nvbio::QGramFilter< system_tag, qgram_index_type, query_iterator, index_iterator > Struct Template Reference

Detailed description

template< typename system_tag, typename qgram_index_type, typename query_iterator, typename index_iterator>
struct nvbio::QGramFilter< system_tag, qgram_index_type, query_iterator, index_iterator >

This class implements a q-gram filter which can be used to find and filter matches between an arbitrary set of indexed query q-grams, representing q-grams of a given text, and a q-gram index. The q-gram index can be either a simple string index or a string-set index.

For string q-gram indices, the filter will return an ordered set of (qgram-pos,query-pos) pairs, where qgram-pos is the index of the hit into the string used to build qgram-index, and query-pos corresponds to one of the input query q-gram indices.

For string-set q-gram indices, the filter will return an ordered set of (string-id,string-pos,query-pos) pairs (encoded as uint4), where string-id is the index of the hit into the string-set used to build qgram-index, and query-pos corresponds to one of the input query q-gram indices.

Template Parameters

qgram_index_type	the type of the qgram-index
query_iterator	the type of the query q-gram iterator
index_iterator	the type of the query index iterator

Definition at line 67 of file filter.h.

#include <filter.h>

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The documentation for this struct was generated from the following file:

• E:/git/nvbio/nvbio/qgram/filter.h