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This commit is contained in:
Heng Li
parent
8e0d73740e
commit
fbfd4a3eff
544
ksw2.c
544
ksw2.c
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#include <stdint.h>
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#include <stdio.h> // for debugging only
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#include "ksw2.h"
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#ifdef HAVE_KALLOC
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#include "kalloc.h"
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#else
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#include <stdlib.h>
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#define kmalloc(km, size) malloc((size))
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#define kcalloc(km, count, size) calloc((count), (size))
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#define krealloc(km, ptr, size) realloc((ptr), (size))
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#define kfree(km, ptr) free((ptr))
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#endif
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void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b)
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{
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int i, j;
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a = a < 0? -a : a;
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b = b > 0? -b : b;
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for (i = 0; i < m - 1; ++i) {
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for (j = 0; j < m - 1; ++j)
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mat[i * m + j] = i == j? a : b;
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mat[i * m + m - 1] = 0;
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}
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for (j = 0; j < m; ++j)
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mat[(m - 1) * m + j] = 0;
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}
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typedef struct {
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int32_t h, e;
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} eh_t;
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/*********************
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* One-way extension *
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*********************/
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int ksw_extend(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w,
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int end_bonus, int zdrop, int h0, int *_qle, int *_tle, int *_gtle, int *_gscore)
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{
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eh_t *eh; // score array
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int8_t *qp; // query profile
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int i, j, k, gapoe = gapo + gape, st, en, max, max_i, max_j, max_j0, max_gap, max_ie, gscore;
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// allocate memory
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qp = kmalloc(km, (long)qlen * m);
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eh = kcalloc(km, qlen + 1, 8);
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// generate the query profile
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for (k = i = 0; k < m; ++k) {
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const int8_t *p = &mat[k * m];
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for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
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}
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// fill the first row
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eh[0].h = h0, eh[0].e = h0 - gapoe - gapoe > 0? h0 - gapoe - gapoe : 0;
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for (j = 1; j <= qlen && j <= w; ++j) {
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eh[j].h = -(gapo + gape * j), eh[j].e = eh[j-1].e - gape;
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if (eh[j].e < 0) eh[j].e = 0;
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if (eh[j].h < 0) {
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eh[j].h = 0;
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break;
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}
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}
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// adjust $w if it is too large
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k = m * m;
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for (i = 0, max = 0; i < k; ++i) // get the max score
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max = max > mat[i]? max : mat[i];
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max_gap = (int)((double)((qlen < tlen? qlen : tlen) * max + end_bonus - gapo) / gape + 1.);
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max_gap = max_gap > 1? max_gap : 1;
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w = w < max_gap? w : max_gap;
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// DP loop
