def __init__(self, root, gopt, popt, max_isize, pairing_batch_size, visitor=None, mmap_enabled=False): if visitor is None: self.visitor = QuietMonitor() else: self.visitor = visitor self.root = root self.gopt = gopt self.popt = popt self.max_isize = max_isize self.pairing_batch_size = pairing_batch_size self.mmap_enabled = mmap_enabled # reference structures, loaded on demand self.__bwts = None # the reference index # the reference itself self.__pacseq = None self.__bnsp = None self.__last_ii = None self.clean_isize_statistics()
def __init__(self): self.event_monitor = QuietMonitor() self.logger = QuietMonitor() self.__gopt = bwa.gap_init_opt() self.__popt = bwa.pe_init_opt() self.__batch = [] self.qformat = "fastq-illumina" self.max_isize = 1000 self.nthreads = 1 self.trim_qual = 0 self.mmap_enabled = False # .reference is the path to the indexed BWA reference to use. Include the # "root name" of the reference files--i.e. the names without the file extensions. # The trailing dot, if included, will be removed. # e.g. my_references/hg_18.bwt # my_references/hg_18.rsax # my_references/hg_18.sax => "my_references/hg_18" # my_references/hg_18.pac # ... self.reference = None self.hit_visitor = None self.__iterator = None