57 lines
2.3 KiB
C
57 lines
2.3 KiB
C
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// Needs to be called only once per program to set up static arrays
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void init_ed_dist() ;
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// The filtering function:
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// Inputs: Reference and query sequences,
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// Initial score (i.e. h0),
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// endBonus (i.e. the extra score if the whole query is aligned)
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// Outputs:
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// Alignment length in query
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// Alignment length in reference
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// Alignment score
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// Confidence: For now, it's either 0.0 or 1.0, corresponding to no/full confidence in outputs
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// Usage:
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// If confidence == 0.0: Partial alignment - need to rerun ksw_extend(...)
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// If confidence == 1.0
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// if alignedQLen == queryLen: Full alignment
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// if alignedQLen == 0: No alignment
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// Notes:
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// For now, the costMatrix and gap penalties are hardcoded.
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//
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void extend_with_edit_dist(uint8_t* refSeq, int refLen, uint8_t* querySeq, int queryLen,
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int initScore, int endBonus,
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int& alignedQLen, int& alignedRLen, int& score, float& confidence) ;
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// Filter-and-extend function:
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// Inputs: Reference and query sequences,
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// Initial score (i.e. h0),
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// endBonus (i.e. the extra score if the whole query is aligned)
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// zdrop value passed to ksw_extend
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// Outputs:
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// Alignment length in query
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// Alignment length in reference
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// Alignment score
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// Behavior:
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// The filtering function will be called internally first.
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// If there is an obvious result, it will be returned.
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// If not, ksw_extend() will be called with feedback from filtering function,
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// and its result will be returned.
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// Notes:
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// For now, the costMatrix and gap penalties are hardcoded.
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// It is assumed that ksw_extend(...) function is linked. In this version,
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// it is defined in bwa_extend.cpp file.
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void filter_and_extend(uint8_t* refSeq, int refLen, uint8_t* querySeq, int queryLen,
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int initScore, int endBonus, int zdrop,
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int& alignedQLen, int& alignedRLen, int& score) ;
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// Declaration needed for filter_and_extend(), defined in bwa_extend.cpp
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extern "C" {
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int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore, int *_max_off) ;
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}
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