updated ksw
This commit is contained in:
Heng Li
parent
372698bb23
commit
d3f17b1e05
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#include <stdint.h>
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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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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, int m, const int8_t *mat, int gapo, int 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 - gapoe; // -gapoe*2: one deletion followed by one insertion
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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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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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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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h1 = st > 0? NEG_INF : -gapoe - gape * (i + 1);
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f = st > 0? NEG_INF : -gapoe - gapoe - gape * i; // similarly, -gapoe*2: one del followed by one ins
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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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@ -0,0 +1,32 @@
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#ifndef KSW2_H_
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#define KSW2_H_
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#ifdef __cplusplus
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extern "C" {
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#endif
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/**
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* Global alignment with moving a band
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*
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* @param km memory pool, when used with kalloc
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* @param qlen query length
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* @param query query sequence with 0 <= query[i] < m
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* @param tlen target length
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* @param target target sequence with 0 <= target[i] < m
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* @param m number of residue types
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* @param mat m*m scoring mattrix in one-dimension array
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* @param gapo gap open penalty; a gap of length l cost "-(gapo+l*gape)"
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* @param gape gap extension penalty
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* @param w band width
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* @param n_cigar (out) number of CIGAR elements
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* @param cigar (out) BAM-encoded CIGAR; caller need to deallocate with kfree(km, )
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*
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* @return score of the alignment
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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, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar_, uint32_t **cigar_);
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#ifdef __cplusplus
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}
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#endif
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#endif
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