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fix memory issue

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chhylp123
2024-10-13 18:47:05 -04:00
parent e8b18560a5
commit 49dd83df2a
6 changed files with 235 additions and 33 deletions
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CommandLines.h
+1 -1
View File
@@ -5,7 +5,7 @@
#include <pthread.h>
#include <stdint.h>
#define HA_VERSION "0.20.0-r631"
#define HA_VERSION "0.20.0-r639"
#define VERBOSE 0
Correct.cpp
+18 -3
View File
@@ -16753,12 +16753,14 @@ char* qstr, char* tstr, bit_extz_t *exz, double e_rate, int64_t ql, int64_t tl,
uint64_t gen_hc_fast_cigar0(overlap_region *z, Candidates_list *cl, uint64_t wl, All_reads *rref, char* qstr, UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, uint64_t rid, int64_t h_khit, int64_t *re)
{
int64_t ch_idx = z->shared_seed, ch_n;
int64_t i, tl, id = z->y_id, m, tot_e, aln;
int64_t i, tl, id = z->y_id, m, tot_e, aln, xe, ye;
k_mer_hit *ch_a = cl->list + ch_idx;
tl = Get_READ_LENGTH((*rref), id);
for (i = ch_idx; i < cl->length && cl->list[i].readID == cl->list[ch_idx].readID; i++); ch_n = i-ch_idx;
if(ch_n <= 0) return 0;
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
// fprintf(stderr, "[M::%s::rid->%ld] utg%.6dl(%c), z::[%u, %u)\n",
// __func__, rid, (int32_t)z->y_id+1, "+-"[z->y_pos_strand], z->x_pos_s, z->x_pos_e+1);
@@ -16799,7 +16801,9 @@ uint64_t gen_hc_fast_cigar0(overlap_region *z, Candidates_list *cl, uint64_t wl,
aux_n = z->w_list.n;
for (i = tot_e = aln = 0; i < aux_n; i++) {
if(is_ualn_win(z->w_list.a[i])) {
tot_e += z->w_list.a[i].x_end + 1 - z->w_list.a[i].x_start;
xe = z->w_list.a[i].x_end + 1 - z->w_list.a[i].x_start;
ye = z->w_list.a[i].y_end + 1 - z->w_list.a[i].y_start;
tot_e += ((xe >= ye)?(xe):(ye));
} else {
tot_e += z->w_list.a[i].error; aln += z->w_list.a[i].x_end + 1 - z->w_list.a[i].x_start;
}
@@ -23495,6 +23499,9 @@ void gen_hc_r_alin_nec(overlap_region_alloc* ol, Candidates_list *cl, All_reads
resize_UC_Read(tu, bs<<1);
// fprintf(stderr, "[M::%s] window_length::%lld\n", __func__, w.window_length);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
for (i = k = 0; i < ol->length; i++) {
z = &(ol->list[i]);
if(z->is_match != 1) {
@@ -23514,11 +23521,19 @@ void gen_hc_r_alin_nec(overlap_region_alloc* ol, Candidates_list *cl, All_reads
if (rr > err) continue;
z->non_homopolymer_errors = re;
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
if(!gen_hc_fast_cigar(z, cl, rref, w.window_length, qu->seq, tu, exz, aux_o, e_rate, ql, rid, khit, &re)) continue;
// if(z->x_id == 3196 && z->y_id == 3199) fprintf(stderr, "-1-[M::%s] tid::%u\t%.*s\trr::%f\tre::%ld\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), rr, re);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
reassign_gaps(z, aux_o, qu->seq, ql, NULL, -1, rref, tu, buf);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
}
// if(z->x_id == 3196 && z->y_id == 3199) fprintf(stderr, "-2-[M::%s] tid::%u\t%.*s\trr::%f\tre::%u\n", __func__, z->y_id, (int)Get_NAME_LENGTH(R_INF, z->y_id), Get_NAME(R_INF, z->y_id), rr, z->non_homopolymer_errors);
Hash_Table.cpp
+14 -8
View File
@@ -2108,7 +2108,7 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
Chain_Data* dp, overlap_region_alloc* res, int64_t max_skip, int64_t max_iter,