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max = h0, max_i = max_j = -1; max_ie = -1, gscore = -1; max_j0 = 0;
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st = 0, en = qlen;
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for (i = 0; i < tlen; ++i) {
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int f = 0, h1, m0 = 0;
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int8_t *q = &qp[target[i] * qlen];
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// apply the band and the constraint (if provided)
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if (st < max_j0 - w) st = max_j0 - w;
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if (en > max_j0 + w + 1) en = max_j0 + w + 1;
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// compute the first column
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if (st == 0) {
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h1 = h0 - (gapo + gape * (i + 1));
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if (h1 < 0) h1 = 0;
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} else h1 = 0;
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for (j = st; j < en; ++j) {
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// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
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// Similar to SSE2-SW, cells are computed in the following order:
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// H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}
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// E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape
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// F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape
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eh_t *p = &eh[j];
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int h = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j)
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p->h = h1; // set H(i,j-1) for the next row
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h += q[j];
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h = h > e? h : e; // e and f are guaranteed to be non-negative, so h>=0 even if h<0
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h = h > f? h : f;
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h1 = h; // save H(i,j) to h1 for the next column
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max_j0 = m0 > h? max_j0 : j; // record the position where max score is achieved
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m0 = m0 > h? m0 : h; // m0 is stored at eh[mj+1]
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h -= gapoe;
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h = h > 0? h : 0;
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e -= gape;
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e = e > h? e : h; // computed E(i+1,j)
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p->e = e; // save E(i+1,j) for the next row
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f -= gape;
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f = f > h? f : h; // computed F(i,j+1)
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}
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eh[en].h = h1; eh[en].e = 0;
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if (j == qlen) {
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max_ie = gscore > h1? max_ie : i;
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gscore = gscore > h1? gscore : h1;
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}
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if (m0 == 0) break;
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if (m0 > max) {
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max = m0, max_i = i, max_j = max_j0;
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} else if (zdrop > 0) {
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int diff = (i - max_i) - (max_j0 - max_j);
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if (max - m0 - (diff < 0? -diff : diff) * gape > zdrop) break;
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}
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// update beg and end for the next round
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for (j = st; j < en && eh[j].h == 0 && eh[j].e == 0; ++j);
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st = j;
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for (j = en; j >= st && eh[j].h == 0 && eh[j].e == 0; --j);
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en = j + 2 < qlen? j + 2 : qlen;
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//beg = 0; end = qlen; // uncomment this line for debugging
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}
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kfree(km, eh); kfree(km, qp);
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if (_qle) *_qle = max_j + 1;
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if (_tle) *_tle = max_i + 1;
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if (_gtle) *_gtle = max_ie + 1;
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if (_gscore) *_gscore = gscore;
