vector<paired_fasta_read> Read() {
vector<paired_fasta_read> reads;
string tmp_str;
string name1, seq1, name2, seq2;
while(!file_handler_.eof()) {
getline(file_handler_, tmp_str);
if(IsFastaName(tmp_str)) {
if(name1 == "" && name2 == "" && seq1 == "" && seq2 == "")
name1 = tmp_str;
else if(name1 != "" && name2 != "" && seq1 != "" && seq2 != "") {
reads.push_back(paired_fasta_read(fasta_read(name1, seq1), fasta_read(name2, seq2)));
name1 = tmp_str;
name2 = "";
seq1 = "";
seq2 = "";
}
else
name2 = tmp_str;
}
else {
assert(name1 != "");
if(name2 == "")
seq1 = seq1 + tmp_str;
else
seq2 = seq2 + tmp_str;
}
}
if(name1 != "" && name2 != "" && seq1 != "" && seq2 != "")
reads.push_back(paired_fasta_read(fasta_read(name1, seq1), fasta_read(name2, seq2)));
return reads;
}
void* pique_thread(void* arg)
{
pique_ctx_t* ctx = arg;
seq_t* seq = seq_create();
twobit_t* tb = twobit_alloc();
rng_t* rng = rng_alloc(1234);
bool r;
while (true) {
pthread_mutex_lock(ctx->f_mutex);
if (ctx->fmt == INPUT_FMT_FASTA) r = fasta_read(ctx->f, seq);
else if (ctx->fmt == INPUT_FMT_FASTQ) r = fastq_read(ctx->f, seq);
pthread_mutex_unlock(ctx->f_mutex);
if (!r) break;
/* TODO: remove sequences with Ns? */
twobit_copy_str_n(tb, seq->seq.s, seq->seq.n);
dbg_add_twobit_seq(ctx->G, rng, tb);
}
rng_free(rng);
seq_free(seq);
return NULL;
}
vector<fasta_read> Read() {
vector<fasta_read> reads;
string tmp_str;
string name, seq;
while(!file_handler_.eof()) {
getline(file_handler_, tmp_str);
if(tmp_str != "") {
if(IsFastaName(tmp_str)) {
if(name != "" && seq != "")
reads.push_back(fasta_read(name, seq));
name = tmp_str;
seq = "";
}
else
seq = seq + tmp_str;
}
}
if(name != "" && seq != "")
reads.push_back(fasta_read(name, seq));
return reads;
}
