12 * A range along with the alignment it represents.
16 top(0xffffffff), bot(0), cost(0), stratum(0), numMms(0),
17 fw(true), mate1(true), ebwt(NULL)
24 return top < 0xffffffff;
31 uint32_t top; // top of range
32 uint32_t bot; // bottom of range
33 uint16_t cost; // cost
34 uint32_t stratum; // stratum
35 uint32_t numMms; // # mismatches
36 bool fw; // the forward orientation of read aligned?
37 bool mate1; // read aligned is #1 mate/single?
38 std::vector<uint32_t> mms; // list of positions with mismatches
39 std::vector<uint8_t> refcs; // reference characters at mismatch positions
40 const Ebwt<seqan::String<seqan::Dna> > *ebwt;
43 assert_eq(refcs.size(), mms.size());
44 assert_eq(numMms, mms.size());
45 assert_leq(stratum, numMms);