Did I find the right examples for you? yes no

All Samples(3)  |  Call(3)  |  Derive(0)  |  Import(0)

src/s/e/seal-0.4.0-rc2/seal/lib/aligner/bwa/bwa_mapping.py   seal(Download)
 
    # Where in the reference is pos?
    self.ref_id, self.__nn = bwa.get_seq_id(self.bns, self.pos, ref_len)
    self.tid = self.bns.anns[self.ref_id].name
    # make the position relative to the start of its reference section
        # XXX: below, self.__mate.len.  Shouldn't it be (self.__mate.get_pos_end() - self.__mate.pos) ??
        # I posted to the list about this and await a response.
        self.m_ref_id, m_nn = bwa.get_seq_id(self.bns, self.__mate.pos, self.__mate.len)
        if self.m_ref_id == self.ref_id:
          self.mtid = '='
  def __analyze_multi(self, i):
    multi_hit_chunk = []
    q = self.__read.multi[i]
    ref_len = q.get_pos_end(len(self.__read)) - q.pos
    ref_id, nn = bwa.get_seq_id(self.bns, q.pos, ref_len)