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return max;
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}
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/********************
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* Global alignment *
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********************/
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#define NEG_INF -0x40000000
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static inline uint32_t *push_cigar(void *km, int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len)
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{
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if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
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if (*n_cigar == *m_cigar) {
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*m_cigar = *m_cigar? (*m_cigar)<<1 : 4;
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cigar = krealloc(km, cigar, (*m_cigar) << 2);
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}
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cigar[(*n_cigar)++] = len<<4 | op;
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} else cigar[(*n_cigar)-1] += len<<4;
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return cigar;
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}
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int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_)
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{
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eh_t *eh;
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int8_t *qp; // query profile
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int32_t i, j, k, max_j = 0, gapoe = gapo + gape, score, n_col, *off = 0, last_en = -1;
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uint8_t *z = 0; // backtrack matrix; in each cell: f<<4|e<<2|h; in principle, we can halve the memory, but backtrack will be more complex
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// allocate memory
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n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix
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qp = kmalloc(km, qlen * m);
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eh = kcalloc(km, qlen + 1, 8);
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if (n_cigar_ && cigar_) {
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*n_cigar_ = 0;
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z = kmalloc(km, (size_t)n_col * tlen);
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off = kcalloc(km, tlen, 4);
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}
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// generate the query profile
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for (k = i = 0; k < m; ++k) {
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const int8_t *p = &mat[k * m];
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for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];
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}
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// fill the first row
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eh[0].h = 0, eh[0].e = -gapoe - gapo;
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for (j = 1; j <= qlen && j <= w; ++j)
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eh[j].h = -(gapo + gape * j), eh[j].e = -(gapoe + gapo + gape * j);
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for (; j <= qlen; ++j) eh[j].h = eh[j].e = NEG_INF; // everything is -inf outside the band
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// DP loop
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for (i = 0; i < tlen; ++i) { // target sequence is in the outer loop
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int32_t f = NEG_INF, h1, st, en, max = NEG_INF;
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int8_t *q = &qp[target[i] * qlen];
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#if 0
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st = max_j > w? max_j - w : 0;
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en = max_j + w + 1 < qlen? max_j + w + 1 : qlen;
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#else
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st = i > w? i - w : 0;
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en = i + w + 1 < qlen? i + w + 1 : qlen;
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#endif
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h1 = st > 0? NEG_INF : -(gapo + gape * i);
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f = st > 0? NEG_INF : -(gapoe + gapo + gape * i);
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off[i] = st;
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if (n_cigar_ && cigar_) {
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uint8_t *zi = &z[(long)i * n_col];
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for (j = st; j < en; ++j) {
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// At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)
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// Cells are computed in the following order:
