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discard internal seeds shorter than half

This commit is contained in:
Heng Li 2013-02-07 19:50:37 -05:00
parent 83a49f3210
commit cd6bd524d4
2 changed files with 17 additions and 8 deletions
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20
bwamem.c
View File

@ -14,6 +14,8 @@
#define MAPQ_COEF 40. #define MAPQ_COEF 40.
int mem_debug = 0;
void mem_fill_scmat(int a, int b, int8_t mat[25]) void mem_fill_scmat(int a, int b, int8_t mat[25])
{ {
int i, j, k; int i, j, k;
@ -30,8 +32,8 @@ mem_opt_t *mem_opt_init()
mem_opt_t *o; mem_opt_t *o;
o = calloc(1, sizeof(mem_opt_t)); o = calloc(1, sizeof(mem_opt_t));
o->a = 1; o->b = 5; o->q = 8; o->r = 1; o->w = 100; o->a = 1; o->b = 5; o->q = 8; o->r = 1; o->w = 100;
o->min_seed_len = 17; o->min_seed_len = 19;
o->max_occ = 10; o->max_occ = 50;
o->max_chain_gap = 10000; o->max_chain_gap = 10000;
o->mask_level = 0.50; o->mask_level = 0.50;
o->chain_drop_ratio = 0.50; o->chain_drop_ratio = 0.50;
@ -84,6 +86,7 @@ void smem_set_query(smem_i *itr, int len, const uint8_t *query)
itr->len = len; itr->len = len;
} }
const bwtintv_v *smem_next(smem_i *itr, int split_len) const bwtintv_v *smem_next(smem_i *itr, int split_len)
{ {
int i, max, max_i; int i, max, max_i;
@ -110,13 +113,15 @@ const bwtintv_v *smem_next(smem_i *itr, int split_len)
if (xi < xj) { if (xi < xj) {
kv_push(bwtintv_t, *a, itr->matches->a[i]); kv_push(bwtintv_t, *a, itr->matches->a[i]);
++i; ++i;
} else { } else if ((uint32_t)itr->sub->a[j].info - (itr->sub->a[j].info>>32) >= max>>1) {
kv_push(bwtintv_t, *a, itr->sub->a[j]); kv_push(bwtintv_t, *a, itr->sub->a[j]);
++j; ++j;
} } else ++j;
} }
for (; i < itr->matches->n; ++i) kv_push(bwtintv_t, *a, itr->matches->a[i]); for (; i < itr->matches->n; ++i) kv_push(bwtintv_t, *a, itr->matches->a[i]);
for (; j < itr->sub->n; ++j) kv_push(bwtintv_t, *a, itr->sub->a[j]); for (; j < itr->sub->n; ++j)
if ((uint32_t)itr->sub->a[j].info - (itr->sub->a[j].info>>32) >= max>>1)
kv_push(bwtintv_t, *a, itr->sub->a[j]);
kv_copy(bwtintv_t, *itr->matches, *a); kv_copy(bwtintv_t, *itr->matches, *a);
} }
return itr->matches; return itr->matches;
@ -407,7 +412,8 @@ void mem_chain2aln(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, int
if (s->qbeg + s->len > a->qe) a->is_all = 0; if (s->qbeg + s->len > a->qe) a->is_all = 0;
} }
*/ */
//printf("[%d] score=%d\t[%d,%d) <=> [%lld,%lld)\n", c->n, a->score, a->qb, a->qe, a->rb, a->re); if (mem_debug >= 2)
printf("[%d] score=%d\t[%d,%d) <=> [%lld,%lld)\n", c->n, a->score, a->qb, a->qe, a->rb, a->re);
free(rseq); free(rseq);
} }
@ -507,7 +513,7 @@ static mem_alnreg_v find_alnreg(const mem_opt_t *opt, const bwt_t *bwt, const bn
s->seq[i] = nst_nt4_table[(int)s->seq[i]]; s->seq[i] = nst_nt4_table[(int)s->seq[i]];
chn = mem_chain(opt, bwt, s->l_seq, (uint8_t*)s->seq); chn = mem_chain(opt, bwt, s->l_seq, (uint8_t*)s->seq);
chn.n = mem_chain_flt(opt, chn.n, chn.a); chn.n = mem_chain_flt(opt, chn.n, chn.a);
// mem_print_chain(bns, &chn); if (mem_debug >= 1) mem_print_chain(bns, &chn);
regs.n = regs.m = chn.n; regs.n = regs.m = chn.n;
regs.a = malloc(regs.n * sizeof(mem_alnreg_t)); regs.a = malloc(regs.n * sizeof(mem_alnreg_t));
for (i = 0; i < chn.n; ++i) { for (i = 0; i < chn.n; ++i) {

5
fastmap.c
View File

@ -11,6 +11,7 @@
KSEQ_DECLARE(gzFile) KSEQ_DECLARE(gzFile)
extern unsigned char nst_nt4_table[256]; extern unsigned char nst_nt4_table[256];
extern int mem_debug;
int main_mem(int argc, char *argv[]) int main_mem(int argc, char *argv[])
{ {
@ -24,8 +25,10 @@ int main_mem(int argc, char *argv[])
bseq1_t *seqs; bseq1_t *seqs;
opt = mem_opt_init(); opt = mem_opt_init();
while ((c = getopt(argc, argv, "k:")) >= 0) { while ((c = getopt(argc, argv, "k:c:D:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg); if (c == 'k') opt->min_seed_len = atoi(optarg);
else if (c == 'c') opt->max_occ = atoi(optarg);
else if (c == 'D') mem_debug = atoi(optarg);
} }
if (optind + 1 >= argc) { if (optind + 1 >= argc) {
fprintf(stderr, "\n"); fprintf(stderr, "\n");