From a3afeec0b2925afc96b50140d47d8acaa26db517 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 30 May 2018 15:25:34 -0400 Subject: [PATCH] r783: reverted to r781 (#155) --- align.c | 2 +- hit.c | 9 +-------- main.c | 2 +- map.c | 6 +++--- mmpriv.h | 2 +- 5 files changed, 7 insertions(+), 14 deletions(-) diff --git a/align.c b/align.c index 52fc260..8ecd4aa 100644 --- a/align.c +++ b/align.c @@ -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); } diff --git a/hit.c b/hit.c index 27ae7cd..6ec8816 100644 --- a/hit.c +++ b/hit.c @@ -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; diff --git a/main.c b/main.c index b4b522d..e11eebd 100644 --- a/main.c +++ b/main.c @@ -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 diff --git a/map.c b/map.c index febbe8d..79f0d0e 100644 --- a/map.c +++ b/map.c @@ -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); } diff --git a/mmpriv.h b/mmpriv.h index 8b51abb..c3c9a6d 100644 --- a/mmpriv.h +++ b/mmpriv.h @@ -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);