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r118: bugfix - regs unsorted before filtering

This commit is contained in:
Heng Li 2017-06-30 12:52:28 -04:00
parent 5dcd8f8965
commit 1a903486b9
5 changed files with 26 additions and 11 deletions
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2
format.c
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@ -125,7 +125,7 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
} else mm_sprintf_lite(s, "*"); } else mm_sprintf_lite(s, "*");
mm_sprintf_lite(s, "\t*\t0\t0\t"); mm_sprintf_lite(s, "\t*\t0\t0\t");
if ((flag & 0x900) == 0) sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev); if ((flag & 0x900) == 0) sam_write_sq(s, t->seq, t->l_seq, r->rev, r->rev);
else if (flag & 0x100) mm_sprintf_lite(s, "\t*"); else if (flag & 0x100) mm_sprintf_lite(s, "*");
else sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev); else sam_write_sq(s, t->seq + r->qs, r->qe - r->qs, r->rev, r->rev);
mm_sprintf_lite(s, "\t*"); // quality mm_sprintf_lite(s, "\t*"); // quality
write_tags(s, r); write_tags(s, r);

29
hit.c
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@ -3,22 +3,37 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "kalloc.h" #include "kalloc.h"
mm_reg1_t *mm_gen_regs(int qlen, int n_u, uint64_t *u, mm128_t *a) // convert chains to hits mm_reg1_t *mm_gen_regs(void *km, int qlen, int n_u, uint64_t *u, mm128_t *a) // convert chains to hits
{ {
mm128_t *z, tmp;
mm_reg1_t *r; mm_reg1_t *r;
int i, k; int i, k;
r = (mm_reg1_t*)calloc(n_u, sizeof(mm_reg1_t));
if (n_u == 0) return 0;
// sort by score
z = (mm128_t*)kmalloc(km, n_u * 16);
for (i = k = 0; i < n_u; ++i) { for (i = k = 0; i < n_u; ++i) {
z[i].x = u[i] >> 32;
z[i].y = (uint64_t)k << 32 | (int32_t)u[i];
k += (int32_t)u[i];
}
radix_sort_128x(z, z + n_u);
for (i = 0; i < n_u>>1; ++i) // reverse, s.t. larger score first
tmp = z[i], z[i] = z[n_u-1-i], z[n_u-1-i] = tmp;
// populate r[]
r = (mm_reg1_t*)calloc(n_u, sizeof(mm_reg1_t));
for (i = 0; i < n_u; ++i) {
mm_reg1_t *ri = &r[i]; mm_reg1_t *ri = &r[i];
ri->id = i; ri->id = i;
ri->parent = MM_PARENT_UNSET; ri->parent = MM_PARENT_UNSET;
ri->subsc = 0; ri->score = z[i].x;
ri->score = u[i]>>32; ri->cnt = (int32_t)z[i].y;
ri->cnt = (int32_t)u[i]; ri->as = z[i].y >> 32;
ri->as = k;
mm_reg_set_coor(ri, qlen, a); mm_reg_set_coor(ri, qlen, a);
k += ri->cnt;
} }
kfree(km, z);
return r; return r;
} }

2
main.c
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@ -10,7 +10,7 @@
#include "minimap.h" #include "minimap.h"
#include "mmpriv.h" #include "mmpriv.h"
#define MM_VERSION "2.0-r117-pre" #define MM_VERSION "2.0-r118-pre"
void liftrlimit() void liftrlimit()
{ {

2
map.c
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@ -235,7 +235,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
kfree(b->km, m); kfree(b->km, m);
n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, n_a, a, &u, b->km); n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, n_a, a, &u, b->km);
regs = mm_gen_regs(qlen, n_u, u, a); regs = mm_gen_regs(b->km, qlen, n_u, u, a);
*n_regs = n_u; *n_regs = n_u;
if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap if (!(opt->flag & MM_F_AVA)) { // don't choose primary mapping(s) for read overlap
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, n_regs, regs);

2
mmpriv.h
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@ -36,7 +36,7 @@ void mm_write_sam(kstring_t *s, const mm_idx_t *mi, const bseq1_t *t, const mm_r
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km); int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km);
mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a); mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);
mm_reg1_t *mm_gen_regs(int qlen, int n_u, uint64_t *u, mm128_t *a); mm_reg1_t *mm_gen_regs(void *km, int qlen, int n_u, uint64_t *u, mm128_t *a);
void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a); 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_sync_regs(void *km, int n_regs, mm_reg1_t *regs);
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 *n_, mm_reg1_t *r);