mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-01 20:08:11 +08:00
r373
This commit is contained in:
chhylp123
+396
-538
@@ -10,14 +10,8 @@
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#define MAX_HIGH_OCC 8 // TODO: don't hard code if we need to tune this parameter
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#define MAX_MAX_HIGH_OCC 16
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#define GMC(a, x,y,xn) ((a)[(x)*(xn)+(y)])
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static inline int mzcmp(const ha_mz1_t *a, const ha_mz1_t *b)
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{
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return a->rid < b->rid? -1 : a->rid > b->rid? 1 : ((a->x > b->x) - (a->x < b->x));
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}
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#define mz_lt(a, b) (mzcmp(&(a), &(b)) < 0)
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KSORT_INIT(mz, ha_mz1_t, mz_lt)
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#define GL(x, i) ((int64_t)((uint32_t)((x).a[(i)])))
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#define A_M(p, i) ((i) >= 0 && (p).a[(i)].rid > 0)
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void debug_refine(ha_mz1_t *ma, uint64_t *mmt, int32_t sn, int32_t n, int32_t m, int32_t end)
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{
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@@ -42,287 +36,6 @@ void debug_refine(ha_mz1_t *ma, uint64_t *mmt, int32_t sn, int32_t n, int32_t m,
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if(nt != tot) fprintf(stderr, "ERROR-TOT, nt: %ld, tot: %ld\n", nt, tot);
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}
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void refine_select(ha_mz1_v *mz, int32_t sidx, int32_t eidx, int32_t sn, int32_t min_freq, st_mt_t *mm,
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int32_t *rsi, int32_t *rei)
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{
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int32_t n = sn, m = eidx + 1 - sidx, i, k, t, mk=-1;
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uint64_t ix, kx, ks;
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kv_resize(uint64_t, *mm, mm->n+n*m);
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ha_mz1_t *ma = mz->a + sidx;
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uint64_t *mmt = mm->a + mm->n;
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// fprintf(stderr, "[M::%s::] ==> +n: %d, m: %d, sn: %d, sidx: %d, eidx: %d\n", __func__, n, m, sn, sidx, eidx);
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for (i = 0; i < n; i++) ///how many selected minimizers
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{
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for (k = 0, mk = -1; k < m; k++) ///how many minimizers in total
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{
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if((int32_t)(ma[k].rid)<min_freq) continue;
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ks = ma[k].pos + 1 - ma[k].span; t = -1;
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if(i > 0)
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{
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for (t = k-1; t >= 0 && (ma[t].pos >= ks||(int32_t)(ma[t].rid)<min_freq); t--);
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}
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ix = (i <= 0?0:(t<0?0xffffffff:(GMC(mmt, i-1,t,m)&0xffffffff)));
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if(ix < 0xffffffff) ix += (ma[k].rid);
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kx = (mk < 0?0xffffffff:(GMC(mmt, i, mk,m)&0xffffffff));
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ks = MIN(ix, kx);
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// fprintf(stderr, "ks: %lu, i: %d (n-%d), k: %d (m-%d), ix: %lu, kx: %lu, t: %d, mk: %d\n",
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// ks, i, n, k, m, ix, kx, t, mk);
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if((ks&0xffffffff) == 0xffffffff) ks |= ((uint64_t)0xffffffff)<<32;
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else if(ks == ix) ks |= (uint64_t)(i>0?(i-1)*m+t:0xffffffff)<<32;
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else if(ks == kx) ks |= (uint64_t)(mk>=0?i*m+mk:0xffffffff)<<32;
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GMC(mmt, i,k,m) = ks;
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mk = k;
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}
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}
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// fprintf(stderr, "[M::%s::] ==> ++n: %d, m: %d, sn: %d, sidx: %d, eidx: %d\n", __func__, n, m, sn, sidx, eidx);
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ks = (n-1)*m + mk; ix = (uint64_t)-1; kx = 0;
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while (ks != 0xffffffff)
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{
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i = ks/m; k = ks%m;
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ks = mmt[ks]>>32;
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// fprintf(stderr, "i: %d, k: %d, ks: %lu\n", i, k, ks);
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if(ks == 0xffffffff || (int32_t)(ks/m) == (i-1))
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{
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mm->a[sidx+k] = 1;
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ix = MIN((uint64_t)k, ix); kx = MAX((uint64_t)k, kx);
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}
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}
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///debug
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// debug_refine(ma, mmt, sn, n, m, (n-1)*m + mk);
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if(rsi) (*rsi) = ix + sidx;
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if(rei) (*rei) = kx + sidx;
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}
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void refine_sketch(ha_mz1_v *p, ha_pt_t *pt, int32_t rlen, int32_t dp_min_len, float er, int32_t min_freq, st_mt_t *mt)
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{
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// fprintf(stderr, "[M::%s::] ==> #########10#########, rlen: %d\n", __func__, rlen);
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int32_t i, n = p->n, bd, len = MIN(rlen, dp_min_len), sublen, cnt, ei, li, ri;
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int32_t sn = len*er + 1;
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kv_resize(uint64_t, *mt, (int64_t)p->n);
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mt->n = p->n; memset(mt->a, 0, sizeof(uint64_t)*p->n);
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for (i = 0; i < n; i++) p->a[i].rid = ha_pt_cnt(pt, p->a[i].x);
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for (i = cnt = 0, bd = -1, ei = -1; i < n; i++)
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{
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if((int32_t)(p->a[i].rid)<min_freq) continue;
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sublen = p->a[i].pos + 1;
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if(sublen > len) break;
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else ei = i;
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if((int32_t)(p->a[i].pos + 1 - p->a[i].span) > bd)
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{
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bd = p->a[i].pos;
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cnt++;
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}
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}
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// fprintf(stderr, "[M::%s::] ==> +cnt: %d, sn: %d, ei: %d, n: %d\n", __func__, cnt, sn, ei, n);
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if(cnt >= sn) refine_select(p, 0, ei, sn, min_freq, mt, NULL, &li);
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else
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{
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li = i-1;
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for (i = 0; i <= li; i++) mt->a[i] = 1;
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}
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if(len < rlen)
