-\r
- // the set of readers and alignments which we operate on, maintained throughout the life of this class\r
- std::vector<std::pair<BamReader*, BamAlignment*> > readers;\r
-\r
- // readers and alignments sorted by reference id and position, to keep track of the lowest (next) alignment\r
- // when a reader reaches EOF, its entry is removed from this index\r
- AlignmentIndex alignments;\r
-\r
- std::vector<std::string> fileNames;\r