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#ifndef _BLASR_MAP_BY_SUFFIX_ARRAY_HPP_
#define _BLASR_MAP_BY_SUFFIX_ARRAY_HPP_
#include <algorithm>
#include <alignment/algorithms/alignment/SWAlign.hpp>
#include <alignment/algorithms/alignment/ScoreMatrices.hpp>
#include <alignment/datastructures/anchoring/AnchorParameters.hpp>
#include <alignment/datastructures/anchoring/MatchPos.hpp>
#include <alignment/suffixarray/SuffixArray.hpp>
/*
* Parameters:
* Eventually this should be strongly typed, since this is specific to
* suffix array searching on DNASequence read/genome types.
* reference - should be of type DNASequence
* sa - shuld be of type SuffixArray
* read - may be of any DNASequence subclass.
* tupleSize - The length of the keyword used to speed up searching.
* Out:
* matchLow - The starting point in the suffix array for the LCP
* match for the read at pos p.
* matchHigh -The same array but for the upper bound.
* saMatchLength - The length of the lcp.
*/
template <typename T_SuffixArray, typename T_RefSequence, typename T_Sequence>
int LocateAnchorBoundsInSuffixArray(T_RefSequence &reference, T_SuffixArray &sa, T_Sequence &read,
unsigned int minPrefixMatchLength,
std::vector<DNALength> &matchLow,
std::vector<DNALength> &matchHigh,
std::vector<DNALength> &matchLength, AnchorParameters ¶ms);
template <typename T_SuffixArray, typename T_RefSequence, typename T_Sequence, typename T_MatchPos>
int MapReadToGenome(T_RefSequence &reference, T_SuffixArray &sa, T_Sequence &read,
unsigned int minPrefixMatchLength, std::vector<T_MatchPos> &matchPosList,
AnchorParameters &anchorParameters);
#include "MapBySuffixArrayImpl.hpp"
#endif
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