4 * Created on: Aug 3, 2009
17 * Encapsulates a sorted list of reference positions that are annotated
18 * somehow (e.g. as a SNP).
22 typedef std::pair<uint32_t, uint32_t> U32Pair;
23 typedef std::pair<char, char> CharPair;
24 typedef std::map<U32Pair, CharPair> AnnotMap;
25 typedef std::map<U32Pair, CharPair>::const_iterator Iter;
27 AnnotationMap(const char *fname) {
33 * Give a reference coordinate in the index, translate it into a
34 * new reference coordinate via the reference map supplied by the
37 Iter lower_bound(const U32Pair& h) const {
38 return map_.lower_bound(h);
52 * Parse an annotation-map file.
56 /// filename of file containing the annotation map
58 /// maps reference positions to character annotations