template<
typename system_tag,
typename fm_index_type>
struct nvbio::MEMFilter< system_tag, fm_index_type >
- This class implements an FM-index filter which can be used to find and filter MEMs between an arbitrary string-set and an FM-index.
- The filter is designed to:
- first find and rank the suffix array ranges containing occurrences of all MEMs, expressed as a series of lists of (SA-begin,SA-end,string-id,string_begin|string-end<<16) tuples: there is one such list for each string in the set, and the entries are stored contiguously in a single vector;
- and then enumerate each individual occurrence of a MEM within the lists, as a set of (index-pos,string-id,string-begin,string-end) tuples.
- Template Parameters
-
| fm_index_type | the type of the fm-index |
Definition at line 156 of file mem.h.
#include <mem.h>
The documentation for this struct was generated from the following file:
- E:/git/nvbio/nvbio/fmindex/mem.h
1.8.4