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