int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate,
uint32_t xid, int64_t xl, int64_t yl, int64_t quick_check, uint32_t apend_be,
int64_t gen_cigar, int64_t enable_mcopy, double mcopy_rate, int64_t mcopy_khit_cutoff,
int64_t gen_cigar, int64_t mcopy_num, double mcopy_rate, int64_t mcopy_khit_cutoff,
int64_t khit_n)
{
if(a_n <= 0) return 0;
@@ -2186,19 +2186,21 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
}
for (i = msc_i, cL = 0; i >= 0; i = p[i]) { ii[i] = 1; t[cL++] = i;}///label the best chain
if((movl < xl) && enable_mcopy/**(movl < yl)**/) {
if(mcopy_num > 1) {
if(cL >= mcopy_khit_cutoff) {///if there are too few k-mers, disable mcopy
msc -= plus; min_sc = msc*mcopy_rate/**0.2**/; ii[msc_i] = 0;
for (i = ch_n = 0; i < a_n; ++i) {///make all f[] positive
f[i] -= plus; if(i >= ch_n) t[i] = 0;
if((!(ii[i])) && (f[i] >= min_sc)) {
if((!(ii[i])) && (f[i] >= min_sc)) {///!(ii[i]): skip the best chain
t[ch_n] = ((uint64_t)f[i])<<32; t[ch_n] += (i<<1); ch_n++;
}
}
if(ch_n > 1) {
int64_t n_v, n_v0, ni, n_u, n_u0 = res->length;
radix_sort_hc64i(t, t + ch_n);
for (k = ch_n-1, n_v = n_u = 0; k >= 0; --k) {
for (k = ch_n-1, n_v = n_u = 0; k >= 0 && n_u < mcopy_num; --k) {
n_v0 = n_v;
for (i = ((uint32_t)t[k])>>1; i >= 0 && (t[i]&1) == 0; ) {
ii[n_v++] = i; t[i] |= 1; i = p[i];
@@ -2209,10 +2211,11 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
kv_pushp_ol(overlap_region, (*res), &z);
push_ovlp_chain_qgen(z, xid, xl, yl, sc+plus, &(a[ii[n_v-1]]), &(a[ii[n_v0]]));
///mcopy_khit_cutoff <= 1: disable the mcopy_khit_cutoff filtering, for the realignment
if((mcopy_khit_cutoff <= 1) || ((z->x_pos_e+1-z->x_pos_s) <= (movl<<2))) {
// if((mcopy_khit_cutoff <= 1) || ((z->x_pos_e+1-z->x_pos_s) <= (movl<<2))) {
if((!n_u) || (n_v - n_v0 > 1)) {
z->align_length = n_v-n_v0; z->x_id = n_v0;
n_u++;
} else {///non-best is too long
} else {///non-best is tiny
res->length--; n_v = n_v0;
}
} else {
@@ -2220,8 +2223,8 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
}
}
if(n_u > 1) ks_introsort_or_sss(n_u, res->list + n_u0);
res->length = n_u0 + filter_non_ovlp_xchains(res->list + n_u0, n_u, &n_v);
// if(n_u > 1) ks_introsort_or_sss(n_u, res->list + n_u0);
// res->length = n_u0 + filter_non_ovlp_xchains(res->list + n_u0, n_u, &n_v);
n_u = res->length;
if(n_u > n_u0 + 1) {
kv_resize_cl(k_mer_hit, (*cl), (n_v+cl->length));
@@ -2264,6 +2267,9 @@ uint64_t lchain_qdp_mcopy_fast(Candidates_list *cl, int64_t a_idx, int64_t a_n,
}
}
}
///a[] has been sorted by self_offset
// i = msc_i; cL = 0;
// while (i >= 0) {t[cL++] = i; i = p[i];}
anchor.cpp
+4 -4
View File
@@ -1920,7 +1920,7 @@ void lchain_qgen_mcopy(Candidates_list* cl, overlap_region_alloc* ol, uint32_t r
void lchain_qgen_mcopy_fast(Candidates_list* cl, overlap_region_alloc* ol, uint32_t rid, uint64_t rl, All_reads* rdb,
uint32_t apend_be, uint64_t max_n_chain, int64_t max_skip, int64_t max_iter,
int64_t max_dis, double chn_pen_gap, double chn_pen_skip, double bw_rate, int64_t quick_check,
uint32_t gen_off, int64_t enable_mcopy, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut, st_mt_t *sp)
uint32_t gen_off, int64_t mcopy_num, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut, st_mt_t *sp)
{
// fprintf(stderr, "+[M::%s] chain_cutoff::%u\n", __func__, chain_cutoff);
uint64_t i, k, l, m, cn = cl->length, yid, ol0, lch; overlap_region *r, t; ///srt = 0
@@ -1931,7 +1931,7 @@ void lchain_qgen_mcopy_fast(Candidates_list* cl, overlap_region_alloc* ol, uint3
if(cl->list[l].readID != rid) {
yid = cl->list[l].readID; ol0 = ol->length;
m += lchain_qdp_mcopy_fast(cl, l, k-l, m, &(cl->chainDP), ol, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_rate,
rid, rl, Get_READ_LENGTH((*rdb), yid), quick_check, apend_be, gen_off, enable_mcopy, mcopy_rate, mcopy_khit_cut, 1);
rid, rl, Get_READ_LENGTH((*rdb), yid), quick_check, apend_be, gen_off, mcopy_num, mcopy_rate, mcopy_khit_cut, 1);
if((chain_cutoff >= 2) && (!lch)) {
for (i = ol0; (i<ol->length) && (!lch); i++) {
if(ol->list[i].align_length < chain_cutoff) lch = 1;
@@ -2224,7 +2224,7 @@ void ul_map_lchain(ha_abufl_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t
}
void h_ec_lchain(ha_abuf_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, All_reads *rref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres,
int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off, int64_t enable_mcopy, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut)
int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off, int64_t mcopy_num, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut)
{
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
@@ -2235,7 +2235,7 @@ void h_ec_lchain(ha_abuf_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz
// lchain_gen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
// lchain_qgen(cl, overlap_list, rid, rl, NULL, uref, apend_be, f_cigar, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off);
///no need to sort here, overlap_list has been sorted at lchain_gen
lchain_qgen_mcopy_fast(cl, overlap_list, rid, rl, rref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off, enable_mcopy, mcopy_rate, chain_cutoff, mcopy_khit_cut, sp);
lchain_qgen_mcopy_fast(cl, overlap_list, rid, rl, rref, apend_be, max_n_chain, max_skip, max_iter, max_dis, chn_pen_gap, chn_pen_skip, bw_thres, quick_check, gen_off, mcopy_num, mcopy_rate, chain_cutoff, mcopy_khit_cut, sp);
}
void h_ec_lchain_amz(ha_abuf_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, All_reads *rref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres,
ecovlp.cpp
+157 -8
View File
@@ -31,7 +31,7 @@ typedef struct {size_t n, m; char *a; UC_Read z;} sl_v;
void h_ec_lchain(ha_abuf_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, All_reads *rref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres,
int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off, int64_t enable_mcopy, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut);
int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off, int64_t mcopy_num, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut);
void h_ec_lchain_amz(ha_abuf_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, All_reads *rref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres,
int max_n_chain, int apend_be, kvec_t_u8_warp* k_flag, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ, uint32_t is_accurate, uint32_t gen_off, int64_t enable_mcopy, double mcopy_rate, uint32_t chain_cutoff, uint32_t mcopy_khit_cut);
void h_ec_lchain_re_gen(ha_abuf_t *ab, uint32_t rid, char* rs, uint64_t rl, uint64_t mz_w, uint64_t mz_k, ha_pt_t *ha_idx, All_reads *rref, overlap_region_alloc *overlap_list, Candidates_list *cl, double bw_thres,
@@ -173,7 +173,7 @@ void prt_chain(overlap_region_alloc *o)
overlap_region *fetch_aux_ovlp(overlap_region_alloc* ol) /// exactly same to gen_aux_ovlp
{
if (ol->length + 1 > ol->size) {
if (ol->length + 1 >= ol->size) {
uint64_t sl = ol->size;
ol->size = ol->length + 1;
kroundup64(ol->size);
@@ -181,6 +181,10 @@ overlap_region *fetch_aux_ovlp(overlap_region_alloc* ol) /// exactly same to gen
/// need to set new space to be 0
memset(ol->list + sl, 0, sizeof(overlap_region)*(ol->size - sl));
}
///debug for memory
// if(ol->length + 1 >= ol->size) {
// fprintf(stderr, "[M::%s] length::%lu, size::%lu\n", __func__, ol->length, ol->size);
// }
return &(ol->list[ol->length+1]);
}
@@ -2723,6 +2727,7 @@ void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *
{
if(ol->length <= 0) return;
// uint64_t k, l, i, s, m, mm_k, *ei, en, *oi, on, tid, trev, nec; int64_t sc, mm_sc, plus, minus; overlap_region *z, t; ma_hit_t *p;
uint64_t k, i, m, *ei, en, *oi, on, tid, trev, nec; overlap_region *z; ma_hit_t *p;
srt->n = 0;
for (k = 0; k < in->length; k++) {
@@ -2735,6 +2740,9 @@ void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *
if(!(srt->n)) {
gen_hc_r_alin(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf);
} else {
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
kv_resize(uint64_t, *srt, (srt->n + ol->length));
ei = srt->a; en = srt->n; oi = srt->a + srt->n; on = ol->length;
for (k = 0; k < on; k++) {
@@ -2761,9 +2769,48 @@ void gen_hc_r_alin_ea(overlap_region_alloc* ol, Candidates_list *cl, All_reads *
}
}
}
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
if(on > nec) gen_hc_r_alin_nec(ol, cl, rref, qu, tu, exz, aux_o, e_rate, wl, rid, khit, move_gap, buf);
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
}
/**
if(ol->length > 1) {///for duplicated chains
overlap_region_sort_y_id(ol->list, ol->length);
for (k = 1, l = m = 0; k <= ol->length; k++) {
if(k == ol->length || ol->list[k].y_id != ol->list[l].y_id) {
// fprintf(stderr, "\n[M::%s::tid->%u] n->%lu\n", __func__, ol->list[l].y_id, k - l);
mm_k = l;
if(k - l > 1) {
for (s = l, mm_sc = INT32_MIN, mm_k = ((uint64_t)-1); s < k; s++) {
z = &(ol->list[s]);
plus = z->x_pos_e + 1 - z->x_pos_s; minus = (z->non_homopolymer_errors) * 12;
sc = plus - minus;
if((sc > mm_sc) || ((sc == mm_sc) && ((ol->list[mm_k].x_pos_e+1-ol->list[mm_k].x_pos_s) < (z->x_pos_e+1-z->x_pos_s)))) {
mm_sc = sc; mm_k = s;
}
// fprintf(stderr, "[M::%s::%c] q::[%u, %u), t::[%u, %u), sc::%ld, err::%u, s::%lu\n", __func__, "+-"[z->y_pos_strand], z->x_pos_s, z->x_pos_e + 1, z->y_pos_s, z->y_pos_e + 1, sc, z->non_homopolymer_errors, s);
}
}
// fprintf(stderr, "[M::%s::tid->%u] mm_k::%lu\n", __func__, ol->list[l].y_id, mm_k);
if(mm_k != ((uint64_t)-1)) {
if(mm_k != m) {
t = ol->list[mm_k];
ol->list[mm_k] = ol->list[m];
ol->list[m] = t;
}
m++;
}
l = k;
}
}
ol->length = m;
}
**/
}
void prt_ovlp_sam_0(char *cm, FILE *fp, char *ref_id, int32_t ref_id_n, char *qry_id, int32_t qry_id_n, char *qry_seq, uint64_t qry_seq_n, uint64_t rs, uint64_t re, uint64_t qs, uint64_t qe, uint64_t flag, uint64_t err, bit_extz_t *ez)
