void PairAlign::Do_Batch(RefSeq &ref)
{
bool detect_pairs;
bool detect_a;
bool detect_b;
strAlign.clear();
strAlign_unpair.clear();
int tt=0;
int filter1, filter2;
if (0==param.trim_lowQ)
{
for (singleAlignSa.readBuffer=singleAlignSa.mreads.begin(), singleAlignSb.readBuffer=singleAlignSb.mreads.begin(); tt<num_reads; singleAlignSa.readBuffer++, singleAlignSb.readBuffer++, tt++)
{
filter1=singleAlignSa.FilterReads();
filter2=singleAlignSb.FilterReads();
if (!(filter1 || filter2))
{
if (RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
}
else
{
if (singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
if (singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
else
{
if (!filter1)
{
if (singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
}
if (!filter2)
{
if (singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
}
}
else if (10>=param.trim_lowQ)
{
for (singleAlignSa.readBuffer=singleAlignSa.mreads.begin(), singleAlignSb.readBuffer=singleAlignSb.mreads.begin(); tt<num_reads; singleAlignSa.readBuffer++, singleAlignSb.readBuffer++, tt++)
{
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-param.trim_lowQ, param.trim_lowQ);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-param.trim_lowQ, param.trim_lowQ);
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-param.trim_lowQ, param.trim_lowQ);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-param.trim_lowQ, param.trim_lowQ);
filter1=singleAlignSa.FilterReads();
filter2=singleAlignSb.FilterReads();
if (!(filter1 || filter2))
{
if (RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
}
else
{
if (singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
if (singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
else
{
if (!filter1)
{
if (singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
}
if (!filter2)
{
if (singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
}
}
else if (20>=param.trim_lowQ)
{
for (singleAlignSa.readBuffer=singleAlignSa.mreads.begin(), singleAlignSb.readBuffer=singleAlignSb.mreads.begin(); tt<num_reads; singleAlignSa.readBuffer++, singleAlignSb.readBuffer++, tt++)
{
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-10), param.trim_lowQ-10);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-10), param.trim_lowQ-10);
singleAlignSa.readBuffer->seq.erase(0,1);
singleAlignSa.readBuffer->qual.erase(0,1);
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-10), param.trim_lowQ-10);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-10), param.trim_lowQ-10);
singleAlignSb.readBuffer->seq.erase(0,1);
singleAlignSb.readBuffer->qual.erase(0,1);
filter1=singleAlignSa.FilterReads();
filter2=singleAlignSb.FilterReads();
if (!(filter1 || filter2))
{
if (RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
}
else
{
if (singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
if (singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
else
{
if (!filter1)
{
if (singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
}
if (!filter2)
{
if (singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
}
}
else if (30>=param.trim_lowQ)
{
for (singleAlignSa.readBuffer=singleAlignSa.mreads.begin(), singleAlignSb.readBuffer=singleAlignSb.mreads.begin(); tt<num_reads; singleAlignSa.readBuffer++, singleAlignSb.readBuffer++, tt++)
{
//store the original seq and qual
singleAlignSa.oriReadSeq = singleAlignSa.readBuffer->seq;
singleAlignSa.oriReadQual = singleAlignSa.readBuffer->qual;
singleAlignSb.oriReadSeq = singleAlignSb.readBuffer->seq;
singleAlignSb.oriReadQual = singleAlignSb.readBuffer->qual;
//try pair-end align first, if no hits, try single-read align later
if (!(singleAlignSa.FilterReads() || singleAlignSb.FilterReads()) && RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
continue;
}
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-20), param.trim_lowQ-20);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-20), param.trim_lowQ-20);
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-20), param.trim_lowQ-20);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-20), param.trim_lowQ-20);
if (!(singleAlignSa.FilterReads() || singleAlignSb.FilterReads()) && RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
continue;
}
// if no hits, try single-read align later
singleAlignSa.readBuffer->seq = singleAlignSa.oriReadSeq;
singleAlignSa.readBuffer->qual = singleAlignSa.oriReadQual;
singleAlignSb.readBuffer->seq = singleAlignSb.oriReadSeq;
singleAlignSb.readBuffer->qual = singleAlignSb.oriReadQual;
