| 72 | template <class SeqPosHashMap> |
| 73 | template <class oiterator> |
| 74 | void Aligner<SeqPosHashMap>::alignRead( |
| 75 | const string& qid, const Sequence& seq, |
| 76 | oiterator dest) |
| 77 | { |
| 78 | coalesceAlignments(qid, seq, |
| 79 | getAlignmentsInternal(seq, false), dest); |
| 80 | Sequence seqrc = reverseComplement(seq); |
| 81 | coalesceAlignments(qid, seqrc, |
| 82 | getAlignmentsInternal(seqrc, true), dest); |
| 83 | } |
| 84 | |
| 85 | /** Store all alignments for a given Kmer in the parameter aligns. |
| 86 | * @param[out] aligns Map of contig IDs to alignment vectors. |
no test coverage detected