mirror of
https://github.com/chhylp123/hifiasm.git
synced 2026-10-03 14:18:12 +08:00
better seeding
This commit is contained in:
chhylp123
+410
-111
@@ -229,7 +229,7 @@ inline void hf_select(ha_mz1_v *p, int32_t si, int32_t ei, int32_t n, int32_t le
|
||||
p->a[b[j].pos].rid = 0;
|
||||
}
|
||||
|
||||
static void select_mz(ha_mz1_v *p, int len, int sample_dist, int32_t dp_min_len)
|
||||
void select_mz(ha_mz1_v *p, int len, int sample_dist, int32_t dp_min_len)
|
||||
{ // for high-occ minimizers, choose up to max_high_occ in each high-occ streak
|
||||
int32_t i, last0 = -1, n = (int32_t)p->n, m = 0, nw[2], min_len;
|
||||
ha_mz1_t b[MAX_MAX_HIGH_OCC]; // this is to avoid a heap allocation
|
||||
@@ -289,6 +289,288 @@ static void select_mz(ha_mz1_v *p, int len, int sample_dist, int32_t dp_min_len)
|
||||
p->n = n;
|
||||
}
|
||||
|
||||
static inline int mzcmp_l(const ha_mz1_v *p, int32_t ai, int32_t bi)
|
||||
{
|
||||
if(ai >= 0 && bi >= 0){
|
||||
ha_mz1_t *a = &(p->a[ai]), *b = &(p->a[bi]);
|
||||
if(a->rid > 0 && b->rid > 0) return mzcmp(a, b);
|
||||
return (a->rid == 0) - (b->rid == 0);
|
||||
}
|
||||
return (ai < 0) - (bi < 0);
|
||||
}
|
||||
|
||||
#define GL(x, i) ((int64_t)((uint32_t)((x).a[(i)])))
|
||||
#define A_M(p, i) ((i) >= 0 && (p).a[(i)].rid > 0)
|
||||
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)
|
||||
{
|
||||
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(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(mzcmp_l(p, *mi, m) == 0) mt->a[m] |= 0x100000000;
|
||||
}
|
||||
}
|
||||
break;
|
||||
}
|
||||
}
|
||||
return i;
|
||||
}
|
||||
|
||||
void dbg_boundary(ha_mz1_v *p, st_mt_t *mt, int32_t w, int32_t k, int32_t tot_l)
|
||||
{
|
||||
if(tot_l < w + k -1) return;
|
||||
int32_t i, m, n = p->n, s, a;
|
||||
for (i = 0; i < n; i++){
|
||||
if(GL(*mt, i) >= w+k-1){
|
||||
for (m = s = a = 0; m <= i; m++){
|
||||
if(!A_M(*p, m)) continue;
|
||||
if(GL(*mt, m) <= w+k-1){
|
||||
a++;
|
||||
if(mt->a[m]&0x100000000) s++;
|
||||
}
|
||||
}
|
||||
if(a > 0 && s == 0){
|
||||
fprintf(stderr, "\nERROR1, s: %d, n: %d, tot_l: %d, end_l: %ld\n", s, n, tot_l, GL(*mt, i));
|
||||
for (m = s = a = 0; m <= i; m++){
|
||||
if(!A_M(*p, m)) continue;
|
||||
if(GL(*mt, m) <= w+k-1){
|
||||
fprintf(stderr, "lp: %ld\n", GL(*mt, m));
|
||||
a++;
|
||||
if(mt->a[m]&0x100000000) s++;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
break;
|
||||
}
|
||||
}
|
||||
if(i == n){
|
||||
for (m = s = a = 0; m < n; m++){
|
||||
if(!A_M(*p, m)) continue;
|
||||
if(GL(*mt, m) <= w+k-1){
|
||||
a++;
|
||||
if(mt->a[m]&0x100000000) s++;
|
||||
}
|
||||
}
|
||||
if(a > 0 && s == 0) fprintf(stderr, "ERROR2\n");
|
||||
}
|
||||
|
||||
for (i = n-1; i >= 0; i--)
|
||||
{
|
||||
if (GL(*mt, i) + w <= tot_l + 1) {
|
||||
for (m = i, s = a = 0; m < n; m++){
|
||||
if(!A_M(*p, m)) continue;
|
||||
if(GL(*mt, m) + w >= tot_l + 1){
|
||||
a++;
|
||||
if(mt->a[m]&0x100000000) s++;
|
||||
}
|
||||
}
|
||||
if(a > 0 && s == 0) {
|
||||
fprintf(stderr, "\nERROR3, s: %d, n: %d, tot_l: %d, end_l: %ld\n", s, n, tot_l, GL(*mt, i));
|
||||
for (m = i, s = a = 0; m < n; m++){
|
||||
if(!A_M(*p, m)) continue;
|
||||
if(GL(*mt, m) + w >= tot_l + 1){
|
||||
fprintf(stderr, "lp: %ld\n", GL(*mt, m));
|
||||
a++;
|
||||
if(mt->a[m]&0x100000000) s++;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if(i < 0){
|
||||
for (m = s = a = 0; m < n; m++){
|
||||
if(!A_M(*p, m)) continue;
|
||||
if(GL(*mt, m) + w >= tot_l + 1){
|
||||
a++;
|
||||
if(mt->a[m]&0x100000000) s++;
|
||||
}
|
||||
}
|
||||
if(a > 0 && s == 0) fprintf(stderr, "ERROR4\n");
|
||||
}
|
||||
}
|
||||
|
||||
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)
|
||||
{ // 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(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
|
||||
|
||||
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 ff;
|
||||
i = 0;
|
||||
i = qfw(p, mt, n, tot_l, ws, i, &mi);
|
||||
if(i == n) goto 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(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(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;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
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;
|
||||
tiny_queue_t tq;
|
||||
memset(&tq, 0, sizeof(tiny_queue_t));
|
||||
uint64_t shift1 = k - 1, mask = (1ULL<<k) - 1, kmer[4] = {0,0,0,0};
