void set(libmaus2::bambam::parallel::FragmentAlignmentBuffer::shared_ptr_type rblock)
{
block = rblock;
std::vector<std::pair<uint8_t *,uint8_t *> > V;
block->getLinearOutputFragments(V);
std::vector<size_t> const fillVector = block->getFillVector();
assert ( fillVector.size() == V.size() );
if ( V.size() > (D?D->size():0) )
{
libmaus2::autoarray::AutoArray<char const *>::shared_ptr_type T(new libmaus2::autoarray::AutoArray<char const *>(V.size(),false));
D = T;
}
if ( V.size() > (S?S->size():0) )
{
libmaus2::autoarray::AutoArray<size_t>::shared_ptr_type T(new libmaus2::autoarray::AutoArray<size_t>(V.size(),false));
S = T;
}
if ( V.size() > (L?L->size():0) )
{
libmaus2::autoarray::AutoArray<size_t>::shared_ptr_type T(new libmaus2::autoarray::AutoArray<size_t>(V.size(),false));
L = T;
}
for ( uint64_t i = 0; i < V.size(); ++i )
{
D->at(i) = reinterpret_cast<char const *>(V[i].first);
S->at(i) = V[i].second-V[i].first;
L->at(i) = fillVector.at(i);
}
numblocks = V.size();
}
::libmaus2::suffixsort::BwtMergeZBlockRequest const & operator[](uint64_t const i) const
{
return requests.at(i);
}