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nvbio::MEMFilter< system_tag, fm_index_type > Struct Template Reference

Detailed description

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_typethe 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: