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 *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);
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 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;
};