SeqTagLib* load_tags(FileReader *fr, uint32_t fix_p1_len, uint32_t fix_p2_len){
SeqTagLib *lib;
Xmer X;
uint32_t i;
char *seq;
lib = malloc(sizeof(SeqTagLib));
lib->p1len = fix_p1_len;
lib->p2len = fix_p2_len;
lib->hash = init_xmerhash(1023);
X.offset = 0;
X.idx = 0;
while(fread_table(fr) != -1){
seq = get_col_str(fr, 0);
lib->kmer_size = get_col_len(fr, 0);
X.cnt = atoi(get_col_str(fr, 1));
X.k1 = 0;
X.k2 = 0;
for(i=0;i<lib->kmer_size;i++){
if(i < 32){
X.k1 |= ((uint64_t)base_bit_table[(int)seq[i]]) << (i << 1);
} else {
X.k2 |= ((uint64_t)base_bit_table[(int)seq[i]]) << ((i - 32) << 1);
}
}
put_xmerhash(lib->hash, X);
X.offset += X.cnt;
}
lib->n_seq = X.offset;
lib->seqs = calloc((lib->n_seq * (lib->p1len + lib->p2len) + 31) / 32, sizeof(uint64_t));
lib->ids = calloc(lib->n_seq, sizeof(uint64_t));
return lib;
}
void prepare_reads(merge_t *merger, FileReader *in, uint32_t lastcid) {
int n_col;
uint32_t cid, ef_id, eid, eflen, id = 0;
ef_id = 0;
contig_t *ctg = NULL;
read_t *rd;
char *efstr, *path;
while ((n_col = fread_table(in)) != -1) {
if (n_col == 0) continue;
cid = atoi(get_col_str(in, 4));
if (cid != lastcid) {
froll_back(in);
return;
}
eid = atoi(get_col_str(in, 1));
if (eid != ef_id) {
ef_id = eid;
efstr = get_col_str(in, 2);
eflen = get_col_len(in, 2);
reverse_dna(efstr, eflen);
ctg = lend_ctgv_merger(merger);
push_contigv(merger->ctgs, ctg);
ctg->id = ef_id;
ctg->closed = 0;
path = get_col_str(in, 5);
append_string(ctg->path, path, strlen(path));
// ctg->path = strdup(get_col_str(in, 5));
// ctg->efctgs = init_vec(sizeof(FContig*), 6);
push_u32list(ctg->m_rds, id++);
rd = next_ref_readv(ctg->rds);
rd->seq_id = atol(get_col_str(in, 0));
rd->rd_len = eflen;
memmove(rd->seq, efstr, rd->rd_len);
rd->seq[rd->rd_len]= '\0';
rd->rank = 1;
}
rd = next_ref_readv(ctg->rds);
rd->rank = 1;
rd->seq_id = atol(get_col_str(in, 0));
rd->rd_len = get_col_len(in, 3);
memmove(rd->seq, get_col_str(in, 3), rd->rd_len);
rd->seq[rd->rd_len]= '\0';
}
}
CtgDB* load_ctgdb(FileReader *fr1, FileReader *fr2) {
uint32_t id = 0, i = 0;
CtgDB *db;
uuhash *map = init_uuhash(1023);
uint32_t key, val;
uuhash_t h;
int len = 0;
char *seq = NULL;
String *line = init_string(1);
while (fread_table(fr2) != -1) {
key = atoi(get_col_str(fr2, 1));
val = atoi(get_col_str(fr2, 4));
h.key = key;
h.val = val;
if (!exists_uuhash(map, h)) {
put_uuhash(map, h);
}
}
db = (CtgDB*)malloc(sizeof(CtgDB));
db->ctgnum = 0;
db->ctgs = init_ctglist(6);
while (fread_line(line, fr1) != -1) {
if (line->string[0] == 'E') {
if (len != 0) {
Ctg contig;
contig.id = id;
contig.cls_id = i;
h.key = id;
h.val = 0;
contig.old_clsid = get_uuhash(map, h)->val;
contig.sz = 1;
contig.seq = strdup(seq);
db->ctgnum++;
push_ctglist(db->ctgs, contig);
i++;
}
free(seq); seq = NULL;
len = 0;
id = atoi(line->string+2);
} else if (line->string[0] == 'S') {
if (len < (int)strlen(line->string+2)) {
len = (int)strlen(line->string+2);
free(seq); seq = NULL;
seq = strdup(line->string+2);
}
}
}
Ctg contig;
contig.id = id;
contig.cls_id = i;
h.key = id;
h.val = 0;
contig.old_clsid = get_uuhash(map, h)->val;
contig.sz = 1;
contig.seq = strdup(seq);
db->ctgnum++;
push_ctglist(db->ctgs, contig);
free(seq);
free_string(line);
free_uuhash(map);
return db;
}
