/usr/include/blasr/algorithms/alignment/SDPAlign.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | #ifndef _BLASR_SDP_ALIGN_HPP_
#define _BLASR_SDP_ALIGN_HPP_
#include "DNASequence.hpp"
#include "tuples/TupleMatching.hpp"
#include "sdp/SDPFragment.hpp"
#include "FASTASequence.hpp"
#include "FASTQSequence.hpp"
#include "DistanceMatrixScoreFunction.hpp"
#define SDP_DETAILED_WORD_SIZE 5
#define SDP_PREFIX_LENGTH 50
#define SDP_SUFFIX_LENGTH 50
template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn>
int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
T_ScoreFn &scoreFn, int wordSize,
int sdpIns, int sdpDel, float indelRate,
blasr::Alignment &alignment,
AlignmentType alignType=Global,
bool detailedAlignment=true,
bool extendFrontByLocalAlignment=true,
DNALength noRecurseUnder=10000,
bool fastSDP=true,
unsigned int minFragmentsToUseGraphPaper=100000);
template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn, typename T_BufferCache>
int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
T_ScoreFn &scoreFn, int wordSize,
int sdpIns, int sdpDel, float indelRate,
blasr::Alignment &alignment,
T_BufferCache &buffers,
AlignmentType alignType=Global,
bool detailedAlignment=true,
bool extendFrontByLocalAlignment=true,
DNALength noRecurseUnder=10000,
bool fastSDP=true,
unsigned int minFragmentsToUseGraphPaper=100000);
template<typename T_QuerySequence, typename T_TargetSequence, typename T_ScoreFn, typename T_TupleList>
int SDPAlign(T_QuerySequence &query, T_TargetSequence &target,
T_ScoreFn &scoreFn,
int wordSize,
int sdpIns, int sdpDel, float indelRate,
blasr::Alignment &alignment,
std::vector<Fragment> &fragmentSet,
std::vector<Fragment> &prefixFragmentSet,
std::vector<Fragment> &suffixFragmentSet,
T_TupleList &targetTupleList,
T_TupleList &targetPrefixTupleList,
T_TupleList &targetSuffixTupleList,
std::vector<int> &maxFragmentChain,
// A few optinal parameters, should delete that last one.
AlignmentType alignType=Global,
bool detailedAlignment=true,
bool extendFrontByLocalAlignment=true,
DNALength noRecurseUnder=10000,
bool fastSDP=true,
unsigned int minFragmentsToUseGraphPaper=100000);
#include "SDPAlignImpl.hpp"
#endif // _BLASR_SDP_ALIGN_HPP_
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