this file won't exist if we can do on the fly splice junction indexing

def _has_sj_index(ref_file):
    """this file won't exist if we can do on the fly splice junction indexing"""
    return (file_exists(os.path.join(ref_file, "sjdbInfo.txt")) and
            (file_exists(os.path.join(ref_file, "transcriptInfo.tab"))))