libStatGen Software
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Public Member Functions | |
GreedyTupleAligner (Weight &wt) | |
int | MatchTuple (const QueryType query, const int queryLength, const ReferenceType reference, const ReferenceIndex searchStartIndex, const int searchSize, int &matchedLength, int &mismatch) |
Match 'query' to the 'reference' from 'searchStartIndex' up to 'searchSize', store matched length to 'matchedLength' and number of mismatch to 'mismatch'. More... | |
void | Align (QueryType query, int queryLength, ReferenceType reference, ReferenceIndex searchStartIndex, int searchSize, CigarRoller &cigarRoller, ReferenceIndex &matchPosition) |
Core local alignment algorithm. More... | |
Definition at line 60 of file GreedyTupleAligner.h.
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inline |
Core local alignment algorithm.
query | input query |
queryLength | length of query |
reference | reference genome |
searchStartIndex | matching starts here |
searchSize | how far we will search |
cigarRoller | store alignment results here |
matchPosition | store match position |
Definition at line 159 of file GreedyTupleAligner.h.
References CigarRoller::Add(), CigarRoller::clear(), Cigar::del, Cigar::insert, Cigar::match, GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >::MatchTuple(), Cigar::mismatch, and Cigar::softClip.
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inline |
Match 'query' to the 'reference' from 'searchStartIndex' up to 'searchSize', store matched length to 'matchedLength' and number of mismatch to 'mismatch'.
query | input query |
queryLength | length of query |
reference | reference sequence |
searchStartIndex | the positino where search starts |
searchSize | the total length in reference sequence that will be examine |
matchedLength | store how many bases are matched |
mismatch | store how many bases are mismatched |
Definition at line 79 of file GreedyTupleAligner.h.
Referenced by GreedyTupleAligner< QueryType, ReferenceType, ReferenceIndex >::Align().