|
||||
|
||||
for (i = l = dbi = 0; i < len; ++i) {
|
||||
int c = seq_nt4_table[(uint8_t)str[i]];
|
||||
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
|
||||
|
||||
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;
|
||||
|
||||
if (l >= k && kmer_span < 256) {
|
||||
uint64_t y;
|
||||
int32_t cnt;
|
||||
y = yak_hash64_64(kmer[z<<1|0]) + yak_hash64_64(kmer[z<<1|1]);
|
||||
cnt = hf? ha_ft_cnt(hf, y) : 0;
|
||||
|
||||
for (dbi = 0; dbi < mt->n; dbi++)
|
||||
{
|
||||
if(p->a[dbi].x == y && p->a[dbi].rid == cnt && p->a[dbi].pos == i && p->a[dbi].rev == z && p->a[dbi].span == kmer_span)
|
||||
{
|
||||
if(l != (int)mt->a[dbi]) fprintf(stderr, "ERROR\n");
|
||||
dbcnt++;
|
||||
}
|
||||
}
|
||||
}
|
||||
} else l = 0, tq.count = tq.front = 0, kmer_span = 0;
|
||||
}
|
||||
|
||||
if(dbcnt != mt->n) fprintf(stderr, "ERROR\n");
|
||||
if(mt->n != (int)p->n) fprintf(stderr, "ERROR\n");
|
||||
for (dbi = 1; dbi < mt->n; dbi++)
|
||||
{
|
||||
if(p->a[dbi].pos <= p->a[dbi-1].pos || (int)mt->a[dbi] <= (int)mt->a[dbi-1])
|
||||
{
|
||||
fprintf(stderr, "ERROR\n");
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Find symmetric (w,k)-minimizers on a DNA sequence
|
||||
*
|
||||
@@ -300,123 +582,140 @@ static void select_mz(ha_mz1_v *p, int len, int sample_dist, int32_t dp_min_len)
|
||||
* @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)
|
||||
{ ///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 };
|
||||
uint64_t shift1 = k - 1, mask = (1ULL<<k) - 1, kmer[4] = {0,0,0,0};
|
||||
int i, j, l, buf_pos, min_pos, kmer_span = 0;
|
||||
ha_mz1_t buf[256], min = dummy;
|
||||
tiny_queue_t tq;
|
||||
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)
|
||||
{ ///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;
|
||||
|
||||
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);
|
||||
}
|
||||
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);
|
||||
}
|
||||
|
||||
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);
|
||||
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 = 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
|
||||
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
|
||||
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;
|
||||
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 (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;
|
||||
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 (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;
|
||||
|
||||
//for non-HPC k-mer, l = i; but for HPC k-mer, l is always less than i
|
||||
//i is the real base iterator, while l is the HPC base iterator
|
||||
//only if l >= k, info is a useful minimizer (ha_mz1_t.x != UINT64_MAX)
|
||||
//but even if l < k, infor is still stored into buf
|
||||
buf[buf_pos] = info; // need to do this here as appropriate buf_pos and buf[buf_pos] are needed below
|
||||
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]);
|
||||
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]);
|
||||
}
|
||||
/**
|
||||
* 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 (info.x <= min.x) { // a new minimum; then write the old min
|
||||
if (l >= w + k && min.x != UINT64_MAX) kv_push(ha_mz1_t, *p, min);
|
||||
min = info, min_pos = 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);
|
||||
///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.x = UINT64_MAX; 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; // >= 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;
|
||||
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]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
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]);
|
||||
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]);
|
||||
}
|
||||
}
|
||||
if (++buf_pos == w) buf_pos = 0;
|
||||
}
|
||||
if (min.x != UINT64_MAX)
|
||||
kv_push(ha_mz1_t, *p, min);
|
||||
if (sample_dist > w) select_mz(p, len, MAX_HIGH_OCC, dp_min_len);
|
||||
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;
|
||||
/**
|
||||
* 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(p, len, MAX_HIGH_OCC, dp_min_len);
|
||||
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;
|
||||
}
|
||||
|
||||
void ha_sketch_worse(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)
|
||||
|
||||
Reference in New Issue
Block a user