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{
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for (i = n-1, cnt = 0, bd = rlen+1, ei = -1; i >= 0; i--)
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{
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if((int32_t)(p->a[i].rid)<min_freq) continue;
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sublen = rlen - (p->a[i].pos + 1 - p->a[i].span);
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if(sublen > len) break;
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else ei = i;
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if((int32_t)(p->a[i].pos) < bd)
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{
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bd = p->a[i].pos + 1 - p->a[i].span;
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cnt++;
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}
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}
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// fprintf(stderr, "[M::%s::] ==> -cnt: %d, sn: %d, ei: %d, n: %d\n", __func__, cnt, sn, ei, n);
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if(cnt >= sn) refine_select(p, ei, n-1, sn, min_freq, mt, &ri, NULL);
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else
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{
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ri = i+1;
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for (i = ri; i <= n-1; i++) mt->a[i] = 1;
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}
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// fprintf(stderr, "[M::%s::] ==> --cnt: %d, sn: %d, ei: %d, n: %d\n", __func__, cnt, sn, ei, n);
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if(ri - li >= 2)
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{
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li++; ri--;
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sn = (p->a[ri].pos - p->a[li].pos + p->a[li].span)*er + 1;
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for (i = li, cnt = 0, bd = -1; i <= ri; i++)
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{
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if((int32_t)(p->a[i].rid)<min_freq) continue;
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if((int32_t)(p->a[i].pos + 1 - p->a[i].span) > bd)
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{
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bd = p->a[i].pos;
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cnt++;
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if(cnt >= sn) break;
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}
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}
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if(cnt >= sn) refine_select(p, li, ri, sn, min_freq, mt, NULL, NULL);
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else for (i = li; i <= ri; i++) mt->a[i] = 1;
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}
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}
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// fprintf(stderr, "[M::%s::] ==> #########20#########, p->n: %u, n: %d\n", __func__, p->n, n);
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for (i = sn = 0; i < n; i++)
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{
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if(mt->a[i])
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{
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p->a[sn] = p->a[i];
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sn++;
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}
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}
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// if(p->n != sn) fprintf(stderr, "[M::%s::] ==> #########21#########, p->n: %u, sn: %d\n", __func__, p->n, sn);
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p->n = sn;
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}
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inline int hf_dp(ha_mz1_v *mz, int32_t sidx, int32_t eidx, int32_t sn, int32_t min_freq, st_mt_t *mm,
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int32_t *rsi, int32_t *rei)
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{
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return 0;
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}
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inline void hf_select(ha_mz1_v *p, int32_t si, int32_t ei, int32_t n, int32_t len, int32_t sample_dist, ha_mz1_t *b, int32_t force)
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{
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if(ei - si <= 1) return;
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int32_t ps = si < 0? 0 : p->a[si].pos;
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int32_t pe = ei == n? len : p->a[ei].pos;
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int32_t j, k, st = si + 1, en = ei;
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int32_t max_high_occ = (int32_t)((double)(pe - ps) / sample_dist + .499);
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if (max_high_occ > MAX_MAX_HIGH_OCC)
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max_high_occ = MAX_MAX_HIGH_OCC;
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for (j = st, k = 0; j < en && k < max_high_occ; ++j, ++k)
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b[k] = p->a[j], b[k].pos = j; // b[].pos keeps the index in p->a[]
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ks_heapmake_mz(k, b); // initialize the binomial heap
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for (; j < en; ++j) { // if there are more, choose top max_high_occ
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if (mz_lt(p->a[j], b[0])) { // then update the heap
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b[0] = p->a[j], b[0].pos = j;
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ks_heapdown_mz(0, k, b);
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}
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}
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//ks_heapsort_mz(k, b); // sorting is not needed for now
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for (j = 0; j < k; ++j)
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if (b[j].rid < pe - ps || force)
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p->a[b[j].pos].rid = 0;
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}
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void select_mz(ha_mz1_v *p, int len, int sample_dist, int32_t dp_min_len)
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{ // for high-occ minimizers, choose up to max_high_occ in each high-occ streak
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int32_t i, last0 = -1, n = (int32_t)p->n, m = 0, nw[2], min_len;
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ha_mz1_t b[MAX_MAX_HIGH_OCC]; // this is to avoid a heap allocation
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if (n == 0 || n == 1) return;
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assert(n < 1<<27); // 27 is the number of bits for ha_mz1_t::pos; this should be safe as there are more bases than minimizers
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for (i = 0; i < n; ++i)
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if (p->a[i].rid != 0) ++m;
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if (m == 0) return; // no high-frequency k-mers; do nothing
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for (i = 0; i <= n; ++i) {
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if (i == n || p->a[i].rid == 0) {
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if (i - last0 > 1) {
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hf_select(p, last0, i, n, len, sample_dist, b, 0);
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// int32_t ps = last0 < 0? 0 : p->a[last0].pos;
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// int32_t pe = i == n? len : p->a[i].pos;
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// int32_t j, k, st = last0 + 1, en = i;
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// int32_t max_high_occ = (int32_t)((double)(pe - ps) / sample_dist + .499);
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// if (max_high_occ > MAX_MAX_HIGH_OCC)
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// max_high_occ = MAX_MAX_HIGH_OCC;
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// for (j = st, k = 0; j < en && k < max_high_occ; ++j, ++k)
