bool del_line(size_t nline)
{
if ( nline >= lines.size() )
return false;
lines.erase(lines.begin()+nline);
return true;
}
bool insert_line(size_t nline, simpleline_t &line)
{
if ( nline >= lines.size() )
return false;
lines.insert(lines.begin()+nline, line);
return true;
}
/** Function generate_super_sketches
*
* Input: a list of read-pair sequences
* Output: super sketches for each fragment
*/
void generate_super_sketches (std::vector<sketch_t>& super_sketches,
const strvec_t& pairs, xny::sketch_list& slistgen,
xny::super_sketch ssgen, jaz::murmur264& hashfunc) {
bool debug = false;
int num_frag = pairs.size()/2;
int fragID = super_sketches.size();
std::vector<sketch_t> batch_sketches (num_frag);
#pragma omp parallel for
for (int i = 0; i < num_frag; ++ i) {
std::string frag = pairs[i] + pairs[i + num_frag];
if (frag.size()) {
if (std::isupper(frag.at(0))) {
std::replace (frag.begin(), frag.end(), 'N', 'A');
} else std::replace (frag.begin(), frag.end(), 'n', 'a');
std::vector<sketch_t> slist = slistgen (frag, hashfunc);
std::sort (slist.begin(), slist.end(), xny::cmp_sketch());
ssgen (batch_sketches[i], slist, hashfunc);
batch_sketches[i].second = fragID + i;
}
}
super_sketches.insert (super_sketches.end(),
batch_sketches.begin(), batch_sketches.end());
} //generate_super_sketches
bool set_line(size_t nline, simpleline_t &sl)
{
if ( nline >= lines.size() )
return false;
lines[nline] = sl;
return true;
}
/** Function generate_seeds ()
*
* Given [pairs] which stores 2*n number of reads, where pairs[i] and
* pairs[i + n] for 0 <= i <= n - 1 form a read pair
*
* Output: [list_seeds] the non-overlapping seeds for each read pair
*/
void generate_seeds (ii64vec_t& list_seeds, const strvec_t& pairs,
int seed_len) {
bool debug = false;
int num_pairs = pairs.size()/2;
int fragID = list_seeds.size();
ii64vec_t batch_seeds (num_pairs);
int debug_cnt = 0;
#pragma omp parallel for
for (int i = 0; i < num_pairs; ++ i) {
std::string frag = pairs[i] + pairs[i + num_pairs];
if (frag.size()) {
if (std::isupper(frag.at(0))) {
std::replace (frag.begin(), frag.end(), 'N', 'A');
} else std::replace (frag.begin(), frag.end(), 'n', 'a');
}
get_seeds_per_fragment (batch_seeds[i], frag, seed_len);
if (debug) { // print out frag and its seeds
std::cout << frag << "\n";
int tmp_last_seed_len = frag.length() - seed_len * (frag.length()/seed_len);
std::cout << "fraglen, seed_len, last_seed_len = " << frag.length() << ", "
<< seed_len << ", " << tmp_last_seed_len << "\n";
for (auto& x : batch_seeds[i]) {
std::string d_fwd = xny::ID2Str<int64_t>(x, seed_len);
std::cout << d_fwd << "\t" << xny::get_rvc_str(d_fwd) << "\n";
}
if (tmp_last_seed_len != 0) {
std::cout << "last str: ";
std::string d_fwd = xny::ID2Str<int64_t>(batch_seeds[i].back(),
tmp_last_seed_len);
std::cout << d_fwd << "\t" << xny::get_rvc_str(d_fwd) << "\n";
}
debug_cnt ++;
if (debug_cnt > 2) exit(1);
}
// append to the seed list the fragment ID
batch_seeds[i].push_back(fragID + i);
if (debug) { // debug print
std::cout << frag << "\n";
for (int j = 0; j < batch_seeds[i].size(); ++ j) {
std::cout << batch_seeds[i][j] << " ";
}
std::cout << "\n\n";
++ debug_cnt;
if (debug_cnt > 50) exit(1);
}
}
list_seeds.insert (list_seeds.end(),
batch_seeds.begin(), batch_seeds.end());
} // generate_seeds
bool patch_line(size_t nline, size_t offs, int value)
{
if ( nline >= lines.size() )
return false;
qstring &L = lines[nline].line;
L[offs] = (uchar) value & 0xFF;
return true;
}
void merge_floats(strvec_t const & tokens_in, strvec_t & tokens_out) {
ptrdiff_t tokcnt = tokens_in.size();
ptrdiff_t i = 0;
for(; i < tokcnt - 2; ++i) {
string const & l = tokens_in[i];
string const & c = tokens_in[i+1];
string const & r = tokens_in[i+2];
if(c == "." && l != "" && r != "") {
tokens_out.push_back(l+c+r);
i += 2;
} else
tokens_out.push_back(l);
}
for(;i < tokcnt; ++i) {
tokens_out.push_back(tokens_in[i]);
}
}
void set_minmax(size_t start=0, size_t end=size_t(-1))
{
if ( start == 0 && end == size_t(-1) )
{
end = lines.size();
pl_min.n = 0;
pl_max.n = end == 0 ? 0 : end - 1;
}
else
{
pl_min.n = start;
pl_max.n = end;
}
}
/** Function duplicate_removal ()
*
* Input: a list of paired fastq files
* Output: a list of paired fastq files with duplicate removed. If the
* num of output files is equal to the input, then dupl removal is applied
* to each input pair; otherwise, 2 paired fastq output files should be
* specified, and the output are combined in these two files.