@@ -2818,6 +2865,54 @@ void prt_ovlp_sam(overlap_region_alloc* ol, UC_Read* tu, char *ref_seq, int32_t
fclose(fp);
}
void dedup_chains(overlap_region_alloc* ol)
{
uint64_t k, l, s, m, mm_k, mm_m, sf; int64_t sc, mm_sc, plus, minus; overlap_region *z, t;
if(ol->length > 1) {///for duplicated chains
overlap_region_sort_y_id(ol->list, ol->length);
for (k = 1, l = m = 0; k <= ol->length; k++) {
if(k == ol->length || ol->list[k].y_id != ol->list[l].y_id) {
// fprintf(stderr, "\n[M::%s::tid->%u] n->%lu\n", __func__, ol->list[l].y_id, k - l);
mm_k = l;
if(k - l > 1) {
for (s = l, mm_sc = INT32_MIN, mm_k = ((uint64_t)-1), mm_m = 3; s < k; s++) {
z = &(ol->list[s]);
plus = z->x_pos_e + 1 - z->x_pos_s; minus = (z->non_homopolymer_errors) * 12;
sc = plus - minus;
sf = 0;
if(z->is_match < mm_m) {
sf = 1;
} else if(z->is_match == mm_m) {
if(sc > mm_sc) {
sf = 1;
} else if((sc == mm_sc) && ((z->x_pos_e+1-z->x_pos_s) > (ol->list[mm_k].x_pos_e+1-ol->list[mm_k].x_pos_s))) {
sf = 1;
}
}
if(sf) {
mm_sc = sc; mm_k = s; mm_m = z->is_match;
}
// fprintf(stderr, "[M::%s::%c] q::[%u, %u), t::[%u, %u), sc::%ld, err::%u, mm::%u, s::%lu\n", __func__, "+-"[z->y_pos_strand], z->x_pos_s, z->x_pos_e + 1, z->y_pos_s, z->y_pos_e + 1, sc, z->non_homopolymer_errors, z->is_match, s);
}
}
// fprintf(stderr, "[M::%s::tid->%u] mm_k::%lu\n", __func__, ol->list[l].y_id, mm_k);
if(mm_k != ((uint64_t)-1)) {
if(mm_k != m) {
t = ol->list[mm_k];
ol->list[mm_k] = ol->list[m];
ol->list[m] = t;
}
m++;
}
l = k;
}
}
ol->length = m;
}
}
static void worker_hap_ec(void *data, long i, int tid)
{
ec_ovec_buf_t0 *b = &(((ec_ovec_buf_t*)data)->a[tid]);
@@ -2825,7 +2920,18 @@ static void worker_hap_ec(void *data, long i, int tid)
uint32_t low_occ = asm_opt.hom_cov * HA_KMER_GOOD_RATIO;
overlap_region *aux_o = NULL; asg64_v buf0; uint32_t qlen = 0;
// if (memcmp(/**"m64062_190807_194840/180552420/ccs"**/"m64062_190803_042216/161743554/ccs", Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
/**
if((i != 1129685) && (i != 1137865) && (i != 1137917) && (i != 1140647) && (i != 1144740) && (i != 1148936) && (i != 1149134) && (i != 1151224) && (i != 1151386) && (i != 1152960) && (i != 1154846) && (i != 1154881) && (i != 1155112) &&
(i != 1156823) && (i != 1157099) && (i != 1157393) && (i != 1158300) && (i != 1158368) && (i != 1160411) && (i != 1160659) && (i != 1161458) && (i != 1163595) && (i != 1164084) && (i != 1164230) && (i != 1165050) && (i != 1168249) &&
(i != 1168304) && (i != 1168514) && (i != 1170447) && (i != 1171377) && (i != 1171387) && (i != 1172376) && (i != 1173566) && (i != 1174275) && (i != 1174434) && (i != 1174511) && (i != 1174860) && (i != 1175306) && (i != 1175314) &&
(i != 1177101) && (i != 1178196) && (i != 1178470) && (i != 1179327) && (i != 1179626) && (i != 1180357) && (i != 1181347) && (i != 1181422) && (i != 1181725) && (i != 1183135) && (i != 1183734) && (i != 1185569) && (i != 1185604) &&
(i != 1186192) && (i != 1188441) && (i != 1188487) && (i != 1189865) && (i != 1189943) && (i != 1192819) && (i != 1193133) && (i != 1196908) && (i != 1197590) && (i != 1200549) && (i != 1200757) && (i != 1205500)) return;
fprintf(stderr, "%ld\t+++\n", i);
**/
// if(i < 1100000 || i > 1400000) return;
