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r428: allow to change the default chain_drop_ratio

This commit is contained in:
Heng Li 2013-12-30 16:18:45 -05:00
parent 3afcdc7746
commit 10cb6b0507
3 changed files with 27 additions and 19 deletions
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40
bwamem.c
View File

@ -232,12 +232,32 @@ static void mem_insert_seed(const mem_opt_t *opt, int64_t l_pac, kbtree_t(chn) *
}
}
int mem_chain_weight(const mem_chain_t *c)
{
int64_t end;
int j, w = 0, tmp;
for (j = 0, end = 0; j < c->n; ++j) {
const mem_seed_t *s = &c->seeds[j];
if (s->qbeg >= end) w += s->len;
else if (s->qbeg + s->len > end) w += s->qbeg + s->len - end;
end = end > s->qbeg + s->len? end : s->qbeg + s->len;
}
tmp = w;
for (j = 0, end = 0; j < c->n; ++j) {
const mem_seed_t *s = &c->seeds[j];
if (s->rbeg >= end) w += s->len;
else if (s->rbeg + s->len > end) w += s->rbeg + s->len - end;
end = end > s->qbeg + s->len? end : s->qbeg + s->len;
}
return w < tmp? w : tmp;
}
void mem_print_chain(const bntseq_t *bns, mem_chain_v *chn)
{
int i, j;
for (i = 0; i < chn->n; ++i) {
mem_chain_t *p = &chn->a[i];
err_printf("CHAIN(%d) n=%d", i, p->n);
err_printf("CHAIN(%d) n=%d w=%d", i, p->n, mem_chain_weight(p));
for (j = 0; j < p->n; ++j) {
bwtint_t pos;
int is_rev, ref_id;
@ -294,22 +314,8 @@ int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain_t *chains)
a = malloc(sizeof(flt_aux_t) * n_chn);
for (i = 0; i < n_chn; ++i) {
mem_chain_t *c = &chains[i];
int64_t end;
int w = 0, tmp;
for (j = 0, end = 0; j < c->n; ++j) {
const mem_seed_t *s = &c->seeds[j];
if (s->qbeg >= end) w += s->len;
else if (s->qbeg + s->len > end) w += s->qbeg + s->len - end;
end = end > s->qbeg + s->len? end : s->qbeg + s->len;
}
tmp = w;
for (j = 0, end = 0; j < c->n; ++j) {
const mem_seed_t *s = &c->seeds[j];
if (s->rbeg >= end) w += s->len;
else if (s->rbeg + s->len > end) w += s->rbeg + s->len - end;
end = end > s->qbeg + s->len? end : s->qbeg + s->len;
}
w = w < tmp? w : tmp;
int w;
w = mem_chain_weight(c);
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;

4
fastmap.c
View File

@ -30,7 +30,7 @@ int main_mem(int argc, char *argv[])
int64_t n_processed = 0;
opt = mem_opt_init();
while ((c = getopt(argc, argv, "paMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:")) >= 0) {
while ((c = getopt(argc, argv, "paMCSPHk:c:v:s:r:t:R:A:B:O:E:U:w:L:d:T:Q:D:")) >= 0) {
if (c == 'k') opt->min_seed_len = atoi(optarg);
else if (c == 'w') opt->w = atoi(optarg);
else if (c == 'A') opt->a = atoi(optarg);
@ -49,6 +49,7 @@ int main_mem(int argc, char *argv[])
else if (c == 'd') opt->zdrop = atoi(optarg);
else if (c == 'v') bwa_verbose = atoi(optarg);
else if (c == 'r') opt->split_factor = atof(optarg);
else if (c == 'D') opt->chain_drop_ratio = atof(optarg);
else if (c == 'C') copy_comment = 1;
else if (c == 'Q') {
opt->mapQ_coef_len = atoi(optarg);
@ -75,6 +76,7 @@ int main_mem(int argc, char *argv[])
fprintf(stderr, " -r FLOAT look for internal seeds inside a seed longer than {-k} * FLOAT [%g]\n", opt->split_factor);
// fprintf(stderr, " -s INT look for internal seeds inside a seed with less than INT occ [%d]\n", opt->split_width);
fprintf(stderr, " -c INT skip seeds with more than INT occurrences [%d]\n", opt->max_occ);
fprintf(stderr, " -D FLOAT drop chains shorter than FLOAT fraction of the longest overlapping chain [%.2f]\n", opt->chain_drop_ratio);
fprintf(stderr, " -S skip mate rescue\n");
fprintf(stderr, " -P skip pairing; mate rescue performed unless -S also in use\n");
fprintf(stderr, " -A INT score for a sequence match [%d]\n", opt->a);

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.5a-r427"
#define PACKAGE_VERSION "0.7.5a-r428"
#endif
int bwa_fa2pac(int argc, char *argv[]);