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prepare for integration with hifiasm

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This commit is contained in:
Heng Li
2020-03-26 11:33:52 -04:00
parent 60d94790a2
commit c3bbaa8a39
3 changed files with 38 additions and 157 deletions
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htab.cpp
+16 -13
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@@ -9,6 +9,7 @@
#include "kseq.h"
#include "ksort.h"
#include "htab.h"
#include "Process_Read.h"
#include "CommandLines.h"
#define YAK_COUNTER_BITS 12
@@ -308,7 +309,6 @@ static void worker_pt_gen(void *data, long i, int tid) // callback for kt_for()
b->n += kh_key(g, k) & YAK_MAX_COUNT;
}
}
// fprintf(stderr, "X\t%ld\t%d\t%ld\n", i, kh_size(g), (long)b->n);
yak_ct_destroy(g);
a->ct->h[i].h = 0;
CALLOC(b->a, b->n);
@@ -464,12 +464,15 @@ static void count_seq_buf_HPC(ch_buf_t *buf, int k, int p, int len, const char *
* K-mer counting *
******************/
KSEQ_INIT(gzFile, gzread)
//KSEQ_INIT(gzFile, gzread)
#define HAF_COUNT_EXACT 0x1
#define HAF_COUNT_ALL 0x2
typedef struct { // global data structure for kt_pipeline()
const yak_copt_t *opt;
const void *flt_tab;
int create_new, is_store;
int flag, create_new, is_store;
uint64_t batch_offset;
uint64_t n_base;
kseq_t *ks;
@@ -608,7 +611,7 @@ static void *worker_count(void *data, int step, void *in) // callback for kt_pip
return 0;
}
static ha_ct_t *yak_count(const char *fn, const yak_copt_t *opt, ha_pt_t *p0, ha_ct_t *c0, const void *flt_tab)
static ha_ct_t *yak_count(const yak_copt_t *opt, const char *fn, int flag, ha_pt_t *p0, ha_ct_t *c0, const void *flt_tab)
{
pl_data_t pl;
gzFile fp;
@@ -633,28 +636,28 @@ static ha_ct_t *yak_count(const char *fn, const yak_copt_t *opt, ha_pt_t *p0, ha
return pl.ct;
}
static ha_ct_t *yak_count_file(const yak_copt_t *opt, ha_pt_t *p0, int n_fn, char **fn, const void *flt_tab)
static ha_ct_t *yak_count_file(const yak_copt_t *opt, int flag, ha_pt_t *p0, int n_fn, char **fn, const void *flt_tab)
{
int i;
ha_ct_t *h = 0;
for (i = 0; i < n_fn; ++i)
h = yak_count(fn[i], opt, p0, h, flt_tab);
h = yak_count(opt, fn[i], flag, p0, h, flt_tab);
if (h && opt->bf_shift > 0)
ha_ct_destroy_bf(h);
return h;
}
ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, ha_pt_t *p0, int is_exact, int count_all, const void *flt_tab)
ha_ct_t *ha_count(const hifiasm_opt_t *asm_opt, int flag, ha_pt_t *p0, const void *flt_tab)
{
yak_copt_t opt;
ha_ct_t *h;
yak_copt_init(&opt);
opt.k = asm_opt->k_mer_length;
opt.is_HPC = !asm_opt->no_HPC;
opt.w = count_all? 1 : asm_opt->mz_win;
opt.bf_shift = is_exact? 0 : asm_opt->bf_shift;
opt.w = flag & HAF_COUNT_ALL? 1 : asm_opt->mz_win;
opt.bf_shift = flag & HAF_COUNT_EXACT? 0 : asm_opt->bf_shift;
opt.n_thread = asm_opt->thread_num;
h = yak_count_file(&opt, p0, asm_opt->num_reads, asm_opt->read_file_names, flt_tab);
h = yak_count_file(&opt, flag, p0, asm_opt->num_reads, asm_opt->read_file_names, flt_tab);
return h;
}
@@ -707,7 +710,7 @@ void *ha_gen_flt_tab(const hifiasm_opt_t *asm_opt)
int64_t cnt[YAK_N_COUNTS];
int peak_hom, peak_het, cutoff;
ha_ct_t *h;
h = ha_count(asm_opt, 0, 0, 1, 0);
h = ha_count(asm_opt, HAF_COUNT_ALL, NULL, NULL);
ha_ct_hist(h, cnt, asm_opt->thread_num);
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);
@@ -727,7 +730,7 @@ void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
int peak_hom, peak_het, i;
ha_ct_t *ct;
ha_pt_t *pt;
ct = ha_count(asm_opt, 0, 1, 0, flt_tab);
ct = ha_count(asm_opt, HAF_COUNT_EXACT, NULL, flt_tab);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> counted %ld distinct minimizer k-mers\n", __func__,
yak_realtime(), yak_cputime() / yak_realtime(), (long)ct->tot);
ha_ct_hist(ct, cnt, asm_opt->thread_num);
@@ -737,7 +740,7 @@ void *ha_gen_mzidx(const hifiasm_opt_t *asm_opt, const void *flt_tab)
ha_ct_shrink(ct, 2, YAK_MAX_COUNT - 1, asm_opt->thread_num);
for (i = 2, tot_cnt = 0; i <= YAK_MAX_COUNT - 1; ++i) tot_cnt += cnt[i] * i;
pt = ha_pt_gen(ct, asm_opt->thread_num);
ha_count(asm_opt, pt, 1, 0, flt_tab);
ha_count(asm_opt, HAF_COUNT_EXACT, pt, flt_tab);
assert((uint64_t)tot_cnt == pt->tot_pos);
ha_pt_sort(pt, asm_opt->thread_num);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> indexed %ld positions\n", __func__,