From 59c822b722e4a6925d6ffbf5323572bc4309a288 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 9 Sep 2017 08:38:39 -0400 Subject: [PATCH] removed some commented code which *might* return at some time later --- map.c | 83 +---------------------------------------------------------- 1 file changed, 1 insertion(+), 82 deletions(-) diff --git a/map.c b/map.c index 2a81352..d7d573a 100644 --- a/map.c +++ b/map.c @@ -102,72 +102,7 @@ static void mm_dust_minier(mm128_v *mini, int l_seq, const char *seq, int sdust_ } mini->n = k; } -#if 0 -int mm_pair_thin_core(mm_tbuf_t *b, uint64_t x, int radius, int rel, int st0, int n, const uint64_t *z, uint64_v *a) -{ - int i, st = st0, en = n, mid = en - 1; - while (st < en) { - uint64_t y; - mid = st + ((en - st) >> 1); - y = z[mid]; - if (y < x && (x - y)>>1 > radius) st = mid + 1; - else if (y >= x && (y - x)>>1 > radius) en = mid; - else break; - } - if (st < en) { - for (en = mid + 1; en < n; ++en) - if (z[en] > x && (z[en] - x)>>1 > radius) - break; - for (st = mid - 1; st >= st0; --st) - if (z[st] < x && (x - z[st])>>1 > radius) - break; - ++st; - for (i = st; i < en; ++i) { - uint64_t y = z[i]; - if (((x ^ y) & 1) == rel) { -// printf("* %d,%d\n", (uint32_t)x>>1, (uint32_t)y>>1); - kv_push(uint64_t, b->km, *a, y); - } - } - return en; - } else return st < n && z[st] < x? st + 1 : en; -} -void mm_pair_thin(mm_tbuf_t *b, int radius, mm_match_t *m1, mm_match_t *m2) -{ - mm_match_t *m[2]; - const uint64_t *z[2]; - uint64_v a[2]; - int i, n[2], k[2], u = 0, rel = (m1->qpos ^ m2->qpos) & 1; - - m[0] = m1, m[1] = m2; - for (i = 0; i < 2; ++i) { - n[i] = m[i]->n; - z[i] = m[i]->x.cr; - k[i] = 0; - kv_init(a[i]); - kv_resize(uint64_t, b->km, a[i], 256); - } - while (k[0] < n[0] && k[1] < n[1]) { - //printf("%d; %d,%d\n", u, k[0], k[1]); - int v = u^1, dist = (int)(m[v]->qpos>>1) - (int)(m[u]->qpos>>1); - uint64_t x = z[u][k[u]]; - int uori = (x ^ m[u]->qpos) & 1, last; - int64_t tpos = x>>1 & 0x7fffffff; - tpos = uori == 0? tpos + dist : tpos - dist; - if (tpos < 0) tpos = 0; - x = x>>32<<32 | tpos<<1 | (x&1); - last = a[v].n; - k[v] = mm_pair_thin_core(b, x, radius, rel, k[v], n[v], z[v], &a[v]); - if (a[v].n > last) kv_push(uint64_t, b->km, a[u], z[u][k[u]]); - ++k[u]; - u ^= 1; - } - for (i = 0; i < 2; ++i) - m[i]->n = a[i].n, m[i]->x.r = a[i].a, m[i]->is_alloc = 1; -// printf("%d,%d; %d,%d\n", m[0]->qpos>>1, m[1]->qpos>>1, m[0]->n, m[1]->n); -} -#endif mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint32_t m_st, uint32_t m_en, const char *qname, int qlen, const char *seq, int *n_regs) { int i, n = m_en - m_st, j, n_u, max_gap_ref; @@ -187,23 +122,7 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, m[i].x.cr = mm_idx_get(mi, p->x>>8, &t); m[i].n = t; } -#if 0 - int last = -1, last2 = -1; - // pair k-mer thinning - for (i = 0; i < n; ++i) { - if (m[i].n >= opt->mid_occ && m[i].n < opt->max_occ) { - if (last2 < 0) last2 = i; - if (last < 0 || m[last].n < m[i].n) last = i; - if (last >= 0 && (m[last].qpos>>1) + (m[last].span>>1) <= m[i].qpos>>1) { - mm_pair_thin(b, opt->bw, &m[last], &m[i]); - last2 = last = -1; - } else if (last2 >= 0 && (m[last2].qpos>>1) + (m[last2].span>>1) <= m[i].qpos>>1) { - mm_pair_thin(b, opt->bw, &m[last2], &m[i]); - last2 = last = -1; - } - } - } -#endif + // fill the _a_ array for (i = 0, n_a = 0; i < n; ++i) // find the length of a[] if (m[i].n < opt->mid_occ) n_a += m[i].n;