chaining with DP
This commit is contained in:
Heng Li
parent
2827c29b48
commit
949d9be872
10
index.c
10
index.c
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@ -60,7 +60,7 @@ const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
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void mm_idx_stat(const mm_idx_t *mi)
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{
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int i, n = 0;
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int i, n = 0, n1 = 0;
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uint64_t sum = 0, len = 0;
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for (i = 0; i < mi->n_seq; ++i)
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len += mi->seq[i].len;
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@ -71,11 +71,13 @@ void mm_idx_stat(const mm_idx_t *mi)
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khint_t k;
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if (h == 0) continue;
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for (k = 0; k < kh_end(h); ++k)
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if (kh_exist(h, k))
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if (kh_exist(h, k)) {
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sum += kh_key(h, k)&1? 1 : (uint32_t)kh_val(h, k);
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if (kh_key(h, k)&1) ++n1;
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}
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}
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fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d; average occurrences: %.3lf; average spacing: %.3lf\n",
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__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, (double)sum / n, (double)len / sum);
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fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf\n",
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__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum);
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}
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uint32_t mm_idx_cal_max_occ(const mm_idx_t *mi, float f)
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64
map.c
64
map.c
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@ -16,8 +16,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
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opt->sdust_thres = 0;
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opt->min_cnt = 2;
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opt->radius = 500;
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opt->max_gap = 10000;
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opt->min_match = 40;
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}
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@ -192,9 +192,59 @@ int mm_liss(int d, int min_L, void *km, int n, mm128_t *a, int *b)
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return m;
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}
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static const char LogTable256[256] = {
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#define LT(n) n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n
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-1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
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LT(4), LT(5), LT(5), LT(6), LT(6), LT(6), LT(6),
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LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7), LT(7)
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};
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static inline int ilog2_32(uint32_t v)
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{
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register uint32_t t, tt;
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if ((tt = v>>16)) return (t = tt>>8) ? 24 + LogTable256[t] : 16 + LogTable256[tt];
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return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
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}
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#define MM_MATCH_SCORE 31
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void mm_chain_dp(int d, int bw, void *km, int n, mm128_t *a)
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{
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int32_t i, j, *f, *p, *t;
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f = (int32_t*)kmalloc(km, n * 4);
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p = (int32_t*)kmalloc(km, n * 4);
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t = (int32_t*)kmalloc(km, n * 4);
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memset(t, 0, n * 4);
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for (i = 0; i < n; ++i) {
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uint64_t ri = a[i].x;
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int32_t qi = (int32_t)a[i].y;
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int32_t max_f = -INT32_MAX, max_j = -1;
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for (j = i - 1; j >= 0; --j) {
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int64_t dr = ri - a[j].x;
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int32_t dq = qi - (int32_t)a[j].y, dd, pen, sc;
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if (dr > d) break;
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if (dq <= 0 || dq > d) continue;
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if (t[j] == i) {
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if (p[j] >= 0) t[p[j]] = i;
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continue;
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}
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dd = dr > dq? dr - dq : dq - dr;
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if (dd > bw) continue;
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pen = ilog2_32(dd);
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sc = f[j] + MM_MATCH_SCORE - pen;
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if (sc > max_f) max_f = sc, max_j = j;
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}
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if (max_j >= 0) f[i] = max_f, p[i] = max_j;
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else f[i] = MM_MATCH_SCORE, p[i] = -1;
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}
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kfree(km, f);
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kfree(km, p);
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kfree(km, t);
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}
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void 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)
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{
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int i, n = m_en - m_st, last = -1, last2 = -1, j, n_a, *t, n_t;
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int i, n = m_en - m_st, last = -1, last2 = -1, j, n_a, *t = 0, n_t;
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mm_match_t *m;
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mm128_t *a;
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@ -252,10 +302,10 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
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continue;
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p = &a[j++];
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if ((r[k]&1) == (q->qpos&1)) { // forward strand
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p->x = r[k];
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p->x = (r[k]&0xffffffff00000000ULL) | (uint32_t)r[k]>>1;
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p->y = (uint64_t)i << 32 | q->qpos >> 1;
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} else { // reverse strand
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p->x = 1ULL<<63 | r[k];
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p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | (uint32_t)r[k]>>1;
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p->y = (uint64_t)i << 32 | (qlen - ((q->qpos>>1) + 1 - q->span) - 1);
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}
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}
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@ -263,6 +313,7 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
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radix_sort_128x(a, a + n_a);
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//for (i = 0; i < n_a; ++i) printf("%c\t%s\t%d\t%d\n", "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (uint32_t)a[i].x>>1, (uint32_t)a[i].y);
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#if 0
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t = (int*)kmalloc(b->km_fixed, (n_a + opt->min_cnt - 1) / opt->min_cnt * sizeof(int));
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n_t = mm_liss(opt->radius, opt->min_cnt, b->km_fixed, n_a, a, t);
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@ -281,9 +332,12 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
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if (a_st) printf("%s:%d-%d", qname, (uint32_t)a_st->y, (uint32_t)(a_en-1)->y);
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else printf("%s:*", qname);
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printf("\t%d\t%d\t", max, max2);
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if (max_i >= 0) printf("%s:%d-%d", mi->seq[a_st->x<<1>>33].name, (uint32_t)a_st->x>>1, (uint32_t)(a_en-1)->x>>1);
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if (max_i >= 0) printf("%s:%d-%d", mi->seq[a_st->x<<1>>33].name, (uint32_t)a_st->x, (uint32_t)(a_en-1)->x);
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else printf("*");
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printf("\t%d\t%d\t%d\t%d\t%d\n", n_tot, n_low, s_low, n, n_t);
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#else
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mm_chain_dp(opt->max_gap, opt->radius, b->km_fixed, n_a, a);
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#endif
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// free
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for (i = 0; i < n; ++i)
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