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chhylp123
2020-11-14 23:35:32 -05:00
parent 35e3423f93
commit ab073aa1fc
5 changed files with 2266 additions and 227 deletions
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Trio.cpp
+8 -5
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@@ -67,7 +67,7 @@ static yak_ch_t *yak_ch_restore_core(yak_ch_t *ch0, const char *fn, int mode, ..
{
va_list ap;
FILE *fp;
uint32_t t[3];
uint32_t t[3], f_tmp = 0;
char magic[4];
int i, j, absent, min_cnt = 0, mid_cnt = 0, mode_err = 0;
uint64_t mask = (1ULL<<YAK_COUNTER_BITS) - 1, n_ins = 0, n_new = 0;
@@ -92,33 +92,36 @@ static yak_ch_t *yak_ch_restore_core(yak_ch_t *ch0, const char *fn, int mode, ..
fclose(fp);
return 0;
}
fread(t, 4, 3, fp);
f_tmp += fread(t, 4, 3, fp);
if (t[2] != YAK_COUNTER_BITS) {
fprintf(stderr, "ERROR: saved counter bits: %d; compile-time counter bits: %d\n", t[2], YAK_COUNTER_BITS);
fclose(fp);
return 0;
}
///t[0] = k; t[1] = pre, t[2] = YAK_COUNTER_BITS;
ch = ch0 == 0? yak_ch_init(t[0], t[1]) : ch0;
assert((int)t[0] == ch->k && (int)t[1] == ch->pre);
for (i = 0; i < 1<<ch->pre; ++i) {
yak_ht_t *h = ch->h[i].h;
fread(t, 4, 2, fp);
f_tmp += fread(t, 4, 2, fp);
///t[0] = kh_capacity(h), t[1] = kh_size(h);
if (ch0 == 0) yak_ht_resize(h, t[0]);
for (j = 0; j < (int)t[1]; ++j) {
uint64_t key;
fread(&key, 8, 1, fp);
f_tmp += fread(&key, 8, 1, fp);
if (mode == YAK_LOAD_ALL) {
++n_ins;
yak_ht_put(h, key, &absent);
if (absent) ++n_new;
} else if (mode == YAK_LOAD_TRIOBIN1 || mode == YAK_LOAD_TRIOBIN2) {
int cnt = key & mask, x, shift = mode == YAK_LOAD_TRIOBIN1? 0 : 2;
//1. filter singleton k-mer; 2. label non-repeat and repeat
if (cnt >= mid_cnt) x = 2<<shift;
else if (cnt >= min_cnt) x = 1<<shift;
else x = -1;
if (x >= 0) {
khint_t k;
///no need cnt at all
key = (key & ~mask) | x;
++n_ins;
k = yak_ht_put(h, key, &absent);