void *t_PairAlign(void *)
{
PairAlign a;
int n1, n2;
bit32_t cur_at;
a.ImportFileFormat(read_a._file_format, read_b._file_format);
while(1) {
pthread_mutex_lock(&mutex_fin);
n1=read_a.LoadBatchReads(fin_a);
n2=read_b.LoadBatchReads(fin_b);
cur_at=read_a._index;
a.ImportBatchReads(n1, read_a.mreads, read_b.mreads);
pthread_mutex_unlock(&mutex_fin);
if(!n1||(n1!=n2))
break;
a.Do_Batch(ref);
pthread_mutex_lock(&mutex_fout);
fout<<a._str_align;
fout_unpair<<a._str_align_unpair;
cout<<cur_at<<" reads finished. "<<Cal_AllTime()<<" secs passed"<<endl;
pthread_mutex_unlock(&mutex_fout);
}
pthread_mutex_lock(&mutex_fout);
n_aligned_pairs+=a.n_aligned_pairs;
n_aligned_a+=a.n_aligned_a;
n_aligned_b+=a.n_aligned_b;
pthread_mutex_unlock(&mutex_fout);
};
void Do_SingleAlign()
{
read_a.CheckFile(fin_a);
SingleAlign a;
a.ImportFileFormat(read_a._file_format);
a.SetFlag('a');
while(read_a.LoadBatchReads(fin_a))
{
a.ImportBatchReads(read_a.num, read_a.mreads);
a.Do_Batch(ref);
fout<<a._str_align;
cout<<read_a._index<<" reads finished. "<<Cal_AllTime()<<" secs passed"<<endl;
}
n_aligned=a.n_aligned;
};
void *t_SingleAlign(void *)
{
SingleAlign a;
int n;
bit32_t cur_at;
a.ImportFileFormat(read_a._file_format);
a.SetFlag('a');
while(1)
{
pthread_mutex_lock(&mutex_fin);
n=read_a.LoadBatchReads(fin_a);
cur_at=read_a._index;
a.ImportBatchReads(read_a.num, read_a.mreads);
pthread_mutex_unlock(&mutex_fin);
if(!n)
break;
a.Do_Batch(ref);
pthread_mutex_lock(&mutex_fout);
fout<<a._str_align;
cout<<cur_at<<" reads finished. "<<Cal_AllTime()<<" secs passed"<<endl;
pthread_mutex_unlock(&mutex_fout);
}
pthread_mutex_lock(&mutex_fout);
n_aligned+=a.n_aligned;
pthread_mutex_unlock(&mutex_fout);
};
void Do_PairAlign()
{
if(param.max_snp_num>0)
param.max_snp_num=2;
read_a.CheckFile(fin_a);
read_b.CheckFile(fin_b);
vector<pthread_t> pthread_ids(param.num_procs);
//create
for(int i=0; i<param.num_procs; i++)
pthread_create(&pthread_ids[i], NULL, t_PairAlign, NULL);
//join
for (int i=0; i<param.num_procs; i++)
pthread_join(pthread_ids[i], NULL);
//
};
void Do_SingleAlign()
{
read_a.CheckFile(fin_a);
vector<pthread_t> pthread_ids(param.num_procs);
//create
for(int i=0; i<param.num_procs; i++)
pthread_create(&pthread_ids[i], NULL, t_SingleAlign, NULL);
//join
for (int i=0; i<param.num_procs; i++)
pthread_join(pthread_ids[i], NULL);
};
void Do_PairAlign()
{
if(param.max_snp_num>0)
param.max_snp_num=2;
read_a.CheckFile(fin_a);
read_b.CheckFile(fin_b);
PairAlign a;
int n1, n2;
while(1)
{
n1=read_a.LoadBatchReads(fin_a);
n2=read_b.LoadBatchReads(fin_b);
if(!n1||(n1!=n2))
break;
a.ImportBatchReads(n1, read_a.mreads, read_b.mreads);
a.Do_Batch(ref);
fout<<a._str_align;
fout_unpair<<a._str_align_unpair;
cout<<read_a._index<<" reads finished. "<<Cal_AllTime()<<" secs passed"<<endl;
}
n_aligned_pairs=a.n_aligned_pairs;
n_aligned_a=a.n_aligned_a;
n_aligned_b=a.n_aligned_b;
};
void RunProcess(void) {
if (!query_a_file.empty())
{
