uint64_t flush()
{
/* flush, compress */
BgzfDeflateZStreamBaseFlushInfo BDZSBFI = base_type::flush(flushmode);
/* write blocks */
streamWrite(inbuf.begin(), outbuf.begin(), BDZSBFI);
if ( flushmode )
{
assert ( ! BDZSBFI.movesize );
}
else
{
if ( BDZSBFI.movesize )
BgzfDeflateInputBufferBase::pc = BDZSBFI.moveUncompressedRest();
else
BgzfDeflateInputBufferBase::pc = BgzfDeflateInputBufferBase::pa;
}
/* return number of compressed bytes written */
return BDZSBFI.getCompressedSize();
}
void * run()
{
while ( true )
{
/* get any id from global list */
BgzfThreadQueueElement defglob;
try
{
defglob = deflatecontext.deflategloblist.deque();
}
catch(std::exception const & ex)
{
/* queue is terminated, break loop */
break;
}
libmaus2_lz_bgzf_op_type op = defglob.op;
uint64_t objectid = 0;
{
libmaus2::parallel::ScopePosixMutex S(deflatecontext.deflateqlock);
switch ( op )
{
case libmaus2_lz_bgzf_op_compress_block:
objectid = deflatecontext.deflatecompqueue.front();
deflatecontext.deflatecompqueue.pop_front();
break;
case libmaus2_lz_bgzf_op_write_block:
{
BgzfThreadQueueElement const btqe = deflatecontext.deflatewritequeue.deque();
objectid = btqe.objectid;
libmaus2::parallel::ScopePosixMutex O(deflatecontext.deflateoutlock);
assert ( deflatecontext.deflateB[objectid]->blockid == deflatecontext.deflatenextwriteid );
break;
}
default:
break;
}
assert ( op != libmaus2_lz_bgzf_op_none );
}
switch ( op )
{
case libmaus2_lz_bgzf_op_compress_block:
{
try
{
BgzfDeflateZStreamBaseFlushInfo const BDZSBFI = deflatecontext.deflateB[objectid]->flush(true /* full flush */);
assert ( !BDZSBFI.movesize );
deflatecontext.deflateB[objectid]->compsize = BDZSBFI.getCompressedSize();
deflatecontext.deflateB[objectid]->flushinfo = BDZSBFI;
}
catch(libmaus2::exception::LibMausException const & ex)
{
libmaus2::parallel::ScopePosixMutex S(deflatecontext.deflateexlock);
if ( deflatecontext.deflateB[objectid]->blockid * 2 + 0 < deflatecontext.deflateexceptionid )
{
deflatecontext.deflateexceptionid = deflatecontext.deflateB[objectid]->blockid * 2 + 0;
libmaus2::exception::LibMausException::unique_ptr_type tex(ex.uclone());
deflatecontext.deflatepse = UNIQUE_PTR_MOVE(tex);
}
deflatecontext.deflateB[objectid]->compsize = 0;
deflatecontext.deflateB[objectid]->flushinfo = BgzfDeflateZStreamBaseFlushInfo();
}
catch(std::exception const & ex)
{
libmaus2::parallel::ScopePosixMutex S(deflatecontext.deflateexlock);
if ( deflatecontext.deflateB[objectid]->blockid * 2 + 0 < deflatecontext.deflateexceptionid )
{
deflatecontext.deflateexceptionid = deflatecontext.deflateB[objectid]->blockid * 2 + 0;
libmaus2::exception::LibMausException se;
se.getStream() << ex.what() << std::endl;
se.finish();
libmaus2::exception::LibMausException::unique_ptr_type tex(se.uclone());
deflatecontext.deflatepse = UNIQUE_PTR_MOVE(tex);
}
deflatecontext.deflateB[objectid]->compsize = 0;
deflatecontext.deflateB[objectid]->flushinfo = BgzfDeflateZStreamBaseFlushInfo();