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// H(i,j) = max{H(i-1,j-1) + S(i,j), E(i,j), F(i,j)}
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// E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape
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// F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape
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eh_t *p = &eh[j];
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int32_t h = p->h, e = p->e;
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uint8_t d; // direction
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p->h = h1;
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h += q[j];
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d = h >= e? 0 : 1;
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h = h >= e? h : e;
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d = h >= f? d : 2;
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h = h >= f? h : f;
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h1 = h;
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max_j = max > h? max_j : j;
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max = max > h? max : h;
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h -= gapoe;
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e -= gape;
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d |= e > h? 1<<2 : 0;
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e = e > h? e : h;
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p->e = e;
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f -= gape;
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d |= f > h? 2<<4 : 0; // if we want to halve the memory, use one bit only, instead of two
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f = f > h? f : h;
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zi[j - st] = d; // z[i,j] keeps h for the current cell and e/f for the next cell
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}
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} else {
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for (j = st; j < en; ++j) {
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eh_t *p = &eh[j];
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int32_t h = p->h, e = p->e;
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p->h = h1;
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h += q[j];
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h = h >= e? h : e;
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h = h >= f? h : f;
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h1 = h;
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max_j = max > h? max_j : j;
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max = max > h? max : h;
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h -= gapoe;
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e -= gape;
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e = e > h? e : h;
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p->e = e;
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f -= gape;
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f = f > h? f : h;
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}
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}
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eh[en].h = h1, eh[en].e = NEG_INF, last_en = en;
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}
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// backtrack
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score = eh[qlen].h;
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if (n_cigar_ && cigar_) {
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int n_cigar = 0, m_cigar = 0, which = 0;
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uint32_t *cigar = 0, tmp;
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i = tlen - 1, k = last_en - 1; // (i,k) points to the last cell; FIXME: with a moving band, we need to take care of last deletion/insertion!!!
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while (i >= 0 && k >= 0) {
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tmp = z[i * n_col + k - off[i]];
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which = tmp >> (which << 1) & 3;
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if (which == 0 && tmp>>6) break;
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if (which == 0) which = tmp & 3;
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if (which == 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --k; // match
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else if (which == 1) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 2, 1), --i; // deletion
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else cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --k; // insertion
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}
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if (i >= 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 2, i + 1); // first deletion
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if (k >= 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 1, k + 1); // first insertion
