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process.cpp
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// STEAK Specific Transposable Element Aligner (HERV-K)
// Copyright (C) 2015 Cindy Santander, Philippe Gambron
// Distributed under the GNU General Public License version 3 (GPLv3.txt or https://www.gnu.org/licenses/gpl-3.0.html)
#include "process.hpp"
#include "smithwaterman.hpp"
#include <map>
#include <boost/algorithm/string.hpp>
#include <omp.h>
using namespace std;
int process_reads_paired(const double& alignment_quality,
const double& match_quality,
int transposon_length,
int host_length,
const vector<LTR>& TE_references,
const vector<Read>& reads,
string& fastq1,
string& fastq2,
string& fastq_te,
string& read_info){
if(reads.empty() || reads.size()>2){
return -1;
}
int i;
for(i=0; i<reads.size(); ++i){
if(reads[i].cigarValue<=alignment_quality){
break;
}
}
if(i==reads.size()){
return -1;
}
int i_ref, i_read;
typedef pair<int, int> pair_t;
map<pair<int, int>, match_result> results;
int max_absolute_score=-1;
pair<int, int> ref_read_pair_max;
string matchRead;
int best_TE_for_read[reads.size()], best_score_for_read[reads.size()];
for(i=0; i<reads.size(); ++i){
best_TE_for_read[i]=-1;
best_score_for_read[i]=0;
}
for(i_ref=0; i_ref<TE_references.size(); ++i_ref){
for(i_read=0; i_read<reads.size(); ++i_read){
#ifdef DEBUG
std::cout << reads[i_read].name << "\n";
#endif
smithwaterman(TE_references[i_ref].sequence, reads[i_read].sequence, results[pair_t(i_ref, i_read)].swr);
if(results[pair_t(i_ref, i_read)].swr.relativeScore>=match_quality){
getTrimmedValues(results[pair_t(i_ref, i_read)].swr, reads[i_read], TE_references[i_ref].direction, results[pair_t(i_ref, i_read)].trimmedRead, results[pair_t(i_ref, i_read)].trimmedPhred, results[pair_t(i_ref, i_read)].trimmedPosition, results[pair_t(i_ref, i_read)].matchRead, results[pair_t(i_ref, i_read)].matchPhred);
}else{
results[pair_t(i_ref, i_read)].trimmedRead=reads[i_read].sequence;
results[pair_t(i_ref, i_read)].trimmedPhred=reads[i_read].phred;
results[pair_t(i_ref, i_read)].trimmedPosition=0;
results[pair_t(i_ref, i_read)].matchRead="";
results[pair_t(i_ref, i_read)].matchPhred="";
}
if(results[pair_t(i_ref, i_read)].trimmedRead.length()>=transposon_length && results[pair_t(i_ref, i_read)].swr.relativeScore>=match_quality){
results[pair_t(i_ref, i_read)].selected=true;
if(results[pair_t(i_ref, i_read)].swr.score>max_absolute_score){
max_absolute_score=results[pair_t(i_ref, i_read)].swr.score;
ref_read_pair_max=pair_t(i_ref, i_read);
}
if(results[pair_t(i_ref, i_read)].swr.score>best_score_for_read[i_read]){
best_score_for_read[i_read]=results[pair_t(i_ref, i_read)].swr.score;
best_TE_for_read[i_read]=i_ref;
}
}
}
}
if(max_absolute_score<0){
return -1;
}
fastq1= "@"+reads[ref_read_pair_max.second].name+"\n";
fastq1=fastq1+results[ref_read_pair_max].trimmedRead+"\n";
fastq1=fastq1+"+\n";
fastq1=fastq1+results[ref_read_pair_max].trimmedPhred+"\n";
int i_other_read=(ref_read_pair_max.second+1)%2;
if(reads.size()>1){
fastq2= "@"+reads[i_other_read].name+"\n";
if(best_TE_for_read[i_other_read]>=0){
fastq2=fastq2+results[pair_t(best_TE_for_read[i_other_read], i_other_read)].trimmedRead+"\n";
fastq2=fastq2+"+\n";
fastq2=fastq2+results[pair_t(best_TE_for_read[i_other_read], i_other_read)].trimmedPhred+"\n";
}else{
fastq2=fastq2+reads[i_other_read].sequence+"\n";
fastq2=fastq2+"+\n";
fastq2=fastq2+reads[i_other_read].phred+"\n";
}
}
fastq_te= "@"+reads[ref_read_pair_max.second].name+"\n";
fastq_te=fastq_te+results[ref_read_pair_max].matchRead+"\n";
