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bug fix

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chhylp123
2021-10-10 14:47:16 -04:00
parent cb320b88f3
commit 908b4f3786
2 changed files with 2 additions and 6 deletions
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htab.cpp
+1 -6
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@@ -676,7 +676,7 @@ static void sf##_worker_for_mz(void *data, long i, int tid)\
(s->p->pt&&(s->p->flag&HAF_COUNT_REFINE))?s->p->pt:NULL, s->p->opt->min_rcnt, asm_opt.dp_min_len, asm_opt.dp_e, &(s->mt[tid]), asm_opt.mz_rewin, s->uq);\
s->mz[i].n = s->mz[i].m = b->n;\
MALLOC(s->mz[i].a, b->n);\
memcpy(s->mz[i].a, b->a, b->n * sizeof(VType));\
MEMCPY(s->mz[i].a, b->a, b->n);\
}\
static inline void sf##_pt_insert_buf(sf##_ch_buf_t *buf, int p, const HType *y){\
/**assign minimizer to one of 4096 bins by low 12 bits**/\
@@ -974,7 +974,6 @@ ha_ct_t *ha_count(const hifiasm_opt_t *asm_o, int flag, int HPC, int k, int w, h
///for ha_pt_gen, shoud be 0
opt.bf_shift = flag & HAF_COUNT_EXACT? 0 : asm_o->bf_shift;
opt.n_thread = asm_o->thread_num;
// opt.n_thread = p0? 1: asm_o->thread_num;
opt.adaLen = (keep_adapter? asm_o->adapterLen : 0);
opt.min_rcnt = (low_freq?*low_freq:-1);
///asm_opt->num_reads is the number of fastq files
@@ -1085,15 +1084,11 @@ ha_pt_t *ha_pt_ug_gen(const hifiasm_opt_t *asm_opt, const void *flt_tab, ma_utg_
ct = ha_count(asm_opt, HAF_COUNT_EXACT|HAF_UG_READ, is_HPC, k, w, NULL, flt_tab, NULL, us, 0, NULL);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> counted %ld distinct minimizer k-mers\n", __func__,
yak_realtime(), yak_cpu_usage(), (long)ct->tot);
exit(1);
///minimizer with YAK_MAX_COUNT occ may apper > YAK_MAX_COUNT times, so it may lead to overflow at ha_pt_gen
ha_ct_shrink(ct, min_freq, YAK_MAX_COUNT - 1, asm_opt->thread_num);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> sb0\n", __func__, yak_realtime(), yak_cpu_usage());
pt = ha_pt_gen(ct, asm_opt->thread_num, 1);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> sb1\n", __func__, yak_realtime(), yak_cpu_usage());
ha_count(asm_opt, HAF_COUNT_EXACT|HAF_UG_READ, is_HPC, k, w, pt, flt_tab, NULL, us, 0, NULL);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> sb2\n", __func__, yak_realtime(), yak_cpu_usage());
//ha_pt_sort(pt, asm_opt->thread_num);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> indexed %ld positions\n", __func__,
yak_realtime(), yak_cpu_usage(), (long)pt->tot_pos);
htab.h
+1
View File
@@ -159,6 +159,7 @@ static inline uint64_t yak_hash_long(uint64_t x[4])
#define CALLOC(ptr, len) ((ptr) = (__typeof__(ptr))calloc((len), sizeof(*(ptr))))
#define MALLOC(ptr, len) ((ptr) = (__typeof__(ptr))malloc((len) * sizeof(*(ptr))))
#define REALLOC(ptr, len) ((ptr) = (__typeof__(ptr))realloc((ptr), (len) * sizeof(*(ptr))))
#define MEMCPY(dest, src, len) (memcpy((dest), (src), (len) * sizeof(*(src))))
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))