// if(i % 100000 == 0) fprintf(stderr, "-a-[M::%s-beg] rid->%ld\n", __func__, i);
// if (memcmp("m64062_190807_194840/180552420/ccs"/**"m64062_190803_042216/161743554/ccs"**//**"m64062_190806_063919/15403289/ccs"**/, Get_NAME((R_INF), i), Get_NAME_LENGTH((R_INF),i)) == 0) {
// fprintf(stderr, "-a-[M::%s-beg] rid->%ld\n", __func__, i);
// } else {
// return;
@@ -2840,13 +2946,16 @@ static void worker_hap_ec(void *data, long i, int tid)
recover_UC_Read(&b->self_read, &R_INF, i); qlen = b->self_read.length;
h_ec_lchain(b->ab, i, b->self_read.seq, b->self_read.length, asm_opt.mz_win, asm_opt.k_mer_length, &R_INF, &b->olist, &b->clist, 0.02, asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 0, 2, /**0**/2, UINT32_MAX);
h_ec_lchain(b->ab, i, b->self_read.seq, b->self_read.length, asm_opt.mz_win, asm_opt.k_mer_length, &R_INF, &b->olist, &b->clist, 0.02, asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 3, 0.7, 2, 32);
// b->num_read_base += b->olist.length;
b->cnt[0] += b->self_read.length;
aux_o = fetch_aux_ovlp(&b->olist);///must be here
///debug for memory
// snprintf(NULL, 0, "dwn::%u\tdcn::%u", (uint32_t)aux_o->w_list.n, (uint32_t)aux_o->w_list.c.n);
// gen_hc_r_alin(&b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_ov_diff_ec, WINDOW_HC, i, E_KHIT/**asm_opt.k_mer_length**/, 1, &b->v16);
gen_hc_r_alin_ea(&b->olist, &b->clist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, aux_o, asm_opt.max_ov_diff_ec, WINDOW_HC, i, E_KHIT/**asm_opt.k_mer_length**/, 1, &b->v16, &b->v64, &(R_INF.paf[i]));
@@ -2865,6 +2974,8 @@ static void worker_hap_ec(void *data, long i, int tid)
rphase_hc(&b->olist, &R_INF, &b->hap, &b->self_read, &b->ovlp_read, &b->pidx, &b->v64, &buf0, 0, WINDOW_MAX_SIZE, b->self_read.length, 1/**, 0**/, i);
copy_asg_arr(b->sp, buf0);
dedup_chains(&b->olist);
copy_asg_arr(buf0, b->sp);
b->cnt[1] += wcns_gen(&b->olist, &R_INF, &b->self_read, &b->ovlp_read, &b->exz, &b->pidx, &b->v64, &buf0, 0, 512, b->self_read.length, 3, 0.500001, aux_o, &b->v32, &b->cns, 256, i);
copy_asg_arr(b->sp, buf0);
@@ -2947,6 +3058,10 @@ static void worker_hap_ec(void *data, long i, int tid)
**/
// exit(1);
refresh_ec_ovec_buf_t0(b, REFRESH_N);
/**
fprintf(stderr, "%ld\t---\n", i);
**/
}
uint32_t adjust_exact_match(asg16_v *in, int64_t xs0, int64_t xe0, int64_t ys0, int64_t ye0, uint64_t *rxs, uint64_t *rxe, uint64_t *rys, uint64_t *rye, uint32_t rev)
@@ -3410,7 +3525,7 @@ static void worker_hap_dc_ec_gen_new_idx(void *data, long i, int tid)
recover_UC_Read(&b->self_read, &R_INF, i);
h_ec_lchain(b->ab, i, b->self_read.seq, b->self_read.length, asm_opt.mz_win, asm_opt.k_mer_length, &R_INF, &b->olist, &b->clist, /**0.02**/0.001, asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 0, 2, /**0**/2, UINT32_MAX);
h_ec_lchain(b->ab, i, b->self_read.seq, b->self_read.length, asm_opt.mz_win, asm_opt.k_mer_length, &R_INF, &b->olist, &b->clist, /**0.02**/0.001, asm_opt.max_n_chain, 1, NULL, NULL, &(b->sp), &high_occ, &low_occ, 1, 1, 3, 0.7, 2, 32);
overlap_region_sort_y_id(b->olist.list, b->olist.length);
@@ -4119,7 +4234,7 @@ void h_ec_lchain_fast_new(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Read *tu,
{
// fprintf(stderr, "-0-[M::%s]\tnew_n::%lu\told_n::%u\n", __func__, ol->length, in0->length + in1->length);