fastq_te=fastq_te+"+\n";
fastq_te=fastq_te+results[ref_read_pair_max].matchPhred+"\n";
string processedRead;
matchRead=results[ref_read_pair_max].matchRead;
boost::to_lower(matchRead);
if(TE_references[ref_read_pair_max.first].direction<0){
processedRead=results[ref_read_pair_max].trimmedRead+matchRead;
}else{
processedRead=matchRead+results[ref_read_pair_max].trimmedRead;
}
string processedMate;
if(reads.size()>1){
if(best_TE_for_read[i_other_read]>=0){
matchRead=results[pair_t(best_TE_for_read[i_other_read], i_other_read)].matchRead;
fastq_te=fastq_te+"@"+reads.front().name+"\n";
fastq_te=fastq_te+matchRead+"\n";
fastq_te=fastq_te+"+\n";
fastq_te=fastq_te+results[pair_t(best_TE_for_read[i_other_read], i_other_read)].matchPhred+"\n";
boost::to_lower(matchRead);
if(TE_references[best_TE_for_read[i_other_read]].direction<0){
processedMate=results[pair_t(best_TE_for_read[i_other_read], i_other_read)].trimmedRead+matchRead;
}else{
processedMate=matchRead+results[pair_t(best_TE_for_read[i_other_read], i_other_read)].trimmedRead;
}
}else{
processedMate=reads[i_other_read].sequence;
}
}else{
processedMate="NA";
}
read_info=reads.front().name+"\t"+TE_references.front().name+"\t"+to_string(results[ref_read_pair_max].trimmedRead.length())+"\t"+to_string(results[ref_read_pair_max].matchRead.length())+"\t"+to_string(results[ref_read_pair_max].swr.relativeScore)+"\t"+processedRead+"\t"+processedMate+"\t"+reads[ref_read_pair_max.second].chromosome+"|"+to_string(reads[ref_read_pair_max.second].position)+"|"+to_string(reads[ref_read_pair_max.second].quality)+"|"+reads[ref_read_pair_max.second].cigarString+"\t"+reads[i_other_read].chromosome+"|"+to_string(reads[i_other_read].position)+"|"+to_string(reads[i_other_read].quality)+"|"+reads[i_other_read].cigarString+"\n";
return 0;
}
int process_reads_unpaired(const double& alignment_quality,
const double& match_quality,
int transposon_length,
int host_length,
const vector<LTR>& TE_references,
const vector<Read>& reads,
string& fastq1,
string& fastq_te,
string& read_info){
if(reads.size()!=1){
return -1;
}
int i;
for(i=0; i<reads.size(); ++i){
if(reads[i].cigarValue<=alignment_quality){
break;
}
}
if(i==reads.size()){
return -1;
}
int i_ref, i_read;
typedef pair<int, int> pair_t;
map<pair<int, int>, match_result> results;
int max_absolute_score=-1;
pair<int, int> ref_read_pair_max;
string matchRead;
int best_TE_for_read[reads.size()], best_score_for_read[reads.size()];
for(i=0; i<reads.size(); ++i){
best_TE_for_read[i]=-1;
best_score_for_read[i]=0;
}
for(i_ref=0; i_ref<TE_references.size(); ++i_ref){
for(i_read=0; i_read<reads.size(); ++i_read){
#ifdef DEBUG
std::cout << reads[i_read].name << "\n";
#endif
smithwaterman(TE_references[i_ref].sequence, reads[i_read].sequence, results[pair_t(i_ref, i_read)].swr);
if(results[pair_t(i_ref, i_read)].swr.relativeScore>=match_quality){
getTrimmedValues(results[pair_t(i_ref, i_read)].swr, reads[i_read], TE_references[i_ref].direction, results[pair_t(i_ref, i_read)].trimmedRead, results[pair_t(i_ref, i_read)].trimmedPhred, results[pair_t(i_ref, i_read)].trimmedPosition, results[pair_t(i_ref, i_read)].matchRead, results[pair_t(i_ref, i_read)].matchPhred);
}else{
results[pair_t(i_ref, i_read)].trimmedRead=reads[i_read].sequence;
results[pair_t(i_ref, i_read)].trimmedPhred=reads[i_read].phred;
results[pair_t(i_ref, i_read)].trimmedPosition=0;
results[pair_t(i_ref, i_read)].matchRead="";
results[pair_t(i_ref, i_read)].matchPhred="";
}
if(results[pair_t(i_ref, i_read)].trimmedRead.length()>=transposon_length && results[pair_t(i_ref, i_read)].swr.relativeScore>=match_quality){
