort, or None.
    """

    avail_memory = None
    if HAVE_PSUTIL == True:
        mem = virtual_memory()
        avail_memory = mem.total
    else:
        try:
            avail_memory = os.sysconf('SC_PAGE_SIZE') * os.sysconf('SC_PHYS_PAGES')  # e.g. 4015976448
        except ValueError:
            logging.error("If you're in Mac OS you need to have the psutil Python library.")
            raise SystemExit

    avail_cpu = multiprocessing.cpu_count()

    sort_memory = avail_memory / avail_cpu / 1024 ** 2

    # samtools default from documentation is 768M, to be conservative
    #    only use -m option when there is more than 1G per CPU.
    if sort_memory < 1024:
        sort_memory = None

    else:
        sort_memory = "%sG" % (int(floor(sort_memory / 1024)))

    return sort_memory

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