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for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
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tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
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*n_cigar_ = n_cigar, *cigar_ = cigar;
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}
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kfree(km, qp); kfree(km, eh);
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if (n_cigar_ && cigar_) {
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kfree(km, z);
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kfree(km, off);
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}
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return score;
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}
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#ifdef __SSE2__
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#include <emmintrin.h>
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#ifdef __SSE4_1__
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#include <smmintrin.h>
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#endif
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int ksw_global2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int *n_cigar_, uint32_t **cigar_)
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{
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int r, t, n_col, *off, score, tlen16;
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int8_t *u, *v, *x, *y, *s;
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uint8_t *p, *qr, *mem;
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__m128i q_, qe2_, zero_, flag1_, flag2_, flag4_, flag32_;
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zero_ = _mm_set1_epi8(0);
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q_ = _mm_set1_epi8(q);
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qe2_ = _mm_set1_epi8((q + e) * 2);
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flag1_ = _mm_set1_epi8(1<<0);
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flag2_ = _mm_set1_epi8(2<<0);
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flag4_ = _mm_set1_epi8(1<<2);
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flag32_ = _mm_set1_epi8(2<<4);
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w = (w + 1 + 15) / 16 * 16 - 1;
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tlen16 = (tlen + 15) / 16 * 16;
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n_col = w + 1 < tlen16? w + 1 : tlen16; // number of columns in the backtrack matrix
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n_col += 16, tlen16 += 16; // leave enough space at the end
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mem = (uint8_t*)kcalloc(km, tlen16 * 5 + 15, 1);
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u = (int8_t*)(((size_t)mem + 15) >> 4 << 4); // 16-byte aligned (though not necessary)
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v = u + tlen16, x = v + tlen16, y = x + tlen16, s = y + tlen16;
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qr = (uint8_t*)kcalloc(km, qlen, 1);
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p = (uint8_t*)kcalloc(km, (qlen + tlen) * n_col, 1);
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off = (int*)kmalloc(km, (qlen + tlen) * sizeof(int));
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for (t = 0; t < qlen; ++t)
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qr[t] = query[qlen - 1 - t];
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for (r = 0; r < qlen + tlen - 1; ++r) {
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int st = 0, en = tlen - 1;
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int8_t x1, v1;
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uint8_t *pr = p + r * n_col;
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__m128i x1_, v1_;
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// find the boundaries
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if (st < r - qlen + 1) st = r - qlen + 1;
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if (en > r) en = r;
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if (st < (r-w+1)>>1) st = (r-w+1)>>1; // take the ceil
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if (en > (r+w)>>1) en = (r+w)>>1; // take the floor
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off[r] = st;
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// set boundary conditions
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if (st != 0) {
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if (r > st + st + w - 1) x1 = v1 = 0;
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else x1 = x[st-1], v1 = v[st-1]; // (r-1, st-1) in the band
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} else x1 = 0, v1 = r? q : 0;
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if (en != r) {
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if (r < en + en - w - 1) y[en] = u[en] = 0; // (r-1,en) out of the band; TODO: is this line necessary?
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} else y[r] = 0, u[r] = r? q : 0;
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// loop fission: set scores first
