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fixed missing read names

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Overlapping not working yet (now confirmed)
This commit is contained in:
Heng Li
2020-03-27 12:51:08 -04:00
parent 78e8f2f28a
commit 1bb174a04e
5 changed files with 11 additions and 16 deletions
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Assembly.cpp
-2
View File
@@ -10,8 +10,6 @@
#include "Output.h" #include "Output.h"
#include "htab.h" #include "htab.h"
void *ha_flt_tab;
ha_pt_t *ha_idx;
void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double band_width_threshold, int keep_whole_chain); void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_region_alloc *overlap_list, Candidates_list *cl, double band_width_threshold, int keep_whole_chain);
All_reads R_INF; All_reads R_INF;
anchor.cpp
+2 -2
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@@ -65,7 +65,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
REALLOC(ab->a, ab->m_a); REALLOC(ab->a, ab->m_a);
} }
for (i = 0, k = 0; i < ab->mz.n; ++i) { for (i = 0, k = 0; i < ab->mz.n; ++i) {
uint32_t j; int j;
ha_mz1_t *z = &ab->mz.a[i]; ha_mz1_t *z = &ab->mz.a[i];
seed1_t *s = &ab->seed[i]; seed1_t *s = &ab->seed[i];
for (j = 0; j < s->n; ++j) { for (j = 0; j < s->n; ++j) {
@@ -96,7 +96,7 @@ void ha_get_new_candidates(ha_abuf_t *ab, int64_t rid, UC_Read *ucr, overlap_reg
} }
// copy over to _cl_ // copy over to _cl_
if (ab->m_a >= cl->size) { if (ab->m_a >= (uint64_t)cl->size) {
cl->size = ab->m_a; cl->size = ab->m_a;
REALLOC(cl->list, cl->size); REALLOC(cl->list, cl->size);
} }
htab.cpp
+4
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@@ -33,6 +33,9 @@ const unsigned char seq_nt4_table[256] = { // translate ACGT to 0123
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
}; };
void *ha_flt_tab;
ha_pt_t *ha_idx;
/*************************** /***************************
* Yak specific parameters * * Yak specific parameters *
***************************/ ***************************/
@@ -571,6 +574,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
if (seq_nt4_table[(uint8_t)p->ks->seq.s[i]] >= 4) if (seq_nt4_table[(uint8_t)p->ks->seq.s[i]] >= 4)
++n_N; ++n_N;
ha_compress_base(Get_READ(*p->rs_out, p->n_seq), p->ks->seq.s, l, &p->rs_out->N_site[p->n_seq], n_N); ha_compress_base(Get_READ(*p->rs_out, p->n_seq), p->ks->seq.s, l, &p->rs_out->N_site[p->n_seq], n_N);
memcpy(&p->rs_out->name[p->rs_out->name_index[p->n_seq]], p->ks->name.s, p->ks->name.l);
} }
} }
if (s->n_seq == s->m_seq) { if (s->n_seq == s->m_seq) {
htab.h
+2
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@@ -23,6 +23,8 @@ struct ha_abuf_s;
typedef struct ha_abuf_s ha_abuf_t; typedef struct ha_abuf_s ha_abuf_t;
extern const unsigned char seq_nt4_table[256]; extern const unsigned char seq_nt4_table[256];
extern void *ha_flt_tab;
extern ha_pt_t *ha_idx;
void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs); void *ha_ft_gen(const hifiasm_opt_t *asm_opt, All_reads *rs);
int ha_ft_isflt(const void *hh, uint64_t y); int ha_ft_isflt(const void *hh, uint64_t y);
main.cpp
+3 -12
View File
@@ -9,21 +9,12 @@
int main(int argc, char *argv[]) int main(int argc, char *argv[])
{ {
int i; int i;
void *flt_tab;
ha_pt_t *idx;
init_opt(&asm_opt); init_opt(&asm_opt);
if (!CommandLine_process(argc, argv, &asm_opt)) return 1; if (!CommandLine_process(argc, argv, &asm_opt)) return 1;
yak_reset_realtime(); yak_reset_realtime();
flt_tab = ha_ft_gen(&asm_opt, &R_INF); ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF);
idx = ha_pt_gen(&asm_opt, flt_tab, 0, &R_INF); Correct_Reads(asm_opt.number_of_round);
ha_pt_destroy(idx); ha_ft_destroy(ha_flt_tab);
ha_ft_destroy(flt_tab);
if (0) {
Correct_Reads(asm_opt.number_of_round);
}
destory_All_reads(&R_INF); destory_All_reads(&R_INF);
destory_opt(&asm_opt); destory_opt(&asm_opt);
fprintf(stderr, "[M::%s] Version: %s\n", __func__, "dummy"); fprintf(stderr, "[M::%s] Version: %s\n", __func__, "dummy");