// fprintf(stderr, "-mm-[M::%s]\tchain_cutoff::%u\n", __func__, chain_cutoff);
uint64_t on = 0, k, i, m, m0, tid, trev, is_match; ma_hit_t *oa = NULL, *p = NULL; overlap_region *z = NULL, t;
uint64_t on = 0, k, i, l, m, m0, tid, trev, is_match, is_usrt = 0; ma_hit_t *oa = NULL, *p = NULL; overlap_region *z = NULL, t;
char* rs = qu->seq; uint64_t rl = qu->length; int64_t om; uint64_t aq[2], at[2], bq[2], bt[2], ovlp, os, oe;
@@ -4143,6 +4258,7 @@ void h_ec_lchain_fast_new(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Read *tu,
k = 0; i = 0;
for (k = m = 0; k < ol->length; k++) {
z = &(ol->list[k]); tid = z->y_id; trev = z->y_pos_strand;
z->non_homopolymer_errors = 0;
for (; (i < srt_i->n) && ((srt_i->a[i]>>32) < ((tid<<1)|trev)); i++);
if((i < srt_i->n) && ((srt_i->a[i]>>32) == ((tid<<1)|trev))) {
om = 1; z->shared_seed = 0; z->is_match = 0;
@@ -4152,7 +4268,7 @@ void h_ec_lchain_fast_new(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Read *tu,
p = &(in0->buffer[((uint32_t)srt_i->a[i])>>1]); is_match = 1;
}
z->strong = p->ml; z->without_large_indel = p->no_l_indel;
aq[0] = (uint32_t)p->qns; aq[1] = p->qe;
at[0] = p->ts; at[1] = p->te;
@@ -4162,10 +4278,12 @@ void h_ec_lchain_fast_new(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Read *tu,
os = MAX(aq[0], bq[0]); oe = MIN(aq[1], bq[1]);
ovlp = ((oe>os)? (oe-os):0);
if(!((ovlp) && (ovlp >= ((aq[1] - aq[0])*sh)) && ((ovlp >= ((bq[1] - bq[0])*sh))))) om = 0;
z->non_homopolymer_errors += ((aq[1] - aq[0]) - ovlp);
os = MAX(at[0], bt[0]); oe = MIN(at[1], bt[1]);
ovlp = ((oe>os)? (oe-os):0);
if(!((ovlp) && (ovlp >= ((at[1] - at[0])*sh)) && ((ovlp >= ((bt[1] - bt[0])*sh))))) om = 0;
z->non_homopolymer_errors += ((at[1] - at[0]) - ovlp);
if(om) {
if(is_match == 1 && p->el == 1) p->el = 0;
@@ -4222,9 +4340,40 @@ void h_ec_lchain_fast_new(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Read *tu,
set_exact_exz(exz, z->x_pos_s, z->x_pos_e + 1, z->y_pos_s, z->y_pos_e + 1); push_alnw(z, exz);
is_usrt = 1;
// if(oa[k].tn == 1945) fprintf(stderr, "-em-[M::%s]\tqn::%u\ttn::%u\terr::%u\n", __func__, rid, oa[k].tn, ol->list[ol->length-1].non_homopolymer_errors);
}
}
if(is_usrt) overlap_region_sort_y_id(ol->list, ol->length);
if(ol->length > 1) {///for duplicated chains
uint64_t mm_k, s; int64_t mm_sc, sc;
for (k = 1, l = m = 0; k <= ol->length; k++) {
if(k == ol->length || ol->list[k].y_id != ol->list[l].y_id) {
mm_k = l;
if(k - l > 1) {
for (s = l, mm_sc = INT32_MIN, mm_k = ((uint64_t)-1); s < k; s++) {
z = &(ol->list[s]);
sc = z->non_homopolymer_errors; sc = - sc;
if((sc > mm_sc) || ((sc == mm_sc) && ((ol->list[mm_k].x_pos_e+1-ol->list[mm_k].x_pos_s) < (z->x_pos_e+1-z->x_pos_s)))) {
mm_sc = sc; mm_k = s;
}
}
}
if(mm_k != ((uint64_t)-1)) {
if(mm_k != m) {
t = ol->list[mm_k];
ol->list[mm_k] = ol->list[m];
ol->list[m] = t;
}
m++;
}
l = k;
}
}
ol->length = m;
}
}
overlap_region* h_ec_lchain_re3(ha_abuf_t *ab, uint32_t rid, UC_Read *qu, UC_Read *tu, uint64_t mz_w, uint64_t mz_k, All_reads *rref, overlap_region_alloc *ol, Candidates_list *cl, bit_extz_t *exz, asg16_v *buf, asg64_v *srt_i, double bw_thres,
@@ -5270,7 +5419,7 @@ void cal_ec_r(uint64_t n_thre, uint64_t round, uint64_t n_round, uint64_t n_a, u
b = gen_ec_ovec_buf_t(n_thre);
(*tot_e) += cal_ec_multiple(b, n_thre, n_a, tot_b); ////exit(1);