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// b[k] = p->a[j], b[k].pos = j; // b[].pos keeps the index in p->a[]
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// ks_heapmake_mz(k, b); // initialize the binomial heap
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// for (; j < en; ++j) { // if there are more, choose top max_high_occ
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// if (mz_lt(p->a[j], b[0])) { // then update the heap
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// b[0] = p->a[j], b[0].pos = j;
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// ks_heapdown_mz(0, k, b);
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// }
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// }
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// //ks_heapsort_mz(k, b); // sorting is not needed for now
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// for (j = 0; j < k; ++j)
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// if (b[j].rid < pe - ps)
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// p->a[b[j].pos].rid = 0;
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}
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last0 = i;
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}
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}
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min_len = MAX(dp_min_len, (p->a[0].pos+1)+sample_dist);
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for (i = 0, nw[0] = nw[1] = 0; i < n; i++)
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{
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nw[(p->a[i].rid!=0)]++;
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if((p->a[i].pos + 1) > min_len) break;
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}
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if(nw[0]==0 && nw[1]>0) hf_select(p, -1, i, n, len, sample_dist, b, 1);
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min_len = MAX(dp_min_len, (len - (p->a[n-1].pos + 1 - p->a[n-1].span))+sample_dist);
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for (i = n-1, nw[0] = nw[1] = 0; i >= 0; i--)
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{
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nw[(p->a[i].rid!=0)]++;
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if((len - (p->a[i].pos + 1 - p->a[i].span)) > min_len) break;
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}
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if(nw[0]==0 && nw[1]>0) hf_select(p, i, n, n, len, sample_dist, b, 1);
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for (i = n = 0; i < (int32_t)p->n; ++i) // squeeze out filtered minimizers
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if (p->a[i].rid == 0)
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p->a[n++] = p->a[i];
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p->n = n;
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}
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static inline int mzcmp_l(const ha_mz1_v *p, int32_t ai, int32_t bi)
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{
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if(ai >= 0 && bi >= 0){
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ha_mz1_t *a = &(p->a[ai]), *b = &(p->a[bi]);
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if(a->rid > 0 && b->rid > 0) return mzcmp(a, b);
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return (a->rid == 0) - (b->rid == 0);
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}
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return (ai < 0) - (bi < 0);
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}
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#define GL(x, i) ((int64_t)((uint32_t)((x).a[(i)])))
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#define A_M(p, i) ((i) >= 0 && (p).a[(i)].rid > 0)
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int32_t qfw(ha_mz1_v *p, st_mt_t *mt, int32_t n, int32_t tot_l, int32_t ws, int32_t i, int32_t *mi)
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{
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int32_t m, si;
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for (si = i, (*mi) = -1; i < n; i++){
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if(GL(*mt, i) >= ws || (i+1 < n && GL(*mt, i) < ws && GL(*mt, i+1) > ws) ||
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(i+1 == n && tot_l >= ws && GL(*mt, i) < ws)){
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for (m = si; m <= i; m++){
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if(!A_M(*p, m)) continue;
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if(mzcmp_l(p, *mi, m) >= 0) (*mi) = m;
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}
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if((*mi) >= 0 && A_M(*p, *mi)){
|
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for (m = si; m <= i; m++){
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if(!A_M(*p, m)) continue;
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if(mzcmp_l(p, *mi, m) == 0) mt->a[m] |= 0x100000000;
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}
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}
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break;
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}
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}
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return i;
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}
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void dbg_boundary(ha_mz1_v *p, st_mt_t *mt, int32_t w, int32_t k, int32_t tot_l)
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{
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if(tot_l < w + k -1) return;
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@@ -401,110 +114,6 @@ void dbg_boundary(ha_mz1_v *p, st_mt_t *mt, int32_t w, int32_t k, int32_t tot_l)
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}
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}
|
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static void select_mz_h(ha_mz1_v *p, st_mt_t *mt, int len, int sample_dist, int32_t w, int32_t k, int32_t tot_l)
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{ // for high-occ minimizers, choose up to max_high_occ in each high-occ streak
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int32_t i, mi = -1, si, last0 = -1, n = (int32_t)p->n, m = 0, ws = w + k - 1;
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if (n == 0) return;
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assert(n < 1<<27); // 27 is the number of bits for ha_mz1_t::pos; this should be safe as there are more bases than minimizers
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for (i = m = 0, last0 = -1; i <= n; ++i) {
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if (i == n || p->a[i].rid == 0) {
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if (i - last0 > 1) {
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int32_t ps = last0 < 0? 0 : p->a[last0].pos;
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int32_t pe = i == n? len : p->a[i].pos;
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if(((int32_t)((double)(pe - ps) / sample_dist + .499)) > 0){
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last0 = -2;
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m++;
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break;
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}
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}
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last0 = i;
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}
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}
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if (m == 0) return; // no high-frequency k-mers; do nothing
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if(last0 >= -1) goto ff;
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i = 0;
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i = qfw(p, mt, n, tot_l, ws, i, &mi);
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if(i == n) goto ff;
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for (si = 0, i++; i < n; i++){
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for (; si < i; si++){
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if(GL(*mt, si) + w > GL(*mt, i)) break;
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}
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// a new minimum; then write the old min
