::libmaus2::util::Histogram::unique_ptr_type libmaus2::util::Utf8String::getHistogram(::libmaus2::autoarray::AutoArray<uint8_t> const & A)
{
#if defined(_OPENMP)
uint64_t const numthreads = omp_get_max_threads();
#else
uint64_t const numthreads = 1;
#endif
::libmaus2::autoarray::AutoArray<uint64_t> const partstarts = computePartStarts(A,numthreads);
uint64_t const numparts = partstarts.size()-1;
::libmaus2::util::Histogram::unique_ptr_type hist(new ::libmaus2::util::Histogram);
::libmaus2::parallel::OMPLock lock;
#if defined(_OPENMP)
#pragma omp parallel for
#endif
for ( int64_t t = 0; t < static_cast<int64_t>(numparts); ++t )
{
::libmaus2::util::Histogram::unique_ptr_type lhist(new ::libmaus2::util::Histogram);
uint64_t codelen = 0;
uint64_t const tcodelen = partstarts[t+1]-partstarts[t];
::libmaus2::util::GetObject<uint8_t const *> G(A.begin()+partstarts[t]);
while ( codelen != tcodelen )
(*lhist)(::libmaus2::util::UTF8::decodeUTF8(G,codelen));
lock.lock();
hist->merge(*lhist);
lock.unlock();
}
return UNIQUE_PTR_MOVE(hist);
}
/**
* compute character histogram in parallel
**/
::libmaus::autoarray::AutoArray<uint64_t> computeCharHist(std::string const & inputfile)
{
uint64_t const n = ::libmaus::util::GetFileSize::getFileSize(inputfile);
#if defined(_OPENMP)
uint64_t const numthreads = omp_get_max_threads();
#else
uint64_t const numthreads = 1;
#endif
uint64_t const packsize = (n + numthreads-1)/numthreads;
::libmaus::parallel::OMPLock lock;
::libmaus::autoarray::AutoArray<uint64_t> ghist(256);
#if defined(_OPENMP)
#pragma omp parallel for
#endif
for ( int64_t t = 0; t < static_cast<int64_t>(numthreads); ++t )
{
uint64_t const low = std::min(n,t*packsize);
uint64_t const high = std::min(n,low+packsize);
uint64_t const range = high-low;
if ( range )
{
::libmaus::autoarray::AutoArray<uint64_t> lhist(ghist.size());
::libmaus::aio::CheckedInputStream CIS(inputfile);
CIS.seekg(low);
uint64_t const blocksize = 8192;
uint64_t const numblocks = ((range)+blocksize-1)/blocksize;
::libmaus::autoarray::AutoArray<uint8_t> B(blocksize);
for ( uint64_t b = 0; b < numblocks; ++b )
{
uint64_t const llow = std::min(low + b*blocksize,high);
uint64_t const lhigh = std::min(llow + blocksize,high);
uint64_t const lrange = lhigh-llow;
CIS.read ( reinterpret_cast<char *>(B.begin()), lrange );
assert ( CIS.gcount() == static_cast<int64_t>(lrange) );
for ( uint64_t i = 0; i < lrange; ++i )
lhist[B[i]]++;
}
lock.lock();
for ( uint64_t i = 0; i < lhist.size(); ++i )
ghist[i] += lhist[i];
lock.unlock();
}
}
return ghist;
}