(*tot_e) += cal_ec_multiple(b, n_thre, n_a, tot_b); ///exit(1);
sl_ec_r(n_thre, n_a);
for (k = 0; k < n_round; k++) {
htab.cpp
+41 -9
View File
@@ -1329,7 +1329,7 @@ int load_ct_index(void **i_ct_idx, char* file_name)
int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t* opt, char* file_name)
{
char* gfa_name = (char*)malloc(strlen(file_name)+25);
char* gfa_name = (char*)malloc(strlen(file_name)+64);
sprintf(gfa_name, "%s.pt_flt", file_name);
FILE* fp = fopen(gfa_name, "w");
if (!fp) {
@@ -1372,15 +1372,29 @@ int write_pt_index(void *flt_tab, ha_pt_t *ha_idx, All_reads* r, hifiasm_opt_t*
write_All_reads(r, gfa_name);
sprintf(gfa_name, "%s.pt_flt.paf.bin", file_name);
fclose(fp); fp = fopen(gfa_name, "w"); uint64_t k;
if (!fp) {
free(gfa_name);
return 0;
}
fwrite(&(r->total_reads), sizeof(r->total_reads), 1, fp);
for (k = 0; k < r->total_reads; k++) {
fwrite(&(r->paf[k].is_fully_corrected), sizeof(r->paf[k].is_fully_corrected), 1, fp);
fwrite(&(r->paf[k].is_abnormal), sizeof(r->paf[k].is_abnormal), 1, fp);
fwrite(&(r->paf[k].length), sizeof(r->paf[k].length), 1, fp);
fwrite(r->paf[k].buffer, sizeof((*(r->paf[k].buffer))), r->paf[k].length, fp);
}
fprintf(stderr, "[M::%s] Index has been written.\n", __func__);
free(gfa_name);
fclose(fp);
return 1;
}
int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads* r, hifiasm_opt_t* opt, char* file_name)
int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads *r, hifiasm_opt_t* opt, char* file_name)
{
char* gfa_name = (char*)malloc(strlen(file_name)+25);
char* gfa_name = (char*)malloc(strlen(file_name)+64);
sprintf(gfa_name, "%s.pt_flt", file_name);
FILE* fp = fopen(gfa_name, "r");
if (!fp) {
@@ -1460,7 +1474,7 @@ int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads* r, hifiasm_op
f_flag += fread(&opt->max_n_chain, sizeof(opt->max_n_chain), 1, fp);
fclose(fp);
// fclose(fp);
if(!load_All_reads(r, gfa_name))
{
@@ -1468,15 +1482,33 @@ int load_pt_index(void **r_flt_tab, ha_pt_t **r_ha_idx, All_reads* r, hifiasm_op
return 0;
}
memset(r->trio_flag, AMBIGU, r->total_reads*sizeof(uint8_t));
sprintf(gfa_name, "%s.pt_flt.paf.bin", file_name);
fclose(fp); fp = fopen(gfa_name, "r"); uint64_t k;
if (!fp) {
free(gfa_name);
return 0;
}
f_flag += fread(&(r->total_reads), sizeof(r->total_reads), 1, fp);
r->paf = (ma_hit_t_alloc*)malloc(sizeof(ma_hit_t_alloc)*r->total_reads);
r->reverse_paf = (ma_hit_t_alloc*)malloc(sizeof(ma_hit_t_alloc)*r->total_reads);
for (i = 0; i < (long long)r->total_reads; i++)
{
init_ma_hit_t_alloc(&(r->paf[i]));
init_ma_hit_t_alloc(&(r->reverse_paf[i]));
for (k = 0; k < r->total_reads; k++) {
// init_ma_hit_t_alloc(&(r->paf[k]));
init_ma_hit_t_alloc(&(r->reverse_paf[k]));
f_flag += fread(&(r->paf[k].is_fully_corrected), sizeof(r->paf[k].is_fully_corrected), 1, fp);
f_flag += fread(&(r->paf[k].is_abnormal), sizeof(r->paf[k].is_abnormal), 1, fp);
f_flag += fread(&(r->paf[k].length), sizeof(r->paf[k].length), 1, fp);
r->paf[k].size = r->paf[k].length;
r->paf[k].buffer = NULL;
if(r->paf[k].length == 0) continue;
r->paf[k].buffer = (ma_hit_t*)malloc(sizeof(ma_hit_t)*r->paf[k].length);
fread(r->paf[k].buffer, sizeof((*(r->paf[k].buffer))), r->paf[k].length, fp);
}
fclose(fp);
fprintf(stderr, "[M::%s] Index has been loaded.\n", __func__);