}
libmaus2::parallel::ScopePosixMutex S(deflatecontext.deflateqlock);
deflatecontext.deflatewritequeue.enque(
BgzfThreadQueueElement(
libmaus2::lz::BgzfThreadOpBase::libmaus2_lz_bgzf_op_write_block,
objectid,
deflatecontext.deflateB[objectid]->blockid
),
&(deflatecontext.deflategloblist)
);
break;
}
case libmaus2_lz_bgzf_op_write_block:
{
libmaus2::parallel::ScopePosixMutex O(deflatecontext.deflateoutlock);
try
{
#if 0
deflatecontext.deflateout.write(
reinterpret_cast<char const *>(deflatecontext.deflateB[objectid]->outbuf.begin()),
deflatecontext.deflateB[objectid]->compsize
);
#endif
deflatecontext.streamWrite(
deflatecontext.deflateB[objectid]->inbuf.begin(),
deflatecontext.deflateB[objectid]->outbuf.begin(),
deflatecontext.deflateB[objectid]->flushinfo
);
deflatecontext.deflateoutbytes += deflatecontext.deflateB[objectid]->compsize;
#if 0
std::cerr << "compsize "
<< deflatecontext.deflateB[objectid]->compsize
<< " outbytes "
<< deflatecontext.deflateoutbytes
<< std::endl;
#endif
#if 0 // this test is done in streamWrite()
if ( ! deflatecontext.deflateout )
{
libmaus2::exception::LibMausException se;
se.getStream() << "BgzfDeflateParallel: output error on output stream." << std::endl;
se.finish();
throw se;
}
#endif
if ( deflatecontext.deflateindexstr )
{
if ( deflatecontext.deflateB[objectid]->flushinfo.blocks == 0 )
{
}
else if ( deflatecontext.deflateB[objectid]->flushinfo.blocks == 1 )
{
libmaus2::util::UTF8::encodeUTF8(deflatecontext.deflateB[objectid]->flushinfo.block_a_u,*(deflatecontext.deflateindexstr));
libmaus2::util::UTF8::encodeUTF8(deflatecontext.deflateB[objectid]->flushinfo.block_a_c,*(deflatecontext.deflateindexstr));
}
else if ( deflatecontext.deflateB[objectid]->flushinfo.blocks == 2 )
{
libmaus2::util::UTF8::encodeUTF8(deflatecontext.deflateB[objectid]->flushinfo.block_a_u,*(deflatecontext.deflateindexstr));
libmaus2::util::UTF8::encodeUTF8(deflatecontext.deflateB[objectid]->flushinfo.block_a_c,*(deflatecontext.deflateindexstr));
libmaus2::util::UTF8::encodeUTF8(deflatecontext.deflateB[objectid]->flushinfo.block_b_u,*(deflatecontext.deflateindexstr));
libmaus2::util::UTF8::encodeUTF8(deflatecontext.deflateB[objectid]->flushinfo.block_b_c,*(deflatecontext.deflateindexstr));
}
}
}
catch(libmaus2::exception::LibMausException const & ex)
{
libmaus2::parallel::ScopePosixMutex S(deflatecontext.deflateexlock);
if ( deflatecontext.deflateB[objectid]->blockid * 2 + 1 < deflatecontext.deflateexceptionid )
{
deflatecontext.deflateexceptionid = deflatecontext.deflateB[objectid]->blockid * 2 + 1;
libmaus2::exception::LibMausException::unique_ptr_type tex(ex.uclone());
deflatecontext.deflatepse = UNIQUE_PTR_MOVE(tex);
}
}
catch(std::exception const & ex)
{
libmaus2::parallel::ScopePosixMutex S(deflatecontext.deflateexlock);
if ( deflatecontext.deflateB[objectid]->blockid * 2 + 1 < deflatecontext.deflateexceptionid )
{
deflatecontext.deflateexceptionid = