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chhylp123
2021-12-29 21:22:43 -05:00
parent dbc72b8c2d
commit 7af0d85258
7 changed files with 521 additions and 34 deletions
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Process_Read.cpp
+23 -15
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@@ -754,10 +754,12 @@ void init_all_ul_t(all_ul_t *x, All_reads *hR) {
void destory_all_ul_t(all_ul_t *x) {
uint64_t i;
for (i = 0; i < x->n; i++) {
free(x->a[i].n_n); free(x->a[i].N_site.a);
free(x->a[i].r_base.a); free(x->a[i].bb.a);
free(x->a[i].N_site.a); free(x->a[i].r_base.a); free(x->a[i].bb.a);
}
free(x->a);
for (i = 0; i < x->nid.n; i++) free(x->nid.a[i].a);
free(x->nid.a);
}
void ha_encode_base(uint8_t* dest, char* src, uint64_t src_l, N_t *nn, uint64_t nn_offset)
@@ -843,23 +845,29 @@ void push_subblock_original_bases(char* str, all_ul_t *x, ul_vec_t *p, uint32_t
void append_ul_t(all_ul_t *x, uint64_t *rid, char* id, int64_t id_l, char* str, int64_t str_l, ul_ov_t *o, int64_t on) {
int64_t i, mine, maxs, ovlp, end;
ul_vec_t *p = NULL;
nid_t *np = NULL;
ul_ov_t *z = NULL, *zp = NULL;
uc_block_t *b = NULL;
if(rid) fprintf(stderr, "rid:%lu\n", *rid);
if(rid == NULL) {
kv_pushp(ul_vec_t, *x, &p);
memset(p, 0, sizeof(*p));
fprintf(stderr, "x->n:%u\n", x->n);
}
else {
p = &(x->a[*rid]);
if(id) {
kv_pushp(nid_t, x->nid, &np);
np->n = id_l; MALLOC(np->a, np->n+1); memcpy(np->a, id, id_l); np->a[id_l] = '\0';
}
if(id && id_l > 0) {
free(p->n_n);
p->n_l = id_l; MALLOC(p->n_n, p->n_l+1); memcpy(p->n_n, id, id_l); p->n_n[id_l] = '\0';
}
if(str && str_l > 0) {
if(str) {
if(rid == NULL) {
kv_pushp(ul_vec_t, *x, &p);
memset(p, 0, sizeof(*p));
} else {
if((*rid) >= x->m) kv_resize(ul_vec_t, *x, (*rid) + 1);
if((*rid) >= x->n) {
memset(x->a+x->n, 0, sizeof(*p)*((*rid) + 1 - x->n));
x->n = (*rid) + 1;
}
p = &(x->a[(*rid)]);
}
p->bb.n = p->N_site.n = p->r_base.n = 0;
p->rlen = str_l;