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chhylp123
2021-09-26 13:51:13 -04:00
parent ed814abf35
commit 7dd4a848b9
13 changed files with 2747 additions and 61 deletions
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Trio.cpp
+77
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@@ -349,6 +349,83 @@ static void ha_triobin_list(const hifiasm_opt_t *opt)
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads with external lists\n", __func__, yak_realtime(), yak_cpu_usage());
}
inline void phrase_hstatus(char *s, char **rname, uint32_t *hid)
{
char *p = NULL, *id = NULL; *rname = NULL; *hid = (uint32_t)-1;
uint32_t tot;
for (p = s, tot = 0; *p; ++p){
if (*p == '\t' || *p == ' '){
*p = 0;
if(!tot) *rname = p+1;
else break;
tot++;
}
}
for (p = s, tot = 0; *p; ++p){
if (*p == '_') id = p + 1;
}
*hid = atoi(id);
}
uint32_t *ha_polybin_list(const hifiasm_opt_t *opt)
{
int64_t i;
khint_t k;
cstr_ht_t *h;
assert(R_INF.total_reads < (uint32_t)-1);
h = cstr_ht_init();
for (i = 0; i < (int64_t)R_INF.total_reads; ++i) {
int absent;
char *str = (char*)calloc(Get_NAME_LENGTH(R_INF, i) + 1, 1);
strncpy(str, Get_NAME(R_INF, i), Get_NAME_LENGTH(R_INF, i));
k = cstr_ht_put(h, str, &absent);
if (absent) kh_val(h, k) = i;
}
fprintf(stderr, "[M::%s::%.3f*%.2f] created the hash table for read names\n", __func__, yak_realtime(), yak_cpu_usage());
gzFile fp;
kstream_t *ks;
kstring_t str = {0,0,0};
char *rname = NULL;
uint32_t hid, *ss = NULL;
int dret;
int64_t n_tot = 0, n_bin = 0;
fp = gzopen(opt->fn_bin_poy, "r");
if (fp == 0) {
fprintf(stderr, "ERROR: failed to open file '%s'\n", opt->fn_bin_poy);
for (k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k))
free((char*)kh_key(h, k));
cstr_ht_destroy(h);
return NULL;
}
CALLOC(ss, R_INF.total_reads);
ks = ks_init(fp);
while (ks_getuntil(ks, KS_SEP_LINE, &str, &dret) >= 0) {
khint_t k; ++n_tot;
phrase_hstatus(str.s, &rname, &hid);
if((!(*rname)) || hid == (uint32_t)-1) {
fprintf(stderr, "ERROR: wrong hap status\n");
continue;
}
k = cstr_ht_get(h, rname);
if (k != kh_end(h)) {
ss[kh_val(h, k)] |= (((uint32_t)1)<<(hid-1));
++n_bin;
}
}
free(str.s);
ks_destroy(ks);
gzclose(fp);
for (k = 0; k < kh_end(h); ++k)
if (kh_exist(h, k))
free((char*)kh_key(h, k));
cstr_ht_destroy(h);
fprintf(stderr, "[M::%s::%.3f*%.2f] ==> partitioned reads with external lists\n", __func__, yak_realtime(), yak_cpu_usage());
return ss;
}
void ha_triobin(const hifiasm_opt_t *opt)
{
memset(R_INF.trio_flag, AMBIGU, R_INF.total_reads * sizeof(uint8_t));