*
* Randomly mutate 'N's in each read into 'A'. This will
* result in reads containing a small number of Ns being considered for
* clustering whereas reads containing a lot of Ns will not be considered
* anyway.
*/
void duplicate_removal (const strvec_t& ifqs, const drm_t& drm, int w,
int w2, xny::low_complexity& lc, int batch, bool silent) {
// sanity check
if ((drm.op.size() != ifqs.size()) && (drm.op.size () != 2)) {
abording ("duplicate_removal ofqs.size() != ifqs.size() and"
"ofqs.size() != 2");
}
// first obtain the length of a read, double it to be fragment length
std::ifstream fh_tmp;
xny::openfile<std::ifstream>(fh_tmp, ifqs[0]);
bio::fastq_input_iterator<> fq(fh_tmp);
int frag_len = 2 * (std::get<1>(*fq)).length();
xny::closefile(fh_tmp);
// calculate the upper bound of mismatches can be tolerated,
// number of seeds & seed length; max seed length will be bounded by 31
// int ub_mismatch = std::min (drm.max_mismatch, frag_len * (100 - drm.perc_sim) /100),
int ub_mismatch = frag_len * (100 - drm.perc_sim) /100,
//num_seed = ub_mismatch + 1,
seed_len = std::min(frag_len / (ub_mismatch + 1), 31);
//num_seed = std::max(num_seed, frag_len/seed_len);
//std::cout << max_mismatch << ", " << frag_len << ", " << perc_sim << "\n";
//std::cout << "ub_mismatch = " << ub_mismatch << "\n";
// process every pair of files
int num_file_pairs = ifqs.size()/2;
xny::sketch_list slistgen (w, false);
xny::super_sketch ssgen (w2);
std::ofstream ofhfq, ofhfq2;
if (drm.op.size() == 2) {
xny::openfile<std::ofstream> (ofhfq, drm.op[0]);
xny::openfile<std::ofstream> (ofhfq2, drm.op[1]);
}
for (int i = 0; i < num_file_pairs; ++ i) {
int fID = 2*i;
if (! silent) {
std::cout << "\tprocess files: " << ifqs[fID] << " and "
<< ifqs[fID + 1] << "\n\n";
}
// --------------- generate seeds for each fragment -------------
// ----------- a compressed form to represent fragments ---------
if (! silent) std::cout << "\tgenerate seeds...\n";
ii64vec_t list_seeds; // stores the list of seeds per fragment,
// the last element stores the fragment ID
get_seeds (list_seeds, ifqs[fID], ifqs[fID + 1], seed_len,
batch, silent);
// ---- initialize the global union-find structure ----
ivec_t uf_clst (list_seeds.size());
for (unsigned int j = 0; j < list_seeds.size(); ++ j) uf_clst[j] = j;
// ------------------ clustering via ss -------------------------
if (! silent) std::cout << "\tclustering via super sketches ...\n";
clustering_via_ss (uf_clst, list_seeds, ifqs[fID], ifqs[fID + 1],
batch, slistgen, ssgen, ub_mismatch, silent);
// --------------- clustering via seeds -----------------
if (!silent) std::cout << "\tclustering via seeds ...\n";
clustering_via_seeds (uf_clst, list_seeds, frag_len/seed_len,
ub_mismatch, silent);
// -------- generate final union find clusters --------------
iivec_t clusters;
uf_generate_cls (clusters, uf_clst);
// ---- generate the duplicated fragment IDs ----------------
iset_t duplIDs; // duplicate fragIDs
int debug_counter = 0;
for (int j = 0; j < (int) clusters.size(); ++ j) {
duplIDs.insert(clusters[j].begin() + 1, clusters[j].end());
/*{ // debug code print out clusters
if (clusters[j].size() > 100) {
debug_print_fragments (clusters[j], ifqs[fID], ifqs[fID+1]);
++ debug_counter;
if (debug_counter > 10) exit(1);
}
}*/
}
clusters.clear();
if (!silent) std::cout << "\n\t\tnum duplicate frags: " << duplIDs.size()
<< "(" << 100 * duplIDs.size()/ list_seeds.size() << "% total)" << "\n\n";
if (!silent) std::cout << "\toutput non-redundant read-pairs...\n";
// ----- output non-redundant read-pairs ---------
if (drm.op.size() > 2) {
xny::openfile<std::ofstream> (ofhfq, drm.op[fID]);
xny::openfile<std::ofstream> (ofhfq2, drm.op[fID + 1]);
}
clean_dupl_frag (ifqs[fID], ifqs[fID+1], ofhfq, ofhfq2,
duplIDs, lc, batch);
if (drm.op.size() > 2) {
xny::closefile(ofhfq);
xny::closefile(ofhfq2);
}
} // for (int i = 0
} // duplicate_removal
void add_line(const char *str)
{
lines.push_back(simpleline_t(str));
}
void add_line(simpleline_t &line)
{
lines.push_back(line);
}
void clear_lines()
{
lines.clear();
set_minmax();
}
const size_t count() const
{
return lines.size();
}
simpleline_t *get_line(size_t nline)
{
return nline >= lines.size() ? NULL : &lines[nline];
}