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if(mzcmp_l(p, i, mi) <= 0) {
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if(A_M(*p, mi)) mt->a[mi] |= 0x100000000;
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mi = i;
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}// old min has moved outside the window
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else if(si > mi){
|
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if(A_M(*p, mi)) mt->a[mi] |= 0x100000000;
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for (m = si, mi = -1; m <= i; m++){
|
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if(mzcmp_l(p, mi, m) >= 0) mi = m;
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||||
}
|
||||
if(A_M(*p, mi)){
|
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for (m = si; m <= i; m++){
|
||||
if(!A_M(*p, m)) continue;
|
||||
if(mzcmp_l(p, mi, m) == 0) mt->a[m] |= 0x100000000;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if(A_M(*p, mi)) mt->a[mi] |= 0x100000000;
|
||||
|
||||
for (i = n - 1; si < n && GL(*mt, si) + w <= tot_l + 1; si++){
|
||||
if(si > mi){
|
||||
if(A_M(*p, mi)) mt->a[mi] |= 0x100000000;
|
||||
for (m = si, mi = -1; m <= i; m++){
|
||||
if(mzcmp_l(p, mi, m) >= 0) mi = m;
|
||||
}
|
||||
if(A_M(*p, mi)){
|
||||
for (m = si; m <= i; m++){
|
||||
if(!A_M(*p, m)) continue;
|
||||
if(mzcmp_l(p, mi, m) == 0) mt->a[m] |= 0x100000000;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
dbg_boundary(p, mt, w, k, tot_l);
|
||||
fprintf(stderr, "\n");
|
||||
for (i = 0; i < (int32_t)p->n; ++i){
|
||||
if(p->a[i].rid == 0) continue;
|
||||
fprintf(stderr, "%cl: %u, pos: %lu, cnt: %lu, key: %lu, i: %d\n", "+-"[!!(mt->a[i]&0x100000000)],
|
||||
(uint32_t)mt->a[i], p->a[i].pos, p->a[i].rid, p->a[i].x, i);
|
||||
// if (mt->a[i]&0x100000000){
|
||||
// fprintf(stderr, "+l: %u, pos: %lu, cnt: %lu\n", (uint32_t)mt->a[i], p->a[i].pos, p->a[i].rid);
|
||||
// }
|
||||
}
|
||||
**/
|
||||
ha_mz1_t b[MAX_MAX_HIGH_OCC];
|
||||
for (i = 0, last0 = -1; i <= n; ++i) {
|
||||
if (i == n || p->a[i].rid == 0) {
|
||||
if (i - last0 > 1) {
|
||||
int32_t ps = last0 < 0? 0 : p->a[last0].pos;
|
||||
int32_t pe = i == n? len : p->a[i].pos;
|
||||
if(((int32_t)((double)(pe - ps) / sample_dist + .499)) > 0){
|
||||
for (m = last0 + 1, mi = 0; m < i; ++m){
|
||||
if(mt->a[m]&0x100000000) p->a[m].rid = 0, mi++;
|
||||
}
|
||||
if(mi == 0) hf_select(p, last0, i, n, len, sample_dist, b, 0);
|
||||
}
|
||||
}
|
||||
last0 = i;
|
||||
}
|
||||
}
|
||||
|
||||
ff:
|
||||
for (i = n = 0; i < (int32_t)p->n; ++i) // squeeze out filtered minimizers
|
||||
if (p->a[i].rid == 0)
|
||||
p->a[n++] = p->a[i];
|
||||
p->n = n;
|
||||
}
|
||||
|
||||
void debug_pl(const char *str, int len, int w, int k, int is_hpc, ha_mz1_v *p, const void *hf, st_mt_t *mt)
|
||||
{
|
||||
int i, l, dbi, dbcnt = 0, kmer_span = 0;
|
||||
@@ -571,153 +180,402 @@ void debug_pl(const char *str, int len, int w, int k, int is_hpc, ha_mz1_v *p, c
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Find symmetric (w,k)-minimizers on a DNA sequence
|
||||
*
|
||||
* @param str DNA sequence
|
||||
* @param len length of $str
|
||||
* @param w find a minimizer for every $w consecutive k-mers
|
||||
* @param k k-mer size
|
||||
* @param rid reference ID; will be copied to the output $p array
|
||||
* @param is_hpc homopolymer-compressed or not
|
||||
* @param p minimizers
|
||||
*/
|
||||
void ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, ha_mz1_v *p, const void *hf, int sample_dist, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, ha_pt_t *pt, int min_freq, int32_t dp_min_len, float dp_e, st_mt_t *mt, int32_t ws, int32_t is_unique)
|
||||
{ ///in default, w = 51, k = 51, is_hpc = 1
|
||||
/**
|
||||
uint64_t x;
|
||||
uint64_t rid:28, pos:27, rev:1, span:8;
|
||||
**/
|
||||
extern void *ha_ct_table;
|
||||
static const ha_mz1_t dummy = { UINT64_MAX, (1<<28) - 1, 0, 0, 0};
|
||||
uint64_t shift1 = k - 1, mask = (1ULL<<k) - 1, kmer[4] = {0,0,0,0};
|
||||
int i, j, l, tl = 0, buf_pos, min_pos, kmer_span = 0;
|
||||
ha_mz1_t buf[256], min = dummy;
|
||||
uint32_t buf_p[256], min_s = (uint32_t)-1;
|
||||
tiny_queue_t tq;
|
||||
static inline int mz1_mzcmp(const ha_mz1_t *a, const ha_mz1_t *b){return a->rid < b->rid? -1 : a->rid > b->rid? 1 : ((a->x > b->x) - (a->x < b->x));}
|
||||
#define mz1_mz_lt(a, b) (mz1_mzcmp(&(a), &(b)) < 0)
|
||||
KSORT_INIT(mz1_mz, ha_mz1_t, mz1_mz_lt)
|
||||
|
||||
assert(len > 0 && len < 1<<27 && rid < 1<<28 && (w > 0 && w < 256) && (k > 0 && k <= 63));
|
||||
if (dbg_ct != NULL) dbg_ct->a.n = 0;
|
||||
if (k_flag != NULL) {
|
||||
kv_resize(uint8_t, k_flag->a, (uint64_t)len);
|
||||
k_flag->a.n = len;
|
||||
memset(k_flag->a.a, 0, k_flag->a.n);
|
||||
}
|
||||
static inline int mz2_mzcmp(const ha_mzl_t *a, const ha_mzl_t *b){return a->rid < b->rid? -1 : a->rid > b->rid? 1 : ((a->x > b->x) - (a->x < b->x));}
|
||||
#define mz2_mz_lt(a, b) (mz2_mzcmp(&(a), &(b)) < 0)
|
||||
KSORT_INIT(mz2_mz, ha_mzl_t, mz2_mz_lt)
|
||||
|
||||
memset(buf, 0xff, w * sizeof(ha_mz1_t));
|
||||
memset(&tq, 0, sizeof(tiny_queue_t));
|
||||
///len/w is the evaluated minimizer numbers
|
||||
kv_resize(ha_mz1_t, *p, p->n + len/w);
|
||||
kv_resize(uint64_t, *mt, (int64_t)p->m); mt->n = p->n;
|
||||
|
||||
for (i = l = tl = buf_pos = min_pos = 0; i < len; ++i) {
|
||||
int c = seq_nt4_table[(uint8_t)str[i]];
|
||||
ha_mz1_t info = dummy;
|
||||
if (c < 4) { // not an ambiguous base
|
||||
int z;
|
||||
if (is_hpc) {
|
||||
int skip_len = 1;
|
||||
if (i + 1 < len && seq_nt4_table[(uint8_t)str[i + 1]] == c) {
|
||||
for (skip_len = 2; i + skip_len < len; ++skip_len)
|
||||
if (seq_nt4_table[(uint8_t)str[i + skip_len]] != c)
|
||||
break;
|
||||
i += skip_len - 1; // put $i at the end of the current homopolymer run
|
||||
}
|
||||
tq_push(&tq, skip_len);
|
||||
kmer_span += skip_len;
|
||||
///how many bases that are covered by this HPC k-mer
|
||||
///kmer_span includes at most k HPC elements
|
||||
if (tq.count > k) kmer_span -= tq_shift(&tq);
|
||||
} else kmer_span = l + 1 < k? l + 1 : k;
|
||||
///kmer_span should be used for HPC k-mer
|
||||
///non-HPC k-mer, kmer_span should be k
|
||||
///kmer_span is used to calculate anchor pos on reverse complementary strand
|
||||
|
||||
if (k_flag != NULL) k_flag->a.a[i] = 1;///lable all useful base, which are not ignored by HPC
|
||||
|
||||
kmer[0] = (kmer[0] << 1 | (c&1)) & mask; // forward k-mer
|
||||
kmer[1] = (kmer[1] << 1 | (c>>1)) & mask;
|
||||
kmer[2] = kmer[2] >> 1 | (uint64_t)(1 - (c&1)) << shift1; // reverse k-mer
|
||||
kmer[3] = kmer[3] >> 1 | (uint64_t)(1 - (c>>1)) << shift1;
|
||||
if (kmer[1] == kmer[3]) continue; // skip "symmetric k-mers" as we don't know it strand
|
||||
z = kmer[1] < kmer[3]? 0 : 1; // strand
|
||||
++l; tl++;
|
||||
if (l >= k && kmer_span < 256) {
|
||||
uint64_t y;
|
||||
int32_t cnt, filtered;
|
||||
y = yak_hash64_64(kmer[z<<1|0]) + yak_hash64_64(kmer[z<<1|1]);
|
||||
cnt = hf? ha_ft_cnt(hf, y) : 0;
|
||||
filtered = (cnt >= 1<<28);
|
||||
if(is_unique){
|
||||
filtered = (cnt == 0);
|
||||
cnt = (cnt == 1? 0:cnt);
|
||||
}
|
||||
if (dbg_ct != NULL) kv_push(uint64_t, dbg_ct->a, ((((uint64_t)(query_ct_index(ha_ct_table, y))<<1)|filtered)<<32)|(uint64_t)(i));
|
||||
if (!filtered) info.x = y, info.rid = cnt, info.pos = i, info.rev = z, info.span = kmer_span; // initially ha_mz1_t::rid keeps the k-mer count
|
||||
if (k_flag != NULL) k_flag->a.a[i]++;
|
||||
if (k_flag != NULL && filtered > 0) k_flag->a.a[i]++;
|
||||
}
|
||||
} else l = 0, tq.count = tq.front = 0, kmer_span = 0;
|
||||
|
||||
buf[buf_pos] = info; // need to do this here as appropriate buf_pos and buf[buf_pos] are needed below
|
||||
buf_p[buf_pos] = l;
|
||||
if (l == w + k - 1 && min.x != UINT64_MAX) { // special case for the first window - because identical k-mers are not stored yet
|
||||
for (j = buf_pos + 1; j < w; ++j){
|
||||
if (mzcmp(&min, &buf[j]) == 0 && buf[j].pos != min.pos){
|
||||
kv_push(ha_mz1_t, *p, buf[j]); kv_push(uint64_t, *mt, buf_p[j]);
|
||||
}
|
||||
}
|
||||
for (j = 0; j < buf_pos; ++j){
|
||||
if (mzcmp(&min, &buf[j]) == 0 && buf[j].pos != min.pos){
|
||||
kv_push(ha_mz1_t, *p, buf[j]); kv_push(uint64_t, *mt, buf_p[j]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* There are three cases:
|
||||
* 1. info.x <= min.x, means info is a new minimizer
|
||||
* 2. info.x > min.x, info is not a new minimizer
|
||||
* (1) buf_pos != min_pos, do nothing
|
||||
* (2) buf_pos == min_pos, means current minimizer has moved outside the window
|
||||
* **/
|
||||
///three cases: 1.