results[pair_t(i_ref, i_read)].selected=true;
if(results[pair_t(i_ref, i_read)].swr.score>max_absolute_score){
max_absolute_score=results[pair_t(i_ref, i_read)].swr.score;
ref_read_pair_max=pair_t(i_ref, i_read);
}
if(results[pair_t(i_ref, i_read)].swr.score>best_score_for_read[i_read]){
best_score_for_read[i_read]=results[pair_t(i_ref, i_read)].swr.score;
best_TE_for_read[i_read]=i_ref;
}
}
}
}
if(max_absolute_score<0){
return -1;
}
fastq1= "@"+reads.front().name+"\n";
fastq1=fastq1+results[ref_read_pair_max].trimmedRead+"\n";
fastq1=fastq1+"+\n";
fastq1=fastq1+results[ref_read_pair_max].trimmedPhred+"\n";
fastq_te= "@"+reads.front().name+"\n";
fastq_te=fastq_te+results[ref_read_pair_max].matchRead+"\n";
fastq_te=fastq_te+"+\n";
fastq_te=fastq_te+results[ref_read_pair_max].matchPhred+"\n";
string processedRead;
matchRead=results[ref_read_pair_max].matchRead;
boost::to_lower(matchRead);
if(TE_references[ref_read_pair_max.first].direction<0){
processedRead=results[ref_read_pair_max].trimmedRead+matchRead;
}else{
processedRead=matchRead+results[ref_read_pair_max].trimmedRead;
}
string processedMate;
processedMate="NA";
read_info=reads.front().name+"\t"+TE_references.front().name+"\t"+to_string(results[ref_read_pair_max].trimmedRead.length())+"\t"+to_string(results[ref_read_pair_max].matchRead.length())+"\t"+to_string(results[ref_read_pair_max].swr.relativeScore)+"\t"+processedRead+"\t"+processedMate+"\t"+reads[ref_read_pair_max.second].chromosome+"|"+to_string(reads[ref_read_pair_max.second].position)+"|"+to_string(reads[ref_read_pair_max.second].quality)+"|"+reads[ref_read_pair_max.second].cigarString+"\tNA\n";
return 0;
}
int process_buffer_paired(const double &alignment_quality, const double &match_quality, int transposon_length, int host_length, const std::vector<LTR> &TE_references, buffer<std::pair<Read, Read>> *b, result_texts* rt){
rt->fastq1_txt="";
rt->fastq2_txt="";
rt->fastq_te_txt="";
rt->read_info_txt="";
int i, j;
int n_threads;
#pragma omp parallel
n_threads=omp_get_num_threads();
std::string fastq1_txt_array[n_threads];
std::string fastq2_txt_array[n_threads];
std::string fastq_te_txt_array[n_threads];
std::string read_info_txt_array[n_threads];
for(i=0; i<n_threads; ++i){
fastq1_txt_array[i]="";
fastq2_txt_array[i]="";
fastq_te_txt_array[i]="";
read_info_txt_array[i]="";
}
std::vector<std::pair<Read, Read>> incoming_pairs;
std::vector<Read> reads1, reads2;
while(b->take(incoming_pairs)>=0){
for(i=0; i<incoming_pairs.size(); ++i){
reads1.push_back(incoming_pairs[i].first);
reads2.push_back(incoming_pairs[i].second);
}
if(reads1.size()>=VECTOR_SIZE){
#pragma omp parallel for
for(i=0; i<reads1.size(); ++i){
std::vector<Read> reads_to_process;
std::string fastq1, fastq2, fastq_te, read_info;
reads_to_process.clear();
reads_to_process.push_back(reads1[i]);
reads_to_process.push_back(reads2[i]);
if(process_reads_paired(alignment_quality, match_quality, transposon_length, host_length, TE_references, reads_to_process, fastq1, fastq2, fastq_te, read_info)>=0){
fastq1_txt_array[omp_get_thread_num()]=fastq1_txt_array[omp_get_thread_num()]+fastq1;
fastq2_txt_array[omp_get_thread_num()]=fastq2_txt_array[omp_get_thread_num()]+fastq2;
fastq_te_txt_array[omp_get_thread_num()]=fastq_te_txt_array[omp_get_thread_num()]+fastq_te;
read_info_txt_array[omp_get_thread_num()]=read_info_txt_array[omp_get_thread_num()]+read_info;
}
}
reads1.clear();
reads2.clear();
}
}
#pragma omp parallel for
for(i=0; i<reads1.size(); ++i){