if (!singleAlignSa.FilterReads() && singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-20), param.trim_lowQ-20);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-20), param.trim_lowQ-20);
if (!singleAlignSa.FilterReads())
{
if (singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
}
}
if (!singleAlignSb.FilterReads() && singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-20), param.trim_lowQ-20);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-20), param.trim_lowQ-20);
if (!singleAlignSb.FilterReads())
{
if (singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
}
}
else if (40>=param.trim_lowQ)
{
for (singleAlignSa.readBuffer=singleAlignSa.mreads.begin(), singleAlignSb.readBuffer=singleAlignSb.mreads.begin(); tt<num_reads; singleAlignSa.readBuffer++, singleAlignSb.readBuffer++, tt++)
{
//store the original seq and qual
singleAlignSa.oriReadSeq = singleAlignSa.readBuffer->seq;
singleAlignSa.oriReadQual = singleAlignSa.readBuffer->qual;
singleAlignSb.oriReadSeq = singleAlignSb.readBuffer->seq;
singleAlignSb.oriReadQual = singleAlignSb.readBuffer->qual;
//try pair-end align first, if no hits, try single-read align later
if (!(singleAlignSa.FilterReads() || singleAlignSb.FilterReads()) && RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
continue;
}
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-30), param.trim_lowQ-30);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-30), param.trim_lowQ-30);
singleAlignSa.readBuffer->seq.erase(0,1);
singleAlignSa.readBuffer->qual.erase(0,1);
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-30), param.trim_lowQ-30);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-30), param.trim_lowQ-30);
singleAlignSb.readBuffer->seq.erase(0,1);
singleAlignSb.readBuffer->qual.erase(0,1);
if (!(singleAlignSa.FilterReads() || singleAlignSb.FilterReads()) && RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
continue;
}
// if no hits, try single-read align later
singleAlignSa.readBuffer->seq = singleAlignSa.oriReadSeq;
singleAlignSa.readBuffer->qual = singleAlignSa.oriReadQual;
singleAlignSb.readBuffer->seq = singleAlignSb.oriReadSeq;
singleAlignSb.readBuffer->qual = singleAlignSb.oriReadQual;
if (!singleAlignSa.FilterReads() && singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-30), param.trim_lowQ-30);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-30), param.trim_lowQ-30);
singleAlignSa.readBuffer->seq.erase(0,1);
singleAlignSa.readBuffer->qual.erase(0,1);
if (!singleAlignSa.FilterReads())
{
if (singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
}
}
if (!singleAlignSb.FilterReads() && singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-30), param.trim_lowQ-30);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-30), param.trim_lowQ-30);
singleAlignSb.readBuffer->seq.erase(0,1);
singleAlignSb.readBuffer->qual.erase(0,1);
if (!singleAlignSb.FilterReads())
{
if (singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}else{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
}
}
else if (50>=param.trim_lowQ)
{
for (singleAlignSa.readBuffer=singleAlignSa.mreads.begin(), singleAlignSb.readBuffer=singleAlignSb.mreads.begin(); tt<num_reads; singleAlignSa.readBuffer++, singleAlignSb.readBuffer++, tt++)
{
//store the original seq and qual
singleAlignSa.oriReadSeq = singleAlignSa.readBuffer->seq;
singleAlignSa.oriReadQual = singleAlignSa.readBuffer->qual;
singleAlignSb.oriReadSeq = singleAlignSb.readBuffer->seq;
singleAlignSb.oriReadQual = singleAlignSb.readBuffer->qual;
//try pair-end align first, if no hits, try single-read align later
if (!(singleAlignSa.FilterReads() || singleAlignSb.FilterReads()) && RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
continue;
}
detect_pairs=0;
while (1)
{
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-40), param.trim_lowQ-40);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-40), param.trim_lowQ-40);
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-40), param.trim_lowQ-40);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-40), param.trim_lowQ-40);
if (singleAlignSa.readBuffer->seq.size()<param.min_read_size)
break;
if (!(singleAlignSa.FilterReads() || singleAlignSb.FilterReads()) && RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
detect_pairs=1;
break;
}
}
if (detect_pairs)
continue;
// if no hits, try single-read align later
singleAlignSa.readBuffer->seq = singleAlignSa.oriReadSeq;