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for (t = st; t <= en; ++t)
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s[t] = mat[target[t] * m + qr[t + qlen - 1 - r]];
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// core loop
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x1_ = _mm_cvtsi32_si128(x1);
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v1_ = _mm_cvtsi32_si128(v1);
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for (t = st; t <= en; t += 16) {
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__m128i d, z, a, b, xt1, vt1, ut, tmp;
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z = _mm_add_epi8(_mm_loadu_si128((__m128i*)&s[t]), qe2_);
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xt1 = _mm_loadu_si128((__m128i*)&x[t]); // xt1 <- x[r-1][t..t+15]
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tmp = _mm_srli_si128(xt1, 15); // tmp <- x[r-1][t+15]
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xt1 = _mm_or_si128(_mm_slli_si128(xt1, 1), x1_); // xt1 <- x[r-1][t-1..t+14]
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x1_ = tmp;
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vt1 = _mm_loadu_si128((__m128i*)&v[t]); // vt1 <- v[r-1][t..t+15]
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tmp = _mm_srli_si128(vt1, 15); // tmp <- v[r-1][t+15]
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vt1 = _mm_or_si128(_mm_slli_si128(vt1, 1), v1_); // vt1 <- v[r-1][t-1..t+14]
|
||||
v1_ = tmp;
|
||||
a = _mm_add_epi8(xt1, vt1); // a <- x[r-1][t-1..t+14] + v[r-1][t-1..t+14]
|
||||
|
||||
ut = _mm_loadu_si128((__m128i*)&u[t]); // ut <- u[t..t+15]
|
||||
b = _mm_add_epi8(_mm_loadu_si128((__m128i*)&y[t]), ut); // b <- y[r-1][t..t+15] + u[r-1][t..t+15]
|
||||
|
||||
d = _mm_and_si128(flag1_, _mm_cmplt_epi8(a, z)); // d = a < z? 1 : 0
|
||||
#ifdef __SSE4_1__
|
||||
z = _mm_max_epi8(z, a); // z = z > a? z : a (signed)
|
||||
tmp = _mm_cmplt_epi8(b, z);
|
||||
d = _mm_blendv_epi8(d, flag2_, tmp); // d = b < z? d : 2
|
||||
#else
|
||||
z = _mm_and_si128(z, _mm_cmpgt_epi8(z, zero_)); // z = z > 0? z : 0;
|
||||
z = _mm_max_epu8(z, a); // z = max(z, a); this works because both are non-negative
|
||||
tmp = _mm_cmplt_epi8(b, z);
|
||||
d = _mm_or_si128(_mm_andnot_si128(tmp, d), _mm_and_si128(tmp, flag2_));
|
||||
#endif
|
||||
z = _mm_max_epu8(z, b); // z = max(z, b); this works because both are non-negative
|
||||
|
||||
_mm_storeu_si128((__m128i*)&u[t], _mm_sub_epi8(z, vt1)); // u[r][t..t+15] <- z - v[r-1][t-1..t+14]
|
||||
_mm_storeu_si128((__m128i*)&v[t], _mm_sub_epi8(z, ut)); // v[r][t..t+15] <- z - u[r-1][t..t+15]
|
||||
|
||||
z = _mm_sub_epi8(z, q_);
|
||||
a = _mm_sub_epi8(a, z);
|
||||
b = _mm_sub_epi8(b, z);
|
||||
tmp = _mm_cmpgt_epi8(a, zero_);
|
||||
d = _mm_or_si128(d, _mm_and_si128(flag4_, tmp));
|
||||
_mm_storeu_si128((__m128i*)&x[t], _mm_and_si128(a, tmp));
|
||||
tmp = _mm_cmpgt_epi8(b, zero_);
|
||||
d = _mm_or_si128(d, _mm_and_si128(flag32_, tmp));
|
||||
_mm_storeu_si128((__m128i*)&y[t], _mm_and_si128(b, tmp));
|
||||
_mm_storeu_si128((__m128i*)&pr[t - st], d);
|
||||
}
|
||||
}
|
||||
kfree(km, mem); kfree(km, qr);
|
||||
{ // backtrack
|
||||
int n_cigar = 0, m_cigar = 0, which = 0, i, j, k, l;
|
||||
uint32_t *cigar = 0, tmp;
|
||||
i = tlen - 1, j = qlen - 1;
|
||||
while (i >= 0 && j >= 0) {
|
||||
r = i + j;
|
||||
tmp = p[r * n_col + i - off[r]];
|
||||
which = tmp >> (which << 1) & 3;
|
||||
if (which == 0 && tmp>>6) break;
|
||||
if (which == 0) which = tmp & 3;
|
||||
if (which == 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match
|
||||
else if (which == 1) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 2, 1), --i; // deletion
|
||||
else cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion
|
||||
}
|
||||
if (i >= 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 2, i + 1); // first deletion
|
||||
if (j >= 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion
|
||||
for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
|
||||
tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
|
||||
*n_cigar_ = n_cigar, *cigar_ = cigar;
|
||||
|
||||
// compute score
|
||||
for (k = 0, score = 0, i = j = 0; k < n_cigar; ++k) {
|
||||
int op = cigar[k] & 0xf, len = cigar[k] >> 4;
|
||||
if (op == 0) {
|
||||
for (l = 0; l < len; ++l)
|
||||
score += mat[target[i + l] * m + query[j + l]];
|
||||
i += len, j += len;
|
||||
} else if (op == 1) {
|
||||
score -= q + len * e;
|
||||
j += len;
|
||||
} else if (op == 2) {
|
||||
score -= q + len * e;
|
||||
i += len;
|
||||
}
|
||||
}
|
||||
}
|
||||
kfree(km, p); kfree(km, off);
|
||||
return score;
|
||||
}
|
||||
#endif // __SSE2__
|
||||
|
||||
int ksw_global2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t q, int8_t e, int w, int *n_cigar_, uint32_t **cigar_)
|
||||
{
|
||||
int qe = q + e, qe2 = qe + qe, r, t, n_col, *off, score;
|
||||
int8_t *u, *v, *x, *y, *s;
|
||||
uint8_t *p, *qr;
|
||||
|
||||
u = (int8_t*)kcalloc(km, tlen + 1, 1);
|
||||
v = (int8_t*)kcalloc(km, tlen + 1, 1);
|
||||
x = (int8_t*)kcalloc(km, tlen + 1, 1);
|
||||
y = (int8_t*)kcalloc(km, tlen + 1, 1);
|
||||
s = (int8_t*)kmalloc(km, tlen);
|
||||
qr = (uint8_t*)kmalloc(km, qlen);
|
||||
n_col = w + 1 < tlen? w + 1 : tlen;
|
||||
p = (uint8_t*)kcalloc(km, (qlen + tlen) * n_col, 1);
