Set-BWTE

Detailed Description

This module contains functions and classes implementing the set-bwte algorithm described in:
"A massively parallel algorithm for constructing the BWT of large string sets"
http://arxiv.org/abs/1410.0562

Classes
struct	nvbio::BWTEBlock
struct	nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >

Functions
template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >
void	nvbio::bwte (const ConcatenatedStringSet< PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, typename std::iterator_traits< offsets_iterator >::value_type >, offsets_iterator > string_set, PagedText< SYMBOL_SIZE, BIG_ENDIAN > &BWT_ext, SparseSymbolSet &BWT_ext_dollars, BWTParams *params=NULL)

Function Documentation

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >

void nvbio::bwte	(	const ConcatenatedStringSet< PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, typename std::iterator_traits< offsets_iterator >::value_type >, offsets_iterator >	string_set,
		PagedText< SYMBOL_SIZE, BIG_ENDIAN > &	BWT_ext,
		SparseSymbolSet &	BWT_ext_dollars,
		BWTParams *	params = NULL
	)

Parallel set-bwte algorithm for computing the BWT of a string-set.

Parameters

string_set	the input set of strings
BWT_ext	the output external BWT, stored into a PagedText
BWT_ext_dollars	the output external BWT dollar symbols, stored as a SparseSymbolSet
params	the BWT construction parameters

Parallel BWTE algorithm for computing the BWT of a string-set.

Parameters

string_set	the input set of strings
output	the output handler for the resulting BWT
params	the BWT construction parameters

Definition at line 896 of file bwte_inl.h.