Exemple #1
0
 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()
Exemple #2
0
    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