fin_a.open(query_a_file.c_str());
if (!fin_a)
{
cerr << "failed to open file: "<< query_a_file << endl;
exit(1);
}
}else if (!query_q_file.empty()){
fin_a.open(query_q_file.c_str());
param.fin_q = true;
if (!fin_a)
{
cerr << "failed to open file: "<< query_q_file << endl;
exit(1);
}
}
else
{
cerr <<"missing query file(s)\n";
exit(1);
}
cerr << "Read recruitment:\n";
cerr << "Query: " << query_a_file << " Reference: " << ref_file << endl;
fout.open(out_align_file.c_str());
if (!fout)
{
cerr << "failed to open file: " << out_align_file << endl;
exit(1);
}
unsigned int n_aligned(0); // Number of reads recruited
read_a.InitialIndex();
n_aligned=Do_ReadAlign();
fin_a.close();
fout.close();
cerr << "Total number of reads recruited: " << n_aligned << " (" << setprecision(2) << 100.0*n_aligned/read_a._index << "%)\n";
cerr << "Done.\n";
cerr << "Finished at " << Curr_Time();
cerr << "Total time consumed: " << Cal_AllTime() << " secs\n";
}
void RunProcess(void)
{
//pair-end alignment
if((!query_a_file.empty()) && (!query_b_file.empty()))
{
cout<<"Pair-end alignment:\n";
cout<<"Query: "<<query_a_file<<" "<<query_b_file<<" Reference: "<<ref_file<<" Output: "<<out_align_file<<" "<<out_align_file_unpair<<endl;
fin_a.open(query_a_file.c_str());
if(!fin_a) {
cerr<<"failed to open file: "<<query_a_file<<endl;
exit(1);
}
fin_b.open(query_b_file.c_str());
if(!fin_b) {
cerr<<"failed to open file: "<<query_b_file<<endl;
exit(1);
}
fout.open(out_align_file.c_str());
if(!fout) {
cerr<<"failed to open file: "<<out_align_file<<endl;
exit(1);
}
fout_unpair.open(out_align_file_unpair.c_str());
if(!fout_unpair) {
cerr<<"failed to open file: "<<out_align_file_unpair<<endl;
exit(1);
}
n_aligned_pairs=n_aligned_a=n_aligned_b=0;
read_a.InitialIndex();
read_b.InitialIndex();
Do_PairAlign();
fin_a.close();
fin_b.close();
fout.close();
fout_unpair.close();
cout<<"Total number of aligned reads: \n"
<<"pairs: "<<n_aligned_pairs<<" ("<<setprecision(2)<<100.0*n_aligned_pairs/read_a._index<<"%)\n"
<<"single a: "<<n_aligned_a<<" ("<<setprecision(2)<<100.0*n_aligned_a/read_a._index<<"%)\n"
<<"single b: "<<n_aligned_b<<" ("<<setprecision(2)<<100.0*n_aligned_b/read_b._index<<"%)\n";
}
//single-read alignment
else
{
if(!query_a_file.empty()) {
fin_a.open(query_a_file.c_str());
if(!fin_a) {
cerr<<"b failed to open file: "<<query_a_file<<endl;
exit(1);
}
}
else
{
cerr<<"missing query file(s)\n";
exit(1);
}
cout<<"Single read alignment:\n";
cout<<"Query: "<<query_a_file<<" Reference: "<<ref_file<<" Output: "<<out_align_file<<endl;
fout.open(out_align_file.c_str());
if(!fout) {
cerr<<"failed to open file: "<<out_align_file<<endl;
exit(1);
}
n_aligned=0;
read_a.InitialIndex();
Do_SingleAlign();
fin_a.close();
fout.close();
cout<<"Total number of aligned reads: "<<n_aligned<<" ("<<setprecision(2)
<<100.0*n_aligned/read_a._index<<"%)\n";
}
cout<<"Done.\n";
cout<<"Finished at "<<Curr_Time();
cout<<"Total time consumed: "<<Cal_AllTime()<<" secs\n";
};