std::vector<Read> reads_to_process;
std::string fastq1, fastq2, fastq_te, read_info;
reads_to_process.clear();
reads_to_process.push_back(reads1[i]);
reads_to_process.push_back(reads2[i]);
if(process_reads_paired(alignment_quality, match_quality, transposon_length, host_length, TE_references, reads_to_process, fastq1, fastq2, fastq_te, read_info)>=0){
fastq1_txt_array[omp_get_thread_num()]=fastq1_txt_array[omp_get_thread_num()]+fastq1;
fastq2_txt_array[omp_get_thread_num()]=fastq2_txt_array[omp_get_thread_num()]+fastq2;
fastq_te_txt_array[omp_get_thread_num()]=fastq_te_txt_array[omp_get_thread_num()]+fastq_te;
read_info_txt_array[omp_get_thread_num()]=read_info_txt_array[omp_get_thread_num()]+read_info;
}
}
for(i=0; i<n_threads; ++i){
rt->fastq1_txt=rt->fastq1_txt+fastq1_txt_array[i];
rt->fastq2_txt=rt->fastq2_txt+fastq2_txt_array[i];
rt->fastq_te_txt=rt->fastq_te_txt+fastq_te_txt_array[i];
rt->read_info_txt=rt->read_info_txt+read_info_txt_array[i];
}
return 0;
}
int process_buffer_unpaired(const double &alignment_quality, const double &match_quality, int transposon_length, int host_length, const std::vector<LTR> &TE_references, buffer<Read> *b, std::string* fastq1_txt, std::string* fastq_te_txt, std::string* read_info_txt){
Read read;
std::vector<Read> reads, incoming_reads;
int i, j;
int n_threads;
#pragma omp parallel
n_threads=omp_get_num_threads();
*fastq1_txt="";
*fastq_te_txt="";
*read_info_txt="";
std::string fastq1_txt_array[n_threads];
std::string fastq_te_txt_array[n_threads];
std::string read_info_txt_array[n_threads];
for(i=0; i<n_threads; ++i){
fastq1_txt_array[i]="";
fastq_te_txt_array[i]="";
read_info_txt_array[i]="";
}
while(b->take(incoming_reads)>=0){
for(i=0; i<incoming_reads.size(); ++i){
reads.push_back(incoming_reads[i]);
}
if(reads.size()>=VECTOR_SIZE){
#pragma omp parallel for
for(i=0; i<reads.size(); ++i){
std::vector<Read> read_to_process;
std::string fastq1, fastq_te, read_info;
read_to_process.clear();
read_to_process.push_back(reads[i]);
if(process_reads_unpaired(alignment_quality, match_quality, transposon_length, host_length, TE_references, read_to_process, fastq1, fastq_te, read_info)>=0){
/*
#pragma omp critical
{
*fastq1_txt=*fastq1_txt+fastq1;
*fastq_te_txt=*fastq_te_txt+fastq_te;
*read_info_txt=*read_info_txt+read_info;
}
*/
fastq1_txt_array[omp_get_thread_num()]=fastq1_txt_array[omp_get_thread_num()]+fastq1;
fastq_te_txt_array[omp_get_thread_num()]=fastq_te_txt_array[omp_get_thread_num()]+fastq_te;
read_info_txt_array[omp_get_thread_num()]=read_info_txt_array[omp_get_thread_num()]+read_info;
}
}
reads.clear();
}
}
#pragma omp parallel for
for(i=0; i<reads.size(); ++i){
std::vector<Read> read_to_process;
std::string fastq1, fastq_te, read_info;
read_to_process.clear();
read_to_process.push_back(reads[i]);
if(process_reads_unpaired(alignment_quality, match_quality, transposon_length, host_length, TE_references, read_to_process, fastq1, fastq_te, read_info)>=0){
/*
#pragma omp critical
{
*fastq1_txt=*fastq1_txt+fastq1;
*fastq_te_txt=*fastq_te_txt+fastq_te;
*read_info_txt=*read_info_txt+read_info;
}
*/
fastq1_txt_array[omp_get_thread_num()]=fastq1_txt_array[omp_get_thread_num()]+fastq1;
fastq_te_txt_array[omp_get_thread_num()]=fastq_te_txt_array[omp_get_thread_num()]+fastq_te;
read_info_txt_array[omp_get_thread_num()]=read_info_txt_array[omp_get_thread_num()]+read_info;
}
}
for(i=0; i<n_threads; ++i){
*fastq1_txt=*fastq1_txt+fastq1_txt_array[i];
*fastq_te_txt=*fastq_te_txt+fastq_te_txt_array[i];
*read_info_txt=*read_info_txt+read_info_txt_array[i];
}
return 0;
}