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https://github.com/attractivechaos/klib
synced 2025-02-20 00:13:58 +03:00
added NW and SW-extension; backported from bwa
This commit is contained in:
Heng Li
parent
04fc53768f
commit
d4c28fd9c6
179
ksw.c
179
ksw.c
@ -351,6 +351,185 @@ kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, con
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return r;
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}
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/********************
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*** SW extension ***
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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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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 h0, int *_qle, int *_tle)
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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, beg, end, max, max_i, max_j, max_gap;
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if (h0 < 0) h0 = 0;
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// allocate memory
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qp = malloc(qlen * m);
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eh = calloc(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[1].h = h0 > gapoe? h0 - gapoe : 0;
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for (j = 2; j <= qlen && eh[j-1].h > gape; ++j)
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eh[j].h = eh[j-1].h - gape;
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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 * max - 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;
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beg = 0, end = qlen;
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for (i = 0; LIKELY(i < tlen); ++i) {
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int f = 0, h1, m = 0, mj = -1;
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int8_t *q = &qp[target[i] * qlen];
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// compute the first column
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h1 = h0 - (gapo + gape * (i + 1));
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if (h1 < 0) h1 = 0;
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// apply the band and the constraint (if provided)
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if (beg < i - w) beg = i - w;
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if (end > i + w + 1) end = i + w + 1;
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if (end > qlen) end = qlen;
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for (j = beg; LIKELY(j < end); ++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;
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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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mj = m > h? mj : j;
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m = m > h? m : h; // m 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[end].h = h1; eh[end].e = 0;
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if (m == 0) break;
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if (m > max) max = m, max_i = i, max_j = mj;
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// update beg and end for the next round
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for (j = mj; j >= beg && eh[j].h; --j);
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beg = j + 1;
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for (j = mj + 2; j <= end && eh[j].h; ++j);
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end = j;
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//beg = 0; end = qlen; // uncomment this line for debugging
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}
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free(eh); free(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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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 MINUS_INF -0x40000000
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static inline uint32_t *push_cigar(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 = realloc(cigar, (*m_cigar) << 4);
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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(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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int i, j, k, gapoe = gapo + gape, score, n_col;
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uint8_t *z; // backtrack matrix; in each cell: f<<4|e<<2|h; in principle, we can halve the memory, but backtrack will be a little more complex
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if (n_cigar_) *n_cigar_ = 0;
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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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z = malloc(n_col * tlen);
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qp = malloc(qlen * m);
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eh = calloc(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 = 0; eh[0].e = MINUS_INF;
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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 = MINUS_INF;
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for (; j <= qlen; ++j) eh[j].h = eh[j].e = MINUS_INF; // everything is -inf outside the band
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// DP loop
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for (i = 0; LIKELY(i < tlen); ++i) { // target sequence is in the outer loop
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int32_t f = MINUS_INF, h1, beg, end;
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int8_t *q = &qp[target[i] * qlen];
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uint8_t *zi = &z[i * n_col];
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beg = i > w? i - w : 0;
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end = i + w + 1 < qlen? i + w + 1 : qlen; // only loop through [beg,end) of the query sequence
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h1 = beg == 0? -(gapo + gape * (i + 1)) : MINUS_INF;
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for (j = beg; LIKELY(j < end); ++j) {
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// This loop is organized in a similar way to ksw_extend() and ksw_sse2(), except:
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// 1) not checking h>0; 2) recording direction for backtracking
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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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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 - beg] = 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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eh[end].h = h1; eh[end].e = MINUS_INF;
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}
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score = eh[qlen].h;
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if (n_cigar_ && cigar_) { // backtrack
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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 = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
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while (i >= 0 && k >= 0) {
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which = z[i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
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if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;
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else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;
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else cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;
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}
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if (i >= 0) push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
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if (k >= 0) push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);
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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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free(eh); free(qp); free(z);
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return score;
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}
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/*******************************************
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* Main function (not compiled by default) *
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*******************************************/
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3
ksw.h
3
ksw.h
@ -62,6 +62,9 @@ extern "C" {
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*/
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kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);
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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 h0, int *_qle, int *_tle);
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int ksw_global(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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