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explicitly use bit to keep bt matrix 

This also simplifies backtracking.
This commit is contained in:
Heng Li 2013-02-05 16:28:15 -05:00
parent 7e1466c885
commit 1bc9712cd8
1 changed files with 19 additions and 32 deletions
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51
ksw.c
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@ -403,10 +403,6 @@ int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
#define MINUS_INF -0x40000000 #define MINUS_INF -0x40000000
typedef struct {
uint8_t h:2, e:1, f:1;
} btmat_t;
static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len) static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len)
{ {
if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) { if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {
@ -419,17 +415,15 @@ static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar,
return cigar; return cigar;
} }
#define cal_j_(i_, k_, w_) ((k_) - ((i_) > (w_)? (i_) - (w_) : 0))
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_) 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_)
{ {
eh_t *eh; eh_t *eh;
int8_t *qp; int8_t *qp;
int i, j, k, gapoe = gapo + gape, score, n_col; int i, j, k, gapoe = gapo + gape, score, n_col;
btmat_t *z; uint8_t *z;
// allocate memory // allocate memory
n_col = qlen < w? qlen : w; n_col = qlen < 2*w+1? qlen : 2*w+1;
z = malloc(n_col * tlen * sizeof(btmat_t)); z = malloc(n_col * tlen);
qp = malloc(qlen * m); qp = malloc(qlen * m);
eh = calloc(qlen + 1, 8); eh = calloc(qlen + 1, 8);
// generate the query profile // generate the query profile
@ -446,58 +440,51 @@ int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
for (i = 0; LIKELY(i < tlen); ++i) { for (i = 0; LIKELY(i < tlen); ++i) {
int32_t f = MINUS_INF, h1, beg, end; int32_t f = MINUS_INF, h1, beg, end;
int8_t *q = &qp[target[i] * qlen]; int8_t *q = &qp[target[i] * qlen];
btmat_t *zi = &z[i * n_col]; uint8_t *zi = &z[i * n_col];
beg = i > w? i - w : 0; beg = i > w? i - w : 0;
end = i + w + 1 < qlen? i + w + 1 : qlen; end = i + w + 1 < qlen? i + w + 1 : qlen;
h1 = beg == 0? -(gapo + gape * (i + 1)) : MINUS_INF; h1 = beg == 0? -(gapo + gape * (i + 1)) : MINUS_INF;
printf("%d", i); printf("%d", i);
for (j = beg; LIKELY(j < end); ++j) { for (j = beg; LIKELY(j < end); ++j) {
eh_t *p = &eh[j]; eh_t *p = &eh[j];
btmat_t *zij = &zi[j - beg];
int32_t h = p->h, e = p->e; int32_t h = p->h, e = p->e;
uint8_t d; // direction
p->h = h1; p->h = h1;
h += q[j]; h += q[j];
zij->h = h > e? 0 : 1; d = h > e? 0 : 1;
h = h > e? h : e; h = h > e? h : e;
zij->h = h > f? zij->h : 2; d = h > f? d : 2;
h = h > f? h : f; h = h > f? h : f;
printf("\t%d:%d:%d", h<-99?-99:h, e<-99?-99:e, f<-99?-99:f); printf("\t[%d],%d:%d:%d", j, h<-99?-99:h, e<-99?-99:e, f<-99?-99:f);
h1 = h; h1 = h;
h -= gapoe; h -= gapoe;
e -= gape; e -= gape;
zij->e = (e > h); // NB: zij->e keeps the direction for the NEXT row, not the current one d |= e > h? 1<<2 : 0;
e = e > h? e : h; e = e > h? e : h;
p->e = e; p->e = e;
f -= gape; f -= gape;
zij->f = (f > h); d |= f > h? 2<<4 : 0;
f = f > h? f : h; f = f > h? f : h;
printf(",%d:%d:%d", zij->h, zij->e, zij->f); zi[j - beg] = d;
printf(",%d:%d:%d", d>>0&3, d>>2&3, d>>4&3);
} }
putchar('\n'); putchar('\n');
eh[end].h = h1; eh[end].e = MINUS_INF; eh[end].h = h1; eh[end].e = MINUS_INF;
} }
score = eh[qlen].h; score = eh[qlen].h;
if (n_cigar_ && cigar_) { // backtrack if (n_cigar_ && cigar_) { // backtrack
int n_cigar = 0, m_cigar = 0, which; int n_cigar = 0, m_cigar = 0, which = 0;
uint32_t *cigar = 0, tmp; uint32_t *cigar = 0, tmp;
i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell
which = z[i * n_col + cal_j_(i, k, w)].h;
while (i >= 0 && k >= 0) { while (i >= 0 && k >= 0) {
which = z[i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;
printf("(%d,%d)\t%d\n", i, k, which); printf("(%d,%d)\t%d\n", i, k, which);
if (which == 0) { if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;
cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1); --i, --k; else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;
if (i >= 0 && k >= 0) which = z[i * n_col + cal_j_(i, k, w)].h; else cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;
} else if (which == 1) {
cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1); --i;
if (i >= 0) which = z[i * n_col + cal_j_(i, k, w)].e? 1 : 0;
} else { // which == 2
cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1); --k;
if (k >= 0) which = z[i * n_col + cal_j_(i, k, w)].f? 2 : 0;
} }
} if (i >= 0) push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);
printf("(%d,%d)\t%d\n", i, k, which); if (k >= 0) push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);
if (i > 0) push_cigar(&n_cigar, &m_cigar, cigar, 2, i);
if (k > 0) push_cigar(&n_cigar, &m_cigar, cigar, 1, k);
for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR 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; tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;
*n_cigar_ = n_cigar, *cigar_ = cigar; *n_cigar_ = n_cigar, *cigar_ = cigar;