|
||||
if (mzcmp(&min, &info) >= 0) { // a new minimum; then write the old min
|
||||
if (l >= w + k && min.x != UINT64_MAX){
|
||||
kv_push(ha_mz1_t, *p, min); kv_push(uint64_t, *mt, min_s);
|
||||
}
|
||||
min = info, min_pos = buf_pos, min_s = buf_p[buf_pos];
|
||||
} else if (buf_pos == min_pos) { // old min has moved outside the window
|
||||
if (l >= w + k - 1 && min.x != UINT64_MAX){
|
||||
kv_push(ha_mz1_t, *p, min); kv_push(uint64_t, *mt, min_s);
|
||||
}
|
||||
///buf_pos == min_pos, means current minimizer has moved outside the window
|
||||
///so for now we need to find a new minimizer at the current window (w k-mers)
|
||||
for (j = buf_pos + 1, min = dummy; j < w; ++j) // the two loops are necessary when there are identical k-mers
|
||||
if (mzcmp(&min, &buf[j]) >= 0) min = buf[j], min_pos = j, min_s = buf_p[j]; // >= is important s.t. min is always the closest k-mer
|
||||
for (j = 0; j <= buf_pos; ++j)
|
||||
if (mzcmp(&min, &buf[j]) >= 0) min = buf[j], min_pos = j, min_s = buf_p[j];
|
||||
|
||||
if (l >= w + k - 1 && min.x != UINT64_MAX) { // write identical k-mers
|
||||
for (j = buf_pos + 1; j < w; ++j) // these two loops make sure the output is sorted
|
||||
if (mzcmp(&min, &buf[j]) == 0 && min.pos != buf[j].pos){
|
||||
kv_push(ha_mz1_t, *p, buf[j]); kv_push(uint64_t, *mt, buf_p[j]);
|
||||
}
|
||||
for (j = 0; j <= buf_pos; ++j)
|
||||
if (mzcmp(&min, &buf[j]) == 0 && min.pos != buf[j].pos){
|
||||
kv_push(ha_mz1_t, *p, buf[j]); kv_push(uint64_t, *mt, buf_p[j]);
|
||||
}
|
||||
}
|
||||
}
|
||||
if (++buf_pos == w) buf_pos = 0;
|
||||
}
|
||||
if (min.x != UINT64_MAX){
|
||||
kv_push(ha_mz1_t, *p, min); kv_push(uint64_t, *mt, min_s);
|
||||
}
|
||||
// debug_pl(str, len, w, k, is_hpc, p, hf, mt);
|
||||
if (sample_dist > w) select_mz_h(p, mt, len, sample_dist, ws, k, tl);
|
||||
if (dp_min_len > 0 && pt && mt) refine_sketch(p, pt, len, dp_min_len, dp_e, min_freq, mt);
|
||||
for (i = 0; i < (int)p->n; ++i) // populate .rid as this was keeping counts
|
||||
p->a[i].rid = rid;
|
||||
#define HA_SC_INIT(sf, HType, VType, RidBits, PosBits)\
|
||||
inline void sf##_hf_select(VType *p, int32_t si, int32_t ei, int32_t n, int32_t len, int32_t sample_dist, HType *b, int32_t force)\
|
||||
{\
|
||||
if(ei - si <= 1) return;\
|
||||
int32_t ps = si < 0? 0 : p->a[si].pos;\
|
||||
int32_t pe = ei == n? len : p->a[ei].pos;\
|
||||
int32_t j, k, st = si + 1, en = ei;\
|
||||
int32_t max_high_occ = (int32_t)((double)(pe - ps) / sample_dist + .499);\
|
||||
if (max_high_occ > MAX_MAX_HIGH_OCC)\
|
||||
max_high_occ = MAX_MAX_HIGH_OCC;\
|
||||
for (j = st, k = 0; j < en && k < max_high_occ; ++j, ++k)\
|
||||
b[k] = p->a[j], b[k].pos = j; /** b[].pos keeps the index in p->a[]**/\
|
||||
ks_heapmake_##sf##_mz(k, b); /** initialize the binomial heap**/\
|
||||
for (; j < en; ++j) { /** if there are more, choose top max_high_occ**/\
|
||||
if (sf##_mz_lt(p->a[j], b[0])) { /** then update the heap**/\
|
||||
b[0] = p->a[j], b[0].pos = j;\
|
||||
ks_heapdown_##sf##_mz(0, k, b);\
|
||||
}\
|
||||
}\
|
||||
/**ks_heapsort_mz(k, b); // sorting is not needed for now**/\
|
||||
for (j = 0; j < k; ++j)\
|
||||
if (b[j].rid < pe - ps || force)\
|
||||
p->a[b[j].pos].rid = 0;\
|
||||
}\
|
||||
static inline int sf##_mzcmp_l(const VType *p, int32_t ai, int32_t bi)\
|
||||
{\
|
||||
if(ai >= 0 && bi >= 0){\
|
||||
HType *a = &(p->a[ai]), *b = &(p->a[bi]);\
|
||||
if(a->rid > 0 && b->rid > 0) return sf##_mzcmp(a, b);\
|
||||
return (a->rid == 0) - (b->rid == 0);\
|
||||
}\
|
||||
return (ai < 0) - (bi < 0);\
|
||||
}\
|
||||
int32_t sf##_qfw(VType *p, st_mt_t *mt, int32_t n, int32_t tot_l, int32_t ws, int32_t i, int32_t *mi)\
|
||||
{\
|
||||
int32_t m, si;\
|
||||
for (si = i, (*mi) = -1; i < n; i++){\
|
||||
if(GL(*mt, i) >= ws || (i+1 < n && GL(*mt, i) < ws && GL(*mt, i+1) > ws) || \
|
||||
(i+1 == n && tot_l >= ws && GL(*mt, i) < ws)){\
|
||||
for (m = si; m <= i; m++){\
|
||||
if(!A_M(*p, m)) continue;\
|
||||
if(sf##_mzcmp_l(p, *mi, m) >= 0) (*mi) = m;\
|
||||
}\
|
||||
if((*mi) >= 0 && A_M(*p, *mi)){\
|
||||
for (m = si; m <= i; m++){\
|
||||
if(!A_M(*p, m)) continue;\
|
||||
if(sf##_mzcmp_l(p, *mi, m) == 0) mt->a[m] |= 0x100000000;\
|
||||
}\
|
||||
}\
|
||||
break;\
|
||||
}\
|
||||
}\
|
||||
return i;\
|
||||
}\
|
||||
static void sf##_select_mz_h(VType *p, st_mt_t *mt, int len, int sample_dist, int32_t w, int32_t k, int32_t tot_l)\
|
||||
{ /**for high-occ minimizers, choose up to max_high_occ in each high-occ streak**/\
|
||||
int32_t i, mi = -1, si, last0 = -1, n = (int32_t)p->n, m = 0, ws = w + k - 1;\
|
||||
if (n == 0) return;\
|
||||
assert((int64_t)(n) < (int64_t)((((uint64_t)1)<<PosBits)));\
|
||||
for (i = m = 0, last0 = -1; i <= n; ++i) {\
|
||||
if (i == n || p->a[i].rid == 0) {\
|
||||
if (i - last0 > 1) {\
|
||||
int32_t ps = last0 < 0? 0 : p->a[last0].pos;\
|
||||
int32_t pe = i == n? len : p->a[i].pos;\
|
||||
