84 lines
3.7 KiB
C++
84 lines
3.7 KiB
C++
#include <stdio.h>
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#include "intel_ext.h"
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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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// 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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void intel_init()
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{
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init_ed_dist();
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}
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void intel_filter(uint8_t *refSeq, int refLen, uint8_t *querySeq, int queryLen, int initScore, int endBonus,
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int *alignedQLen, int *alignedRLen, int *score, float *confidence)
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{
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if (queryLen < INTEL_MIN_LEN || queryLen > INTEL_MAX_LEN) {
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*confidence = 0.0;
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return;
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}
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extend_with_edit_dist(refSeq, refLen, querySeq, queryLen, initScore, endBonus, *alignedQLen, *alignedRLen, *score, *confidence);
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}
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int intel_extend(int qlen, uint8_t *query, int tlen, 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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if (qlen >= INTEL_MIN_LEN && qlen <= INTEL_MAX_LEN && tlen >= INTEL_MIN_LEN && tlen <= INTEL_MAX_LEN) {
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int score, a = mat[0];
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filter_and_extend(target, tlen, query, qlen, h0/a, !!(end_bonus > 0), zdrop/a, *qle, *tle, score);
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*max_off = 0; *gtle = *tle; *gscore = score;
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score *= a;
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int score2 = score, qle2 = *qle, tle2 = *tle;
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score = ksw_extend(qlen, query, tlen, target, m, mat, gapo, gape, w, end_bonus, zdrop, h0, qle, tle, gtle, gscore, max_off);
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fprintf(stderr, "[%d,%d,%d] %d:%d; %d:%d; %d:%d\n", qlen, tlen, h0, score, score2, *qle, qle2, *tle, tle2);
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return score;
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} else return ksw_extend(qlen, query, tlen, target, m, mat, gapo, gape, w, end_bonus, zdrop, h0, qle, tle, gtle, gscore, max_off);
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}
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