static std::pair<uint64_t,uint64_t> getParamPair(std::string const & filename, uint64_t const offset)
{
libmaus2::aio::InputStreamInstance istr(filename);
istr.seekg ( offset, std::ios::beg );
uint64_t const b = deserializeNumber(istr);
uint64_t const n = deserializeNumber(istr);
return std::pair<uint64_t,uint64_t>(b,n);
}
static std::pair<uint64_t,uint64_t> getParamPair(std::string const & filename, uint64_t const offset)
{
std::ifstream istr(filename.c_str(),std::ios::binary);
assert ( istr.is_open() );
istr.seekg ( offset, std::ios::beg );
uint64_t const b = deserializeNumber(istr);
uint64_t const n = deserializeNumber(istr);
istr.close();
return std::pair<uint64_t,uint64_t>(b,n);
}
libmaus2::util::Array864::Array864(std::istream & in)
: n(deserializeNumber(in)), B(in), R(new ::libmaus2::rank::ERank222B(B.get(),B.size()*64)), A8(in), A64(in)
{
}
static unique_ptr_type concat(
std::string const & filename,
::libmaus::autoarray::AutoArray<uint64_t> const & offsets,
uint64_t const li, uint64_t const ri
)
{
unique_ptr_type ptr;
if ( ri != li )
{
assert ( ri > li );
uint64_t const b = getParamPair(filename,offsets[0]).first;
uint64_t n = 0;
for ( uint64_t i = li; i < ri; ++i )
{
std::pair<uint64_t,uint64_t> const p = getParamPair(filename,offsets[i]);
assert ( b == p.first );
n += p.second;
}
ptr = unique_ptr_type(new this_type(n,b));
uint64_t totalbits = 0;
for ( uint64_t i = li; i < ri; ++i )
{
std::ifstream istr(filename.c_str(),std::ios::binary);
istr.seekg ( offsets[i], std::ios::beg );
assert ( istr.is_open() );
uint64_t const b = deserializeNumber(istr);
uint64_t const n = deserializeNumber(istr);
uint64_t const s = deserializeNumber(istr);
uint64_t const as = deserializeNumber(istr);
assert ( s == as );
uint64_t const blocksize = 16*1024;
uint64_t wordsleft = (n*b+63)/64;
::libmaus::autoarray::AutoArray<uint64_t> B(blocksize,false);
unsigned int const mod = totalbits % 64;
unsigned int const mod64 = 64-mod;
uint64_t * D = ptr->D + (totalbits/64);
if ( !mod )
{
while ( wordsleft )
{
uint64_t const wordstoread = std::min(wordsleft,blocksize);
uint64_t const bytestoread = wordstoread*sizeof(uint64_t);
istr.read ( reinterpret_cast<char *>(B.get()), bytestoread );
assert ( istr );
assert ( istr.gcount() == static_cast<int64_t>(bytestoread) );
for ( uint64_t z = 0; z < wordstoread; ++z )
*(D++) = B[z];
wordsleft -= wordstoread;
}
}
else
{
while ( wordsleft )
{
uint64_t const wordstoread = std::min(wordsleft,blocksize);
uint64_t const bytestoread = wordstoread*sizeof(uint64_t);
istr.read ( reinterpret_cast<char *>(B.get()), bytestoread );
assert ( istr );
assert ( istr.gcount() == static_cast<int64_t>(bytestoread) );
for ( uint64_t z = 0; z < wordstoread; ++z )
{
*(D++) |= (B[z] >> mod);
*D |= B[z] << (mod64);
}
wordsleft -= wordstoread;
}
}
istr.close();
totalbits += n*b;
}
}