|
||||
off = (int*)kmalloc(km, (qlen + tlen) * sizeof(int));
|
||||
|
||||
for (t = 0; t < qlen; ++t)
|
||||
qr[t] = query[qlen - 1 - t];
|
||||
|
||||
for (r = 0; r < qlen + tlen - 1; ++r) {
|
||||
int st = 0, en = tlen - 1;
|
||||
int8_t x1, v1;
|
||||
uint8_t *pr = p + r * n_col;
|
||||
// find the boundaries
|
||||
if (st < r - qlen + 1) st = r - qlen + 1;
|
||||
if (en > r) en = r;
|
||||
if (st < (r-w+1)>>1) st = (r-w+1)>>1; // take the ceil
|
||||
if (en > (r+w)>>1) en = (r+w)>>1; // take the floor
|
||||
off[r] = st;
|
||||
// set boundary conditions
|
||||
if (st != 0) {
|
||||
if (r > st + st + w - 1) x1 = v1 = 0;
|
||||
else x1 = x[st-1], v1 = v[st-1]; // (r-1, st-1) in the band
|
||||
} else x1 = 0, v1 = r? q : 0;
|
||||
if (en != r) {
|
||||
if (r < en + en - w - 1) y[en] = u[en] = 0; // (r-1,en) out of the band; TODO: is this line necessary?
|
||||
} else y[r] = 0, u[r] = r? q : 0;
|
||||
// loop fission: set scores first
|
||||
for (t = st; t <= en; ++t)
|
||||
s[t] = mat[target[t] * m + qr[t + qlen - 1 - r]];
|
||||
// core loop
|
||||
for (t = st; t <= en; ++t) {
|
||||
/* At the beginning of the loop, v1=v(r-1,t-1), x1=x(r-1,t-1), u[t]=u(r-1,t), v[t]=v(r-1,t), x[t]=x(r-1,t), y[t]=y(r-1,t)
|
||||
a = x(r-1,t-1) + v(r-1,t-1)
|
||||
b = y(r-1,t) + u(r-1,t)
|
||||
z = max{ S(t,r-t) + 2q + 2r, a, b }
|
||||
u(r,t) = z - v(r-1,t-1)
|
||||
v(r,t) = z - u(r-1,t)
|
||||
x(r,t) = max{ 0, a - z + q }
|
||||
y(r,t) = max{ 0, b - z + q }
|
||||
*/
|
||||
uint8_t d;
|
||||
int8_t u1;
|
||||
int8_t z = s[t] + qe2;
|
||||
int8_t a = x1 + v1;
|
||||
int8_t b = y[t] + u[t];
|
||||
d = z >= a? 0 : 1;
|
||||
z = z >= a? z : a;
|
||||
d = z >= b? d : 2;
|
||||
z = z >= b? z : b;
|
||||
u1 = u[t]; // u1 = u(r-1,t) (temporary variable)
|
||||
u[t] = z - v1; // u[t] = u(r,t)
|
||||
v1 = v[t]; // v1 = v(r-1,t) (set for the next iteration)
|
||||
v[t] = z - u1; // v[t] = v(r,t)
|
||||
z -= q;
|
||||
a -= z;
|
||||
b -= z;
|
||||
x1 = x[t]; // x1 = x(r-1,t) (set for the next iteration)
|
||||
d |= a > 0? 1<<2 : 0;
|
||||
x[t] = a > 0? a : 0; // x[t] = x(r,t)
|
||||
d |= b > 0? 2<<4 : 0;
|
||||
y[t] = b > 0? b : 0; // y[t] = y(r,t)
|
||||
pr[t - st] = d;
|
||||
}
|
||||
}
|
||||
kfree(km, u); kfree(km, v); kfree(km, x); kfree(km, y); kfree(km, s); kfree(km, qr);
|
||||
{ // backtrack
|
||||
int n_cigar = 0, m_cigar = 0, which = 0, i, j, k, l;
|
||||
uint32_t *cigar = 0, tmp;
|
||||
i = tlen - 1, j = qlen - 1;
|
||||
while (i >= 0 && j >= 0) {
|
||||
r = i + j;
|
||||
tmp = p[r * n_col + i - off[r]];
|
||||
which = tmp >> (which << 1) & 3;
|
||||
if (which == 0 && tmp>>6) break;
|
||||
if (which == 0) which = tmp & 3;
|
||||
if (which == 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 0, 1), --i, --j; // match
|
||||
else if (which == 1) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 2, 1), --i; // deletion
|
||||
else cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 1, 1), --j; // insertion
|
||||
}
|
||||
if (i >= 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 2, i + 1); // first deletion
|
||||
if (j >= 0) cigar = push_cigar(km, &n_cigar, &m_cigar, cigar, 1, j + 1); // first insertion
|
||||
for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR
|
||||
tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
|
||||
*n_cigar_ = n_cigar, *cigar_ = cigar;
|
||||
|
||||
// compute score
|
||||
for (k = 0, score = 0, i = j = 0; k < n_cigar; ++k) {
|
||||
int op = cigar[k] & 0xf, len = cigar[k] >> 4;
|
||||
if (op == 0) {
|
||||
for (l = 0; l < len; ++l)
|
||||
score += mat[target[i + l] * m + query[j + l]];
|
||||
i += len, j += len;
|
||||
} else if (op == 1) {
|
||||
score -= q + len * e;
|
||||
j += len;
|
||||
} else if (op == 2) {
|
||||
score -= q + len * e;
|
||||
i += len;
|
||||
}
|
||||
}
|
||||
}
|
||||
kfree(km, p); kfree(km, off);
|
||||
return score;
|
||||
}
|
||||
38
ksw2.h
38
ksw2.h
|
|
@ -1,38 +0,0 @@
|
|||
#ifndef KSW2_H_
|
||||
#define KSW2_H_
|
||||
|
||||
#include <stdint.h>
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
/**
|
||||
* Global alignment with moving a band
|
||||
*
|
||||
* @param km memory pool, when used with kalloc
|
||||
* @param qlen query length
|
||||
* @param query query sequence with 0 <= query[i] < m
|
||||
* @param tlen target length
|
||||
* @param target target sequence with 0 <= target[i] < m
|
||||
* @param m number of residue types
|
||||
* @param mat m*m scoring mattrix in one-dimension array
|
||||
* @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
|
||||
* @param gape gap extension penalty
|
||||
* @param w band width
|
||||
* @param n_cigar (out) number of CIGAR elements
|
||||
* @param cigar (out) BAM-encoded CIGAR; caller need to deallocate with kfree(km, )
|
||||
*
|
||||
* @return score of the alignment
|
||||
*/
|
||||
int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);
|
||||
int ksw_global2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);
|
||||
int ksw_global2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat, int8_t gapo, int8_t gape, int w, int *n_cigar_, uint32_t **cigar_);
|
||||
|
||||
void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b);
|
||||
|
||||
#ifdef __cplusplus
|
||||
}
|
||||
#endif
|
||||
|
||||
#endif
|
||||
Loading…
Reference in New Issue