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r215: prepare for list-based binning

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Heng Li
2020-04-10 00:12:19 -04:00
parent 7a35bd7fcc
commit f32bfc904a
6 changed files with 50 additions and 33 deletions
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29
Trio.cpp
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@@ -24,6 +24,9 @@
#define yak_ch_hash(a) ((a)>>YAK_COUNTER_BITS)
KHASHL_SET_INIT(static klib_unused, yak_ht_t, yak_ht, uint64_t, yak_ch_hash, yak_ch_eq)
typedef const char *ha_cstr_t;
KHASHL_MAP_INIT(static klib_unused, cstr_ht_t, cstr_ht, ha_cstr_t, int64_t, kh_hash_str, kh_eq_str)
typedef struct {
struct yak_ht_t *h;
} yak_ch1_t;
@@ -248,23 +251,18 @@ static void tb_worker(void *_data, long k, int tid)
if(type == 'm') aux->seq->trio_flag[k] = MOTHER;
}
void trio_partition(void)
static void ha_triobin_yak(const hifiasm_opt_t *opt)
{
if (asm_opt.pat_index == NULL || asm_opt.mat_index == NULL) {
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads*sizeof(uint8_t));
return;
}
yak_ch_t *ch;
int i /**, min_cnt = 2, mid_cnt = 5**/;
tb_shared_t aux;
memset(&aux, 0, sizeof(tb_shared_t));
aux.n_threads = asm_opt.thread_num, aux.print_diff = 0;
aux.n_threads = opt->thread_num, aux.print_diff = 0;
aux.ratio_thres = 0.33;
aux.seq = &R_INF;
ch = yak_ch_restore_core(0, asm_opt.pat_index, YAK_LOAD_TRIOBIN1, asm_opt.min_cnt, asm_opt.mid_cnt);
ch = yak_ch_restore_core(ch, asm_opt.mat_index, YAK_LOAD_TRIOBIN2, asm_opt.min_cnt, asm_opt.mid_cnt);
ch = yak_ch_restore_core(0, opt->fn_bin_yak[0], YAK_LOAD_TRIOBIN1, opt->min_cnt, opt->mid_cnt);
ch = yak_ch_restore_core(ch, opt->fn_bin_yak[1], YAK_LOAD_TRIOBIN2, opt->min_cnt, opt->mid_cnt);
aux.k = ch->k;
aux.ch = ch;
@@ -285,3 +283,16 @@ void trio_partition(void)
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads using yak dumps\n", __func__, yak_realtime(), yak_cpu_usage());
}
static void ha_triobin_list(const hifiasm_opt_t *opt)
{
}
void ha_triobin(const hifiasm_opt_t *opt)
{
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads * sizeof(uint8_t));
if (opt->fn_bin_list[0] && opt->fn_bin_list[1])
ha_triobin_list(opt);
else if (opt->fn_bin_yak[0] && opt->fn_bin_yak[1])
ha_triobin_yak(opt);
}