Convert CRAM files to fastq, potentially within sub regions.

    Returns multiple fastq files that can be merged back together.

def _cram_to_fastq_regions(regions, cram_file, dirs, data):
    """Convert CRAM files to fastq, potentially within sub regions.

    Returns multiple fastq files that can be merged back together.
    """
    base_name = utils.splitext_plus(os.path.basename(cram_file))[0]
    work_dir = utils.safe_makedir(os.path.join(dirs["work"], "align_prep",
                                               "%s-parts" % base_name))
    fnames = run_multicore(_cram_to_fastq_region,
                           [(cram_file, work_dir, base_name, region, data) for region in regions],
                           data["config"])
    # check if we have paired or single end data
    if any(not _is_gzip_empty(p1) for p1, p2, s in fnames):
        out = [[p1, p2] for p1, p2, s in fnames]
    else:
        out = [[s] for p1, p2, s in fnames]
    return out, work_dir