if(((int32_t)((double)(pe - ps) / sample_dist + .499)) > 0){\
|
||||
last0 = -2;\
|
||||
m++;\
|
||||
break;\
|
||||
}\
|
||||
}\
|
||||
last0 = i;\
|
||||
}\
|
||||
}\
|
||||
if (m == 0) return; /**no high-frequency k-mers; do nothing**/\
|
||||
if(last0 >= -1) goto sf##_ff;\
|
||||
i = 0;\
|
||||
i = sf##_qfw(p, mt, n, tot_l, ws, i, &mi);\
|
||||
if(i == n) goto sf##_ff;\
|
||||
for (si = 0, i++; i < n; i++){\
|
||||
for (; si < i; si++){\
|
||||
if(GL(*mt, si) + w > GL(*mt, i)) break;\
|
||||
}\
|
||||
/**a new minimum; then write the old min**/\
|
||||
if(sf##_mzcmp_l(p, i, mi) <= 0) {\
|
||||
if(A_M(*p, mi)) mt->a[mi] |= 0x100000000;\
|
||||
mi = i;\
|
||||
}/**old min has moved outside the window**/\
|
||||
else if(si > mi){\
|
||||
if(A_M(*p, mi)) mt->a[mi] |= 0x100000000;\
|
||||
for (m = si, mi = -1; m <= i; m++){\
|
||||
if(sf##_mzcmp_l(p, mi, m) >= 0) mi = m;\
|
||||
}\
|
||||
if(A_M(*p, mi)){\
|
||||
for (m = si; m <= i; m++){\
|
||||
if(!A_M(*p, m)) continue;\
|
||||
if(sf##_mzcmp_l(p, mi, m) == 0) mt->a[m] |= 0x100000000;\
|
||||
}\
|
||||
}\
|
||||
}\
|
||||
}\
|
||||
if(A_M(*p, mi)) mt->a[mi] |= 0x100000000;\
|
||||
for (i = n - 1; si < n && GL(*mt, si) + w <= tot_l + 1; si++){\
|
||||
if(si > mi){\
|
||||
if(A_M(*p, mi)) mt->a[mi] |= 0x100000000;\
|
||||
for (m = si, mi = -1; m <= i; m++){\
|
||||
if(sf##_mzcmp_l(p, mi, m) >= 0) mi = m;\
|
||||
}\
|
||||
if(A_M(*p, mi)){\
|
||||
for (m = si; m <= i; m++){\
|
||||
if(!A_M(*p, m)) continue;\
|
||||
if(sf##_mzcmp_l(p, mi, m) == 0) mt->a[m] |= 0x100000000;\
|
||||
}\
|
||||
}\
|
||||
}\
|
||||
}\
|
||||
/**dbg_boundary(p, mt, w, k, tot_l);**/\
|
||||
HType b[MAX_MAX_HIGH_OCC];\
|
||||
for (i = 0, last0 = -1; i <= n; ++i) {\
|
||||
if (i == n || p->a[i].rid == 0) {\
|
||||
if (i - last0 > 1) {\
|
||||
int32_t ps = last0 < 0? 0 : p->a[last0].pos;\
|
||||
int32_t pe = i == n? len : p->a[i].pos;\
|
||||
if(((int32_t)((double)(pe - ps) / sample_dist + .499)) > 0){\
|
||||
for (m = last0 + 1, mi = 0; m < i; ++m){\
|
||||
if(mt->a[m]&0x100000000) p->a[m].rid = 0, mi++;\
|
||||
}\
|
||||
if(mi == 0) sf##_hf_select(p, last0, i, n, len, sample_dist, b, 0);\
|
||||
}\
|
||||
}\
|
||||
last0 = i;\
|
||||
}\
|
||||
}\
|
||||
sf##_ff:\
|
||||
for (i = n = 0; i < (int32_t)p->n; ++i) /**squeeze out filtered minimizers**/\
|
||||
if (p->a[i].rid == 0)\
|
||||
p->a[n++] = p->a[i];\
|
||||
p->n = n;\
|
||||
}\
|
||||
void sf##_refine_select(VType *mz, int32_t sidx, int32_t eidx, int32_t sn, int32_t min_freq, st_mt_t *mm, int32_t *rsi, int32_t *rei)\
|
||||
{\
|
||||
int32_t n = sn, m = eidx + 1 - sidx, i, k, t, mk=-1;\
|
||||
uint64_t ix, kx, ks;\
|
||||
kv_resize(uint64_t, *mm, mm->n+n*m);\
|
||||
HType *ma = mz->a + sidx;\
|
||||
uint64_t *mmt = mm->a + mm->n;\
|
||||
/**fprintf(stderr, "[M::%s::] ==> +n: %d, m: %d, sn: %d, sidx: %d, eidx: %d\n", __func__, n, m, sn, sidx, eidx);**/\
|
||||
for (i = 0; i < n; i++) /**how many selected minimizers**/\
|
||||
{\
|
||||
for (k = 0, mk = -1; k < m; k++) /**how many minimizers in total**/\
|
||||
{\
|
||||
if((int32_t)(ma[k].rid)<min_freq) continue;\
|
||||
ks = ma[k].pos + 1 - ma[k].span; t = -1;\
|
||||
if(i > 0){\
|
||||
for (t = k-1; t >= 0 && (ma[t].pos >= ks||(int32_t)(ma[t].rid)<min_freq); t--);\
|
||||
}\
|
||||
ix = (i <= 0?0:(t<0?0xffffffff:(GMC(mmt, i-1,t,m)&0xffffffff)));\
|
||||
if(ix < 0xffffffff) ix += (ma[k].rid);\
|
||||
kx = (mk < 0?0xffffffff:(GMC(mmt, i, mk,m)&0xffffffff));\
|
||||
ks = MIN(ix, kx);\
|
||||
/**fprintf(stderr, "ks: %lu, i: %d (n-%d), k: %d (m-%d), ix: %lu, kx: %lu, t: %d, mk: %d\n", ks, i, n, k, m, ix, kx, t, mk);**/\
|
||||
if((ks&0xffffffff) == 0xffffffff) ks |= ((uint64_t)0xffffffff)<<32;\
|
||||
else if(ks == ix) ks |= (uint64_t)(i>0?(i-1)*m+t:0xffffffff)<<32;\
|
||||
else if(ks == kx) ks |= (uint64_t)(mk>=0?i*m+mk:0xffffffff)<<32;\
|
||||
GMC(mmt, i,k,m) = ks;\
|
||||
mk = k;\
|
||||
}\
|
||||
}\
|
||||
/**fprintf(stderr, "[M::%s::] ==> ++n: %d, m: %d, sn: %d, sidx: %d, eidx: %d\n", __func__, n, m, sn, sidx, eidx);**/\
|
||||
ks = (n-1)*m + mk; ix = (uint64_t)-1; kx = 0;\
|
||||
while (ks != 0xffffffff)\
|
||||
{\
|
||||
i = ks/m; k = ks%m;\
|
||||
ks = mmt[ks]>>32;\
|
||||
/**fprintf(stderr, "i: %d, k: %d, ks: %lu\n", i, k, ks);**/\
|
||||
if(ks == 0xffffffff || (int32_t)(ks/m) == (i-1)){\
|
||||
mm->a[sidx+k] = 1;\
|
||||
ix = MIN((uint64_t)k, ix); kx = MAX((uint64_t)k, kx);\
|
||||
}\
|
||||
}\
|
||||
/**debug_refine(ma, mmt, sn, n, m, (n-1)*m + mk);**/\
|
||||
if(rsi) (*rsi) = ix + sidx;\
|
||||
if(rei) (*rei) = kx + sidx;\
|
||||
}\
|
||||
void sf##_refine_sketch(VType *p, ha_pt_t *pt, int32_t rlen, int32_t dp_min_len, float er, int32_t min_freq, st_mt_t *mt)\
|
||||
{\
|
||||
/**fprintf(stderr, "[M::%s::] ==> #########10#########, rlen: %d\n", __func__, rlen);**/\
|
||||
int32_t i, n = p->n, bd, len = MIN(rlen, dp_min_len), sublen, cnt, ei, li, ri;\
|
||||
int32_t sn = len*er + 1;\
|
||||
kv_resize(uint64_t, *mt, (int64_t)p->n);\
