void DindelUtil::doMultipleReadHaplotypeAlignment(const std::vector<DindelRead> & dReads,
const StringVector & haplotypes)
{
// globally align haplotypes to the first haplotype (arbitrary)
assert(haplotypes.size()>0);
for (size_t h = 0; h < haplotypes.size(); ++h)
{
std::cout << "ALIGNING EVERYTHING AGAINST HAPLOTYPE " << h << "\n";
MultipleAlignment ma;
const std::string rootSequence = haplotypes[h];
ma.addBaseSequence("root", rootSequence, "");
std::string hid;
for(size_t j = 0; j < haplotypes.size(); j++)
{
std::stringstream ss;
if (j!=h)
ss << "haplotype-" << j;
else
ss << "HAPLOTYPE-" << j;
SequenceOverlap o = Overlapper::computeOverlap(rootSequence, haplotypes[j]);
ma.addOverlap(ss.str(), haplotypes[j], "", o);
}
for(size_t r = 0; r < dReads.size(); ++r)
{
std::stringstream ss;
if (r<dReads.size()/2)
ss << "read-" << r << "(" << dReads[r].getID() << ")";
else
ss << "MATE read-" << r;
SequenceOverlap o = Overlapper::computeOverlap(rootSequence, dReads[r].getSequence());
ma.addOverlap(ss.str(), dReads[r].getSequence(), "", o);
}
ma.print(100000);
}
}
