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explain DP

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This commit is contained in:
Heng Li
2017-06-15 19:37:48 -04:00
parent 78fe89d1ab
commit c4564c31a2
2 changed files with 253 additions and 0 deletions
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ksw2.c
+87
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@@ -275,3 +275,90 @@ int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t
}
return score;
}
#include <stdio.h>
int ksw_global2(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int 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;
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, 1);
qr = (uint8_t*)kmalloc(km, qlen, 1);
n_col = 2 * w < tlen + 1? 2 * w : tlen + 1;
p = (uint8_t*)kmalloc(km, (qlen + tlen) * n_col);
for (t = 0; t < qlen; ++t)
qr[t] = query[qlen - 1 - t];
for (r = 0; r <= qlen + tlen; ++r) {
int st = 0, en = tlen;
int8_t x1 = 0, v1 = 0;
uint8_t *pr = p + r * n_col;
if (st < r - qlen) st = r - qlen;
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;
for (t = st; t <= en; ++t)
s[t] = mat[target[t] * m + qr[t + qlen - 1 - r]];
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;
}
}
if (n_cigar_ && cigar_) {
int n_cigar = 0, m_cigar = 0, which = 0, i, j;
uint32_t *cigar = 0, tmp;
i = tlen - 1, j = qlen - 1; // (i,k) points to the last cell;
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;
}
kfree(km, u); kfree(km, v); kfree(km, x); kfree(km, y); kfree(km, s); kfree(km, qr); kfree(km, p);
return 0;
}