|
||||
mt->n = p->n; memset(mt->a, 0, sizeof(uint64_t)*p->n);\
|
||||
for (i = 0; i < n; i++) p->a[i].rid = ha_pt_cnt(pt, p->a[i].x);\
|
||||
for (i = cnt = 0, bd = -1, ei = -1; i < n; i++){\
|
||||
if((int32_t)(p->a[i].rid)<min_freq) continue;\
|
||||
sublen = p->a[i].pos + 1;\
|
||||
if(sublen > len) break;\
|
||||
else ei = i;\
|
||||
if((int32_t)(p->a[i].pos + 1 - p->a[i].span) > bd){\
|
||||
bd = p->a[i].pos;\
|
||||
cnt++;\
|
||||
}\
|
||||
}\
|
||||
/**fprintf(stderr, "[M::%s::] ==> +cnt: %d, sn: %d, ei: %d, n: %d\n", __func__, cnt, sn, ei, n);**/\
|
||||
if(cnt >= sn) sf##_refine_select(p, 0, ei, sn, min_freq, mt, NULL, &li);\
|
||||
else{\
|
||||
li = i-1;\
|
||||
for (i = 0; i <= li; i++) mt->a[i] = 1;\
|
||||
}\
|
||||
if(len < rlen){\
|
||||
for (i = n-1, cnt = 0, bd = rlen+1, ei = -1; i >= 0; i--){\
|
||||
if((int32_t)(p->a[i].rid)<min_freq) continue;\
|
||||
sublen = rlen - (p->a[i].pos + 1 - p->a[i].span);\
|
||||
if(sublen > len) break;\
|
||||
else ei = i;\
|
||||
if((int32_t)(p->a[i].pos) < bd){\
|
||||
bd = p->a[i].pos + 1 - p->a[i].span;\
|
||||
cnt++;\
|
||||
}\
|
||||
}\
|
||||
/**fprintf(stderr, "[M::%s::] ==> -cnt: %d, sn: %d, ei: %d, n: %d\n", __func__, cnt, sn, ei, n);**/\
|
||||
if(cnt >= sn) sf##_refine_select(p, ei, n-1, sn, min_freq, mt, &ri, NULL);\
|
||||
else {\
|
||||
ri = i+1;\
|
||||
for (i = ri; i <= n-1; i++) mt->a[i] = 1;\
|
||||
}\
|
||||
/**fprintf(stderr, "[M::%s::] ==> --cnt: %d, sn: %d, ei: %d, n: %d\n", __func__, cnt, sn, ei, n);**/\
|
||||
if(ri - li >= 2){\
|
||||
li++; ri--;\
|
||||
sn = (p->a[ri].pos - p->a[li].pos + p->a[li].span)*er + 1;\
|
||||
for (i = li, cnt = 0, bd = -1; i <= ri; i++){\
|
||||
if((int32_t)(p->a[i].rid)<min_freq) continue;\
|
||||
if((int32_t)(p->a[i].pos + 1 - p->a[i].span) > bd){\
|
||||
bd = p->a[i].pos;\
|
||||
cnt++;\
|
||||
if(cnt >= sn) break;\
|
||||
}\
|
||||
}\
|
||||
if(cnt >= sn) sf##_refine_select(p, li, ri, sn, min_freq, mt, NULL, NULL);\
|
||||
else for (i = li; i <= ri; i++) mt->a[i] = 1;\
|
||||
}\
|
||||
}\
|
||||
/**fprintf(stderr, "[M::%s::] ==> #########20#########, p->n: %u, n: %d\n", __func__, p->n, n);**/\
|
||||
for (i = sn = 0; i < n; i++){\
|
||||
if(mt->a[i]){\
|
||||
p->a[sn] = p->a[i];\
|
||||
sn++;\
|
||||
}\
|
||||
}\
|
||||
/**if(p->n != sn) fprintf(stderr, "[M::%s::] ==> #########21#########, p->n: %u, sn: %d\n", __func__, p->n, sn);**/\
|
||||
p->n = sn;\
|
||||
}\
|
||||
/**\
|
||||
* Find symmetric (w,k)-minimizers on a DNA sequence\
|
||||
*\
|
||||
* @param str DNA sequence\
|
||||
* @param len length of $str\
|
||||
* @param w find a minimizer for every $w consecutive k-mers\
|
||||
* @param k k-mer size\
|
||||
* @param rid reference ID; will be copied to the output $p array\
|
||||
* @param is_hpc homopolymer-compressed or not\
|
||||
* @param p minimizers\
|
||||
*/\
|
||||
void sf##_ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is_hpc, VType *p, const void *hf, int sample_dist, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, ha_pt_t *pt, int min_freq, int32_t dp_min_len, float dp_e, st_mt_t *mt, int32_t ws, int32_t is_unique)\
|
||||
{ /**in default, w = 51, k = 51, is_hpc = 1**/\
|
||||
extern void *ha_ct_table;\
|
||||
static const HType dummy = { UINT64_MAX, (((uint64_t)1)<<RidBits) - 1, 0, 0, 0};\
|
||||
uint64_t shift1 = k - 1, mask = (1ULL<<k) - 1, kmer[4] = {0,0,0,0};\
|
||||
int i, j, l, tl = 0, buf_pos, min_pos, kmer_span = 0;\
|
||||
HType buf[256], min = dummy;\
|
||||
uint32_t buf_p[256], min_s = (uint32_t)-1;\
|
||||
tiny_queue_t tq;\
|
||||
assert(len > 0 && (int64_t)(len) < (int64_t)((((uint64_t)1)<<PosBits)) && (int64_t)(rid) < (int64_t)((((uint64_t)1)<<RidBits)) && (w > 0 && w < 256) && (k > 0 && k <= 63));\
|
||||
if (dbg_ct != NULL) dbg_ct->a.n = 0;\
|
||||
if (k_flag != NULL) {\
|
||||
kv_resize(uint8_t, k_flag->a, (uint64_t)len);\
|
||||
k_flag->a.n = len;\
|
||||
memset(k_flag->a.a, 0, k_flag->a.n);\
|
||||
}\
|
||||
memset(buf, 0xff, w * sizeof(HType));\
|
||||
memset(&tq, 0, sizeof(tiny_queue_t));\
|
||||
/**len/w is the evaluated minimizer numbers**/\
|
||||
kv_resize(HType, *p, p->n + len/w);\
|
||||
kv_resize(uint64_t, *mt, (int64_t)p->m); mt->n = p->n;\
|
||||
for (i = l = tl = buf_pos = min_pos = 0; i < len; ++i) {\
|
||||
int c = seq_nt4_table[(uint8_t)str[i]];\
|
||||
HType info = dummy;\
|
||||
if (c < 4) { /**not an ambiguous base**/\
|
||||
int z;\
|
||||
if (is_hpc) {\
|
||||
int skip_len = 1;\
|
||||
if (i + 1 < len && seq_nt4_table[(uint8_t)str[i + 1]] == c) {\
|
||||
for (skip_len = 2; i + skip_len < len; ++skip_len)\
|
||||
if (seq_nt4_table[(uint8_t)str[i + skip_len]] != c)\
|
||||
break;\
|
||||
i += skip_len - 1; /**put $i at the end of the current homopolymer run**/\
|
||||
}\
|
||||
tq_push(&tq, skip_len);\
|
||||
kmer_span += skip_len;\
|
||||
/**how many bases that are covered by this HPC k-mer\
|
||||
kmer_span includes at most k HPC elements**/\
|
||||
