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chhylp123
2022-01-17 18:29:48 -05:00
parent 7af0d85258
commit 0ce5a7ba5b
18 changed files with 2884 additions and 385 deletions
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sketch.cpp
+21 -20
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@@ -6,6 +6,7 @@
#include "htab.h"
#include "ksort.h"
#include "Correct.h"
#include "kalloc.h"
#define MAX_HIGH_OCC 8 // TODO: don't hard code if we need to tune this parameter
#define MAX_MAX_HIGH_OCC 16
@@ -327,11 +328,11 @@ static void sf##_select_mz_h(VType *p, st_mt_t *mt, int len, int sample_dist, in
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)\
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, void *km)\
{\
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);\
kv_resize_km(km, 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);**/\
@@ -372,12 +373,12 @@ void sf##_refine_select(VType *mz, int32_t sidx, int32_t eidx, int32_t sn, int32
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)\
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, void *km)\
{\
/**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);\
kv_resize_km(km, 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++){\
@@ -391,7 +392,7 @@ void sf##_refine_sketch(VType *p, ha_pt_t *pt, int32_t rlen, int32_t dp_min_len,
}\
}\
/**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);\
if(cnt >= sn) sf##_refine_select(p, 0, ei, sn, min_freq, mt, NULL, &li, km);\
else{\
li = i-1;\
for (i = 0; i <= li; i++) mt->a[i] = 1;\
@@ -408,7 +409,7 @@ void sf##_refine_sketch(VType *p, ha_pt_t *pt, int32_t rlen, int32_t dp_min_len,
}\
}\
/**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);\
if(cnt >= sn) sf##_refine_select(p, ei, n-1, sn, min_freq, mt, &ri, NULL, km);\
else {\
ri = i+1;\
for (i = ri; i <= n-1; i++) mt->a[i] = 1;\
@@ -425,7 +426,7 @@ void sf##_refine_sketch(VType *p, ha_pt_t *pt, int32_t rlen, int32_t dp_min_len,
if(cnt >= sn) break;\
}\
}\
if(cnt >= sn) sf##_refine_select(p, li, ri, sn, min_freq, mt, NULL, NULL);\
if(cnt >= sn) sf##_refine_select(p, li, ri, sn, min_freq, mt, NULL, NULL, km);\
else for (i = li; i <= ri; i++) mt->a[i] = 1;\
}\
}\
@@ -450,7 +451,7 @@ void sf##_refine_sketch(VType *p, ha_pt_t *pt, int32_t rlen, int32_t dp_min_len,
* @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)\
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, void *km)\
{ /**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};\
@@ -462,15 +463,15 @@ void sf##_ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is
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);\
kv_resize_km(km, 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;\
kv_resize_km(km, HType, *p, p->n + len/w);\
kv_resize_km(km, 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;\
@@ -511,7 +512,7 @@ void sf##_ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is
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 (dbg_ct != NULL) kv_push_km(km, 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]++;\
@@ -522,12 +523,12 @@ void sf##_ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is
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]);\
kv_push_km(km, HType, *p, buf[j]); kv_push_km(km, 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]);\
kv_push_km(km, HType, *p, buf[j]); kv_push_km(km, uint64_t, *mt, buf_p[j]);\
}\
}\
}\
@@ -541,12 +542,12 @@ void sf##_ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is
/**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);\
kv_push_km(km, HType, *p, min); kv_push_km(km, 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);\
kv_push_km(km, HType, *p, min); kv_push_km(km, 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)**/\
@@ -557,22 +558,22 @@ void sf##_ha_sketch(const char *str, int len, int w, int k, uint32_t rid, int is
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]);\
kv_push_km(km, HType, *p, buf[j]); kv_push_km(km, 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]);\
kv_push_km(km, HType, *p, buf[j]); kv_push_km(km, 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);\
kv_push_km(km, HType, *p, min); kv_push_km(km, 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);\
if (dp_min_len > 0 && pt && mt) sf##_refine_sketch(p, pt, len, dp_min_len, dp_e, min_freq, mt, km);\
for (i = 0; i < (int)p->n; ++i) /**populate .rid as this was keeping counts**/\
p->a[i].rid = rid;\
}