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src/s/e/seal-0.4.0-rc2/seal/lib/aligner/bwa/bwa_aligner.py   seal(Download)
import bwa_core as bwa
from bwa_iterator import BWAIterator
from seal.lib.event_monitor import QuietMonitor
 
BWA_INDEX_MANDATORY_EXT = set(["amb", "ann", "bwt", "pac", "rbwt", "rpac"])
  def __init__(self):
    self.event_monitor = QuietMonitor()
    self.logger = QuietMonitor()
    self.__gopt = bwa.gap_init_opt()
    self.__popt = bwa.pe_init_opt()

src/s/e/seal-0.4.0-rc2/seal/lib/aligner/bwa/bwa_iterator.py   seal(Download)
from bwa_mapping import BwaMapping
 
from seal.lib.event_monitor import QuietMonitor
 
class BWAIterator(object):
 
  def __init__(self, root, gopt, popt, max_isize, pairing_batch_size,
               visitor=None, mmap_enabled=False):
    if visitor is None:
      self.visitor = QuietMonitor()