singleAlignSa.readBuffer->qual = singleAlignSa.oriReadQual;
singleAlignSb.readBuffer->seq = singleAlignSb.oriReadSeq;
singleAlignSb.readBuffer->qual = singleAlignSb.oriReadQual;
if (!singleAlignSa.FilterReads() && singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
while(1)
{
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-40), param.trim_lowQ-40);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-40), param.trim_lowQ-40);
if (singleAlignSa.readBuffer->seq.size()<param.min_read_size)
break;
if (!singleAlignSa.FilterReads() && singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
detect_a=1;
break;
}
else
{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
}
}
if (!singleAlignSb.FilterReads() && singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
while(1)
{
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-40), param.trim_lowQ-40);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-40), param.trim_lowQ-40);
if (singleAlignSb.readBuffer->seq.size()<param.min_read_size)
break;
if (!singleAlignSb.FilterReads() && singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
detect_b=1;
break;
}else{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
}
}
else if (60>=param.trim_lowQ)
{
for (singleAlignSa.readBuffer=singleAlignSa.mreads.begin(), singleAlignSb.readBuffer=singleAlignSb.mreads.begin(); tt<num_reads; singleAlignSa.readBuffer++, singleAlignSb.readBuffer++, tt++)
{
//store the original seq and qual
singleAlignSa.oriReadSeq = singleAlignSa.readBuffer->seq;
singleAlignSa.oriReadQual = singleAlignSa.readBuffer->qual;
singleAlignSb.oriReadSeq = singleAlignSb.readBuffer->seq;
singleAlignSb.oriReadQual = singleAlignSb.readBuffer->qual;
//try pair-end align first, if no hits, try single-read align later
if (!(singleAlignSa.FilterReads() || singleAlignSb.FilterReads()) && RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
continue;
}
detect_pairs=0;
singleAlignSa.readBuffer->seq.erase(0,1);
singleAlignSa.readBuffer->qual.erase(0,1);
singleAlignSb.readBuffer->seq.erase(0,1);
singleAlignSb.readBuffer->qual.erase(0,1);
while(1)
{
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-50), param.trim_lowQ-50);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-50), param.trim_lowQ-50);
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-50), param.trim_lowQ-50);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-50), param.trim_lowQ-50);
if (singleAlignSa.readBuffer->seq.size()<param.min_read_size)
break;
if (!(singleAlignSa.FilterReads() || singleAlignSb.FilterReads()) && RunAlign(ref))
{
StringAlign(ref, strAlign);
n_aligned_pairs++;
detect_pairs=1;
break;
}
}
if (detect_pairs)
continue;
// if no hits, try single-read align later
singleAlignSa.readBuffer->seq = singleAlignSa.oriReadSeq;
singleAlignSa.readBuffer->qual = singleAlignSa.oriReadQual;
singleAlignSb.readBuffer->seq = singleAlignSb.oriReadSeq;
singleAlignSb.readBuffer->qual = singleAlignSb.oriReadQual;
if (!singleAlignSa.FilterReads() && singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
}
else
{
singleAlignSa.readBuffer->seq.erase(0,1);
singleAlignSa.readBuffer->qual.erase(0,1);
while(1)
{
singleAlignSa.readBuffer->seq.erase(singleAlignSa.readBuffer->seq.size()-(param.trim_lowQ-50), param.trim_lowQ-50);
singleAlignSa.readBuffer->qual.erase(singleAlignSa.readBuffer->qual.size()-(param.trim_lowQ-50), param.trim_lowQ-50);
if (singleAlignSa.readBuffer->seq.size()<param.min_read_size)
break;
if (!singleAlignSa.FilterReads() && singleAlignSa.RunAlign(ref))
{
singleAlignSa.StringAlign(ref, strAlign_unpair);
n_aligned_a++;
detect_a=1;
break;
}else{
as.collect_unalign_reads(singleAlignSa.readBuffer->name,singleAlignSa.readBuffer->seq);
}
}
}
if (!singleAlignSb.FilterReads() && singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
}
else
{
singleAlignSb.readBuffer->seq.erase(0,1);
singleAlignSb.readBuffer->qual.erase(0,1);
while(1)
{
singleAlignSb.readBuffer->seq.erase(singleAlignSb.readBuffer->seq.size()-(param.trim_lowQ-50), param.trim_lowQ-50);
singleAlignSb.readBuffer->qual.erase(singleAlignSb.readBuffer->qual.size()-(param.trim_lowQ-50), param.trim_lowQ-50);
if (singleAlignSb.readBuffer->seq.size()<param.min_read_size)
break;
if (!singleAlignSb.FilterReads() && singleAlignSb.RunAlign(ref))
{
singleAlignSb.StringAlign(ref, strAlign_unpair);
n_aligned_b++;
detect_b=1;
break;
}
else
{
as.collect_unalign_reads(singleAlignSb.readBuffer->name,singleAlignSb.readBuffer->seq);
}
}
}
}
}
// cout<<strAlign<<endl;
}
