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a bit code cleanup

This commit is contained in:
Heng Li 2013-02-06 13:59:32 -05:00
parent e65b2096f7
commit a9292d674d
3 changed files with 30 additions and 34 deletions
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51
bwamem.c
View File

@ -211,34 +211,32 @@ typedef struct {
#define flt_lt(a, b) ((a).w > (b).w)
KSORT_INIT(mem_flt, flt_aux_t, flt_lt)
void mem_chain_flt(const mem_opt_t *opt, mem_chain_t *chn)
int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain1_t *chains)
{
flt_aux_t *a;
int i, j, n;
if (chn->n <= 1) return; // no need to filter
a = malloc(sizeof(flt_aux_t) * chn->n);
for (i = 0; i < chn->n; ++i) {
mem_chain1_t *c = &chn->chains[i];
if (n_chn <= 1) return n_chn; // no need to filter
a = malloc(sizeof(flt_aux_t) * n_chn);
for (i = 0; i < n_chn; ++i) {
mem_chain1_t *c = &chains[i];
int w = 0;
for (j = 0; j < c->n; ++j) w += c->seeds[j].len; // FIXME: take care of seed overlaps
a[i].beg = c->seeds[0].qbeg;
a[i].end = c->seeds[c->n-1].qbeg + c->seeds[c->n-1].len;
a[i].w = w;
a[i].p = c;
a[i].p2 = 0;
a[i].w = w; a[i].p = c; a[i].p2 = 0;
}
ks_introsort(mem_flt, chn->n, a);
ks_introsort(mem_flt, n_chn, a);
{ // reorder chains such that the best chain appears first
mem_chain1_t *swap;
swap = malloc(sizeof(mem_chain1_t) * chn->n);
for (i = 0; i < chn->n; ++i) {
swap = malloc(sizeof(mem_chain1_t) * n_chn);
for (i = 0; i < n_chn; ++i) {
swap[i] = *((mem_chain1_t*)a[i].p);
a[i].p = &chn->chains[i]; // as we will memcpy() below, a[i].p is changed
a[i].p = &chains[i]; // as we will memcpy() below, a[i].p is changed
}
memcpy(chn->chains, swap, sizeof(mem_chain1_t) * chn->n);
memcpy(chains, swap, sizeof(mem_chain1_t) * n_chn);
free(swap);
}
for (i = 1, n = 1; i < chn->n; ++i) {
for (i = 1, n = 1; i < n_chn; ++i) {
for (j = 0; j < n; ++j) {
int b_max = a[j].beg > a[i].beg? a[j].beg : a[i].beg;
int e_min = a[j].end < a[i].end? a[j].end : a[i].end;
@ -260,20 +258,20 @@ void mem_chain_flt(const mem_opt_t *opt, mem_chain_t *chn)
if (c && c->n > 0) c->n = -c->n;
}
free(a);
for (i = 0; i < chn->n; ++i) { // free discarded chains
mem_chain1_t *c = &chn->chains[i];
for (i = 0; i < n_chn; ++i) { // free discarded chains
mem_chain1_t *c = &chains[i];
if (c->n >= 0) {
free(c->seeds);
c->n = c->m = 0;
} else c->n = -c->n;
}
for (i = n = 0; i < chn->n; ++i) { // squeeze out discarded chains
if (chn->chains[i].n > 0) {
if (n != i) chn->chains[n++] = chn->chains[i];
for (i = n = 0; i < n_chn; ++i) { // squeeze out discarded chains
if (chains[i].n > 0) {
if (n != i) chains[n++] = chains[i];
else ++n;
}
}
chn->n = n;
return n;
}
/****************************************
@ -286,14 +284,14 @@ static inline int cal_max_gap(const mem_opt_t *opt, int qlen)
return l > 1? l : 1;
}
void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c, mem_aln_t *a)
void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c, mem_alnreg_t *a)
{ // FIXME: in general, we SHOULD check funny seed patterns such as contained seeds. When that happens, we should use a SW or extend more seeds
int i, j, qbeg;
int64_t rlen, rbeg, rmax[2], tmp;
const mem_seed_t *s;
uint8_t *rseq = 0;
memset(a, 0, sizeof(mem_aln_t));
memset(a, 0, sizeof(mem_alnreg_t));
// get the start and end of the seeded region
rbeg = c->seeds[0].rbeg; qbeg = c->seeds[0].qbeg;
// get the max possible span
@ -347,17 +345,14 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
a->qe = qe + qle; a->re = rmax[0] + re + tle;
free(qw);
} else a->qe = l_query, a->re = s->rbeg + s->len;
/*
a->is_all = 1;
if (c->n > 1) { // check if all the seeds have been included
s = &c->seeds[c->n - 1];
if (s->qbeg + s->len > a->qe) a->is_all = 0;
}
//printf("[Q] "); for (i = a->qb; i < a->qe; ++i) putchar("ACGTN"[(int)query[i]]); putchar('\n');
//printf("[R] "); for (i = a->rb; i < a->re; ++i) putchar("ACGTN"[(int)rseq[i - rmax[0]]]); putchar('\n');
printf("[%d] score=%d\t[%d,%d) <=> [%lld,%lld)\tis_all=%d\t", c->n, a->score, a->qb, a->qe, a->rb, a->re, a->is_all);
putchar('\n');
*/
printf("[%d] score=%d\t[%d,%d) <=> [%lld,%lld)\n", c->n, a->score, a->qb, a->qe, a->rb, a->re);
free(rseq);
}

9
bwamem.h
View File

@ -31,8 +31,8 @@ typedef struct {
typedef struct {
int64_t rb, re;
int score, qb, qe, is_all;
} mem_aln_t;
int score, qb, qe;
} mem_alnreg_t;
#ifdef __cplusplus
extern "C" {
@ -47,8 +47,9 @@ mem_opt_t *mem_opt_init(void);
void mem_fill_scmat(int a, int b, int8_t mat[25]);
mem_chain_t mem_chain(const mem_opt_t *opt, const bwt_t *bwt, int len, const uint8_t *seq);
void mem_chain_flt(const mem_opt_t *opt, mem_chain_t *chn);
void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c, mem_aln_t *a);
int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain1_t *chains);
void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, const uint8_t *query, const mem_chain1_t *c, mem_alnreg_t *a);
uint32_t *mem_gen_cigar(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar);
#ifdef __cplusplus
}

4
fastmap.c
View File

@ -51,10 +51,10 @@ int main_mem(int argc, char *argv[])
for (i = 0; i < seq->seq.l; ++i)
seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
chain = mem_chain(opt, bwt, seq->seq.l, (uint8_t*)seq->seq.s);
mem_chain_flt(opt, &chain);
chain.n = mem_chain_flt(opt, chain.n, chain.chains);
for (i = 0; i < chain.n; ++i) {
mem_chain1_t *p = &chain.chains[i];
mem_aln_t a;
mem_alnreg_t a;
mem_chain2aln(opt, bns->l_pac, pac, seq->seq.l, (uint8_t*)seq->seq.s, p, &a);
printf("%d\t%d", i, p->n);
for (j = 0; j < p->n; ++j) {