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minimizer filtering apparently works

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Heng Li
2020-03-25 00:38:13 -04:00
parent 84361ba6dd
commit 3e897560c4
5 changed files with 26 additions and 0 deletions
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2
Assembly.h
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@@ -9,6 +9,8 @@
#define Get_Cigar_Length(RECORD) (RECORD>>2)
void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt);
void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab);
void Counting_multiple_thr();
void Build_hash_table_multiple_thr();
void Overlap_calculate_multipe_thr();

1
CommandLines.cpp
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@@ -65,6 +65,7 @@ void init_opt(hifiasm_opt_t* asm_opt)
asm_opt->mat_index = NULL;
asm_opt->thread_num = 1;
asm_opt->k_mer_length = 41;
asm_opt->mz_win = 41;
asm_opt->bf_shift = 37;
asm_opt->high_factor = 10.0f;
asm_opt->no_HPC = 0;

1
CommandLines.h
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@@ -15,6 +15,7 @@ typedef struct {
char* mat_index;
int thread_num;
int k_mer_length;
int mz_win;
int bf_shift;
float high_factor;
int no_HPC;

1
main.cpp
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@@ -17,6 +17,7 @@ int main(int argc, char *argv[])
yak_reset_realtime();
flt_tab = ha_gen_flt_tab(&asm_opt);
ha_gen_mzidx(&asm_opt, flt_tab);
ha_hf_destroy(flt_tab);
if (0) {
Correct_Reads(asm_opt.number_of_round);

21
yak-count.cpp
View File

@@ -496,3 +496,24 @@ void ha_hf_destroy(void *h)
{
yak_hh_destroy((yak_hh_t*)h);
}
void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
{
int64_t cnt[YAK_N_COUNTS];
int peak_hom, peak_het;
yak_copt_t opt;
yak_ch_t *h;
yak_copt_init(&opt);
opt.is_HPC = !asm_opt->no_HPC;
opt.k = asm_opt->k_mer_length;
opt.w = asm_opt->mz_win;
opt.n_thread = asm_opt->thread_num;
opt.bf_shift = asm_opt->bf_shift;
h = yak_count_file(&opt, asm_opt->num_reads, asm_opt->read_file_names, flt_tab);
yak_ch_hist(h, cnt, opt.n_thread);
fprintf(stderr, "[M::%s] count[%d] = %ld (for sanity check)\n", __func__, YAK_MAX_COUNT, (long)cnt[YAK_MAX_COUNT]);
peak_hom = yak_analyze_count(YAK_N_COUNTS, cnt, &peak_het);
if (peak_hom > 0) fprintf(stderr, "[M::%s] peak_hom: %d; peak_het: %d\n", __func__, peak_hom, peak_het);
yak_ch_destroy(h);
return 0;
}