//////////////////////////////////////////////////////////////////////////
// internalWrite
//virtual
void BcLogFile::internalWrite( const BcChar* pText )
{
BcLog::internalWrite( pText );
if( OutputFile_.isOpen() )
{
OutputFile_.write( pText, BcStrLength( pText ) );
internalFlush();
}
}
void write(const char* data, size_t len) {
if ((len + buffer_used) > buffer_size) {
internalFlush();
}
if (len > buffer_size) {
directWrite(data, len);
} else {
memcpy(buffer_ptr, data, len);
buffer_used += len;
buffer_ptr += len;
}
}
void put(libmaus::fastx::FastQReader::pattern_type const & pattern)
{
uint64_t const patlen = getFastQLength(pattern);
while ( (C.end() - pc) < static_cast<ptrdiff_t>(patlen) )
{
uint64_t const off = pc-C.begin();
uint64_t const newclen = std::max(2*C.size(),static_cast<uint64_t>(1ull));
C.resize(newclen);
pc = C.begin()+off;
}
*(pc)++ = '@';
std::copy(pattern.sid.begin(),pattern.sid.end(),pc);
pc += pattern.sid.size();
*(pc++) = '\n';
std::copy(pattern.spattern.begin(), pattern.spattern.end(),pc);
pc += pattern.spattern.size();
*(pc++) = '\n';
*(pc)++ = '+';
std::copy(pattern.plus.begin(), pattern.plus.end(),pc);
pc += pattern.plus.size();
*(pc++) = '\n';
std::copy(pattern.quality.begin(), pattern.quality.end(),pc);
pc += pattern.quality.size();
*(pc++) = '\n';
assert ( pc <= C.end() );
lnumsyms += pattern.spattern.size();
minlen = std::min(minlen,static_cast<uint64_t>(pattern.spattern.size()));
maxlen = std::max(maxlen,static_cast<uint64_t>(pattern.spattern.size()));
pathigh++;
if ( pathigh - patlow == patperblock )
internalFlush();
}
void flush() {
internalFlush();
directFlush();
}
void flush()
{
if ( bgzfenc )
{
internalFlush();
bgzfenc->flush();
bgzfenc->addEOFBlock();
bgzfenc.reset();
fioutstr->flush();
fioutstr.reset();
libmaus::aio::CheckedOutputStream indexCOS(indexfilename);
::libmaus::util::NumberSerialisation::serialiseNumber(indexCOS,blockcnt);
libmaus::aio::CheckedInputStream fiCIS(fifilename);
#if defined(LIBMAUS_FASTX_FASTQBGZFWRITER_PARALLEL)
bgzfidoutstr->flush();
bgzfidoutstr.reset();
bgzfidxcntoutstr->flush();
bgzfidxcntoutstr.reset();
libmaus::aio::CheckedInputStream bgzfidxCIS(bgzfidxfilename);
libmaus::aio::CheckedInputStream bgzfidxcntCIS(bgzfidxcntfilename);
uint64_t uncompacc = 0;
uint64_t compacc = 0;
for ( uint64_t i = 0; i < blockcnt; ++i )
{
uint64_t const bgzfblocks = libmaus::util::UTF8::decodeUTF8(bgzfidxcntCIS);
uint64_t uncomp = 0;
uint64_t comp = 0;
for ( uint64_t j = 0; j < bgzfblocks; ++j )
{
uncomp += libmaus::util::UTF8::decodeUTF8(bgzfidxCIS);
comp += libmaus::util::UTF8::decodeUTF8(bgzfidxCIS);
}
libmaus::fastx::FastInterval FI = libmaus::fastx::FastInterval::deserialise(fiCIS);
FI.fileoffset = compacc;
FI.fileoffsethigh = compacc + comp;
uncompacc += uncomp;
compacc += comp;
indexCOS << FI.serialise();
}
#else
for ( uint64_t i = 0; i < blockcnt; ++i )
{
libmaus::fastx::FastInterval FI = libmaus::fastx::FastInterval::deserialise(fiCIS);
indexCOS << FI.serialise();
}
#endif
indexCOS.flush();
}
}