if (tq.count > k) kmer_span -= tq_shift(&tq);\
|
||||
} else kmer_span = l + 1 < k? l + 1 : k;\
|
||||
/**kmer_span should be used for HPC k-mer\
|
||||
non-HPC k-mer, kmer_span should be k\
|
||||
kmer_span is used to calculate anchor pos on reverse complementary strand**/\
|
||||
if (k_flag != NULL) k_flag->a.a[i] = 1;/**lable all useful base, which are not ignored by HPC**/\
|
||||
kmer[0] = (kmer[0] << 1 | (c&1)) & mask;/**forward k-mer**/\
|
||||
kmer[1] = (kmer[1] << 1 | (c>>1)) & mask;\
|
||||
kmer[2] = kmer[2] >> 1 | (uint64_t)(1 - (c&1)) << shift1; /**reverse k-mer**/\
|
||||
kmer[3] = kmer[3] >> 1 | (uint64_t)(1 - (c>>1)) << shift1;\
|
||||
if (kmer[1] == kmer[3]) continue; /** skip "symmetric k-mers" as we don't know it strand**/\
|
||||
z = kmer[1] < kmer[3]? 0 : 1; /** strand**/\
|
||||
++l; tl++;\
|
||||
if (l >= k && kmer_span < 256) {\
|
||||
uint64_t y;\
|
||||
int32_t cnt, filtered;\
|
||||
y = yak_hash64_64(kmer[z<<1|0]) + yak_hash64_64(kmer[z<<1|1]);\
|
||||
cnt = hf? ha_ft_cnt(hf, y) : 0;\
|
||||
filtered = (cnt >= 1<<28);\
|
||||
if(is_unique){\
|
||||
filtered = (cnt < is_unique);\
|
||||
cnt = (cnt == is_unique? 0:cnt);\
|
||||
}\
|
||||
if (dbg_ct != NULL) kv_push(uint64_t, dbg_ct->a, ((((uint64_t)(query_ct_index(ha_ct_table, y))<<1)|filtered)<<32)|(uint64_t)(i));\
|
||||
if (!filtered) info.x = y, info.rid = cnt, info.pos = i, info.rev = z, info.span = kmer_span; /** initially ha_mz1_t::rid keeps the k-mer count**/\
|
||||
if (k_flag != NULL) k_flag->a.a[i]++;\
|
||||
if (k_flag != NULL && filtered > 0) k_flag->a.a[i]++;\
|
||||
}\
|
||||
} else l = 0, tq.count = tq.front = 0, kmer_span = 0;\
|
||||
buf[buf_pos] = info; /**need to do this here as appropriate buf_pos and buf[buf_pos] are needed below**/\
|
||||
buf_p[buf_pos] = l;\
|
||||
if (l == w + k - 1 && min.x != UINT64_MAX) { /**special case for the first window - because identical k-mers are not stored yet**/\
|
||||
for (j = buf_pos + 1; j < w; ++j){\
|
||||
if (sf##_mzcmp(&min, &buf[j]) == 0 && buf[j].pos != min.pos){\
|
||||
kv_push(HType, *p, buf[j]); kv_push(uint64_t, *mt, buf_p[j]);\
|
||||
}\
|
||||
}\
|
||||
for (j = 0; j < buf_pos; ++j){\
|
||||
if (sf##_mzcmp(&min, &buf[j]) == 0 && buf[j].pos != min.pos){\
|
||||
kv_push(HType, *p, buf[j]); kv_push(uint64_t, *mt, buf_p[j]);\
|
||||
}\
|
||||
}\
|
||||
}\
|
||||
/**\
|
||||
* There are three cases:\
|
||||
* 1. info.x <= min.x, means info is a new minimizer\
|
||||
* 2. info.x > min.x, info is not a new minimizer\
|
||||
* (1) buf_pos != min_pos, do nothing\
|
||||
* (2) buf_pos == min_pos, means current minimizer has moved outside the window\
|
||||
* **/\
|
||||
/**three cases: 1.**/\
|
||||
if (sf##_mzcmp(&min, &info) >= 0) { /**a new minimum; then write the old min**/\
|
||||
if (l >= w + k && min.x != UINT64_MAX){\
|
||||
kv_push(HType, *p, min); kv_push(uint64_t, *mt, min_s);\
|
||||
}\
|
||||
min = info, min_pos = buf_pos, min_s = buf_p[buf_pos];\
|
||||
} else if (buf_pos == min_pos) { /**old min has moved outside the window**/\
|
||||
if (l >= w + k - 1 && min.x != UINT64_MAX){\
|
||||
kv_push(HType, *p, min); kv_push(uint64_t, *mt, min_s);\
|
||||
}\
|
||||
/**buf_pos == min_pos, means current minimizer has moved outside the window\
|
||||
so for now we need to find a new minimizer at the current window (w k-mers)**/\
|
||||
for (j = buf_pos + 1, min = dummy; j < w; ++j) /**the two loops are necessary when there are identical k-mers**/\
|
||||
if (sf##_mzcmp(&min, &buf[j]) >= 0) min = buf[j], min_pos = j, min_s = buf_p[j]; /** >= is important s.t. min is always the closest k-mer**/\
|
||||
for (j = 0; j <= buf_pos; ++j)\
|
||||
if (sf##_mzcmp(&min, &buf[j]) >= 0) min = buf[j], min_pos = j, min_s = buf_p[j];\
|
||||
if (l >= w + k - 1 && min.x != UINT64_MAX) { /**write identical k-mers**/\
|
||||
for (j = buf_pos + 1; j < w; ++j) /**these two loops make sure the output is sorted**/\
|
||||
if (sf##_mzcmp(&min, &buf[j]) == 0 && min.pos != buf[j].pos){\
|
||||
kv_push(HType, *p, buf[j]); kv_push(uint64_t, *mt, buf_p[j]);\
|
||||
}\
|
||||
for (j = 0; j <= buf_pos; ++j)\
|
||||
if (sf##_mzcmp(&min, &buf[j]) == 0 && min.pos != buf[j].pos){\
|
||||
kv_push(HType, *p, buf[j]); kv_push(uint64_t, *mt, buf_p[j]);\
|
||||
}\
|
||||
}\
|
||||
}\
|
||||
if (++buf_pos == w) buf_pos = 0;\
|
||||
}\
|
||||
if (min.x != UINT64_MAX){\
|
||||
kv_push(HType, *p, min); kv_push(uint64_t, *mt, min_s);\
|
||||
}\
|
||||
/**debug_pl(str, len, w, k, is_hpc, p, hf, mt);**/\
|
||||
if (sample_dist > w) sf##_select_mz_h(p, mt, len, sample_dist, ws, k, tl);\
|
||||
if (dp_min_len > 0 && pt && mt) sf##_refine_sketch(p, pt, len, dp_min_len, dp_e, min_freq, mt);\
|
||||
for (i = 0; i < (int)p->n; ++i) /**populate .rid as this was keeping counts**/\
|
||||
p->a[i].rid = rid;\
|
||||
}
|
||||
|
||||
HA_SC_INIT(mz1, ha_mz1_t, ha_mz1_v, 28, 27)
|
||||
HA_SC_INIT(mz2, ha_mzl_t, ha_mzl_v, 31, 32)
|
||||
Reference in New Issue
Block a user