void scan_tags(SeqTagLib *lib, FileReader *fwd, FileReader *rev, int is_fq, int pdirs){
Sequence *seq1, *seq2;
uint64_t id;
uint32_t i, len1, len2;
uint8_t *buf1, *buf2, v;
__n_seqs = lib->n_seq;
id = 0;
seq1 = seq2 = NULL;
buf1 = malloc(lib->p1len);
buf2 = malloc(lib->p2len);
while(is_fq? (fread_fastq_adv(&seq1, fwd, FASTQ_FLAG_NO_NAME | FASTQ_FLAG_NO_QUAL) &&
fread_fastq_adv(&seq2, rev, FASTQ_FLAG_NO_NAME | FASTQ_FLAG_NO_QUAL)) :
(fread_fasta_adv(&seq1, fwd, FASTA_FLAG_NO_NAME) && fread_fasta_adv(&seq2, rev, FASTA_FLAG_NO_NAME))){
id ++;
__n_scan ++;
len1 = seq1->seq.size;
if(len1 > lib->p1len) len1 = lib->p1len;
for(i=0;i<len1;i++){
v = base_bit_table[(int)seq1->seq.string[i]];
if(v == 4) v = lrand48() & 0x03;
buf1[i] = v;
}
len2 = seq2->seq.size;
if(len2 > lib->p2len) len2 = lib->p2len;
for(i=0;i<len2;i++){
v = base_bit_table[(int)seq2->seq.string[i]];
if(v == 4) v = lrand48() & 0x03;
buf2[i] = v;
}
if(pdirs & 0x01){ scan_tag_core(lib, id, buf1, len1, buf2, len2, 0); }
if(pdirs & 0x02){ scan_tag_core(lib, id, buf1, len1, buf2, len2, 1); }
}
free(buf1);
free(buf2);
if(seq1) free_sequence(seq1);
if(seq2) free_sequence(seq2);
}
SeqDB* load_seqdb(FileReader *fr, int is_fq, int fix_rd_len){
SeqDB *sdb;
Sequence *seq;
u64list *seqs;
uint64_t offset;
uint8_t len;
sdb = malloc(sizeof(SeqDB));
sdb->n_rd = 0;
sdb->rd_len = 0;
sdb->max_rd_len = 0;
if(!fix_rd_len){
sdb->seqoffs = init_u64list(1024);
sdb->seqlens = init_u8list(1024);
} else {
sdb->rd_len = fix_rd_len;
sdb->max_rd_len = fix_rd_len;
sdb->seqoffs = NULL;
sdb->seqlens = NULL;
}
seq = NULL;
seqs = init_u64list(1024);
offset = 0;
while(is_fq? fread_fastq_adv(&seq, fr, 5) : fread_fasta_adv(&seq, fr, 1)){
sdb->n_rd ++;
len = seq->seq.size;
if(fix_rd_len){
if(len < sdb->rd_len){
continue;
} else if(len > sdb->rd_len){
len = sdb->rd_len;
}
} else {
if(sdb->max_rd_len < len) sdb->max_rd_len = len;
push_u64list(sdb->seqoffs, offset);
push_u8list(sdb->seqlens, len);
}
encap_u64list(seqs, (offset + len + 31) / 32 + 2);
seq2bits(seqs->buffer, offset, seq->seq.string, len);
offset += len;
if((sdb->n_rd & 0xFFF) == 0){ fprintf(stderr, "\r %u k reads ", (sdb->n_rd >> 10)); fflush(stderr); }
}
