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src/s/e/seal-0.4.0-rc2/tests/seal/lib/aligner/bwa/test_bwa_mapping.py   seal(Download)
 
import seal.lib.aligner.bwa.bwa_core as bwa
from seal.lib.aligner.bwa.bwa_mapping import BwaMapping
from seal.lib.aligner.sam_flags import *
 
        self.hits = []
        for s1, s2 in izip( self.bwa_seqs[0::2], self.bwa_seqs[1::2] ):
            self.hits.append( BwaMapping(self.gap_opts, self.reference, s1, s2) )
            self.hits.append( BwaMapping(self.gap_opts, self.reference, s2, s1) )
 
    def test_base_qualities_out_of_range(self):
        bwa_seq = self.bwa_seqs[0]
        for i in xrange(0, bwa_seq.len):
            bwa_seq.qual[i] = 1 # insert a bad encoded quality value
        mapping = BwaMapping(self.gap_opts, self.reference, bwa_seq, self.bwa_seqs[1])
 
        # create a new BwaMapping object
        mapping = BwaMapping(self.gap_opts, self.reference, bwa_seq, mate)
 
        # get the XA tag and test its value