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fixed bug when retaining 2ndary aln; still buggy

This commit is contained in:
Heng Li 2017-07-02 19:08:30 -04:00
parent da90b614db
commit 74d306a596
5 changed files with 31 additions and 15 deletions
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25
hit.c
View File

@ -134,13 +134,13 @@ void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs) // keep mm_reg1_t::{id,
kfree(km, tmp);
}
void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1_t *r)
void mm_select_sub(void *km, float mask_level, float pri_ratio, int best_n, int *n_, mm_reg1_t *r)
{
if (pri_ratio > 0.0f && *n_ > 0) {
int i, k, n = *n_;
int i, k, n = *n_, n_2nd = 0;
for (i = k = 0; i < n; ++i)
if (r[i].parent == i || r[i].score >= r[r[i].parent].score * pri_ratio)
r[k++] = r[i];
if (r[i].parent == i) r[k++] = r[i];
else if (r[i].score >= r[r[i].parent].score * pri_ratio && n_2nd++ < best_n) r[k++] = r[i];
else if (r[i].p) free(r[i].p);
if (k != n) mm_sync_regs(km, k, r); // removing hits requires sync()
*n_ = k;
@ -192,9 +192,9 @@ int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a)
return as;
}
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg1_t *regs, mm128_t *a)
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs_, mm_reg1_t *regs, mm128_t *a)
{
int i, n_aux;
int i, n_aux, n_regs = *n_regs_, n_drop = 0;
uint64_t *aux;
if (n_regs < 2) return; // nothing to join
@ -228,8 +228,21 @@ void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg
r0->cnt += r1->cnt, r0->score += r1->score;
mm_reg_set_coor(r0, qlen, a);
r1->cnt = 0;
r1->parent = r0->id;
++n_drop;
}
kfree(km, aux);
if (n_drop > 0) { // then fix the hits hierarchy
for (i = 0; i < n_regs; ++i) { // adjust the mm_reg1_t::parent
mm_reg1_t *r = &regs[i];
if (r->parent >= 0 && r->id != r->parent) { // fix for secondary hits only
if (regs[r->parent].parent >= 0 && regs[r->parent].parent != r->parent)
r->parent = regs[r->parent].parent;
}
}
mm_filter_regs(km, opt, n_regs_, regs);
}
}
void mm_set_mapq(int n_regs, mm_reg1_t *regs)

5
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r141-pre"
#define MM_VERSION "2.0-r142-pre"
void liftrlimit()
{
@ -68,7 +68,7 @@ int main(int argc, char *argv[])
mm_realtime0 = realtime();
mm_mapopt_init(&opt);
while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:", long_options, &long_idx)) >= 0) {
while ((c = getopt_long(argc, argv, "aw:k:t:r:f:Vv:g:I:d:ST:s:x:Hcp:M:n:z:A:B:O:E:m:D:N:", long_options, &long_idx)) >= 0) {
if (c == 'w') w = atoi(optarg);
else if (c == 'k') k = atoi(optarg);
else if (c == 'H') is_hpc = 1;
@ -78,6 +78,7 @@ int main(int argc, char *argv[])
else if (c == 't') n_threads = atoi(optarg);
else if (c == 'v') mm_verbose = atoi(optarg);
else if (c == 'g') opt.max_gap = atoi(optarg);
else if (c == 'N') opt.best_n = atoi(optarg);
else if (c == 'p') opt.pri_ratio = atof(optarg);
else if (c == 'D') opt.min_seedcov_ratio = atof(optarg);
else if (c == 'M') opt.mask_level = atof(optarg);

9
map.c
View File

@ -22,8 +22,9 @@ void mm_mapopt_init(mm_mapopt_t *opt)
opt->max_chain_skip = 15;
opt->min_seedcov_ratio = 0.0f;
opt->pri_ratio = 2.0f;
opt->mask_level = 0.5f;
opt->pri_ratio = 2.0f;
opt->best_n = 5;
opt->max_join_long = 20000;
opt->max_join_short = 2000;
@ -240,14 +241,14 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
*n_regs = n_u;
if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
mm_set_parent(b->km, opt->mask_level, *n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, n_regs, regs);
mm_join_long(b->km, opt, qlen, *n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, opt->best_n, n_regs, regs);
mm_join_long(b->km, opt, qlen, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
}
if (opt->flag & MM_F_CIGAR) {
regs = mm_align_skeleton(b->km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
if (!(opt->flag & MM_F_AVA)) {
mm_update_parent(b->km, opt->mask_level, *n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, n_regs, regs);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, opt->best_n, n_regs, regs);
}
} else mm_filter_regs(b->km, opt, n_regs, regs);
mm_set_mapq(*n_regs, regs);

3
minimap.h
View File

@ -77,8 +77,9 @@ typedef struct {
int min_chain_score;
float min_seedcov_ratio;
float pri_ratio;
float mask_level;
float pri_ratio;
int best_n;
int max_join_long, max_join_short;
int min_join_flank_sc;

4
mmpriv.h
View File

@ -41,9 +41,9 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a);
void mm_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r);
void mm_update_parent(void *km, float mask_level, int n, mm_reg1_t *r);
void mm_select_sub(void *km, float mask_level, float pri_ratio, int *n_, mm_reg1_t *r);
void mm_select_sub(void *km, float mask_level, float pri_ratio, int best_n, int *n_, mm_reg1_t *r);
void mm_filter_regs(void *km, const mm_mapopt_t *opt, int *n_regs, mm_reg1_t *regs);
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int n_regs, mm_reg1_t *regs, mm128_t *a);
void mm_join_long(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs, mm128_t *a);
void mm_set_mapq(int n_regs, mm_reg1_t *regs);
#ifdef __cplusplus