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r783: reverted to r781 (#155)

This commit is contained in:
Heng Li 2018-05-30 15:25:34 -04:00
parent 3573784b4d
commit a3afeec0b2
5 changed files with 7 additions and 14 deletions
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2
align.c
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@ -496,7 +496,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
mm_fix_bad_ends(r, a, opt->bw, opt->min_chain_score * 2, &as1, &cnt1);
}
mm_filter_bad_seeds(km, as1, cnt1, a, 10, 40, opt->max_gap>>1, 10);
mm_filter_bad_seeds_alt(km, as1, cnt1, a, 30, opt->max_gap);
mm_filter_bad_seeds_alt(km, as1, cnt1, a, 30, opt->max_gap>>1);
mm_adjust_minier(mi, qseq0, &a[as1], &rs, &qs);
mm_adjust_minier(mi, qseq0, &a[as1 + cnt1 - 1], &re, &qe);
}

9
hit.c
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@ -106,7 +106,7 @@ void mm_split_reg(mm_reg1_t *r, mm_reg1_t *r2, int n, int qlen, mm128_t *a)
r->split |= 1, r2->split |= 2;
}
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff, int test_ref_ovlp) // and compute mm_reg1_t::subsc
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff) // and compute mm_reg1_t::subsc
{
int i, j, k, *w;
uint64_t *cov;
@ -146,13 +146,6 @@ void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff
ol = si < sj? (ei < sj? 0 : ei < ej? ei - sj : ej - sj) : (ej < si? 0 : ej < ei? ej - si : ei - si); // overlap length; TODO: this can be simplified
if ((float)ol / min - (float)uncov_len / max > mask_level) {
int cnt_sub = 0;
if (test_ref_ovlp && rp->rid == ri->rid && (rp->re > ri->rs && rp->rs < ri->re)) { // have overlap on the reference sequence
int min_r = rp->re - rp->rs < ri->re - ri->rs? rp->re - rp->rs : ri->re - ri->rs;
int min_e = rp->re < ri->re? rp->re : ri->re;
int max_s = rp->rs > ri->rs? rp->rs : ri->rs;
int rl = min_e - max_s;
if (rl > min_r * mask_level) continue;
}
ri->parent = rp->parent;
rp->subsc = rp->subsc > ri->score? rp->subsc : ri->score;
if (ri->cnt >= rp->cnt) cnt_sub = 1;

2
main.c
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@ -10,7 +10,7 @@
#include "getopt.h"
#endif
#define MM_VERSION "2.10-r782-dirty"
#define MM_VERSION "2.10-r783-dirty"
#ifdef __linux__
#include <sys/resource.h>

6
map.c
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@ -239,7 +239,7 @@ static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ,
static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_idx_t *mi, void *km, int qlen, int n_segs, const int *qlens, int *n_regs, mm_reg1_t *regs, mm128_t *a)
{
if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b, 1);
mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, max_chain_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
if (!(opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN))) // long join not working well without primary chains
@ -252,7 +252,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
if (!(opt->flag & MM_F_CIGAR)) return regs;
regs = mm_align_skeleton(km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b, 0);
mm_set_parent(km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
mm_set_sam_pri(*n_regs, regs);
}
@ -348,7 +348,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
seg = mm_seg_gen(b->km, hash, n_segs, qlens, n_regs0, regs0, n_regs, regs, a); // split fragment chain to separate segment chains
free(regs0);
for (i = 0; i < n_segs; ++i) {
mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b, 0); // update mm_reg1_t::parent
mm_set_parent(b->km, opt->mask_level, n_regs[i], regs[i], opt->a * 2 + opt->b); // update mm_reg1_t::parent
regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a);
mm_set_mapq(b->km, n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len, is_sr);
}

2
mmpriv.h
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@ -72,7 +72,7 @@ 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);
int mm_squeeze_a(void *km, int n_regs, mm_reg1_t *regs, mm128_t *a);
int mm_set_sam_pri(int n, mm_reg1_t *r);
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff, int test_ref_ovlp);
void mm_set_parent(void *km, float mask_level, int n, mm_reg1_t *r, int sub_diff);
void mm_select_sub(void *km, float pri_ratio, int min_diff, int best_n, int *n_, mm_reg1_t *r);
void mm_select_sub_multi(void *km, float pri_ratio, float pri1, float pri2, int max_gap_ref, int min_diff, int best_n, int n_segs, const int *qlens, int *n_, mm_reg1_t *r);
void mm_filter_regs(void *km, const mm_mapopt_t *opt, int qlen, int *n_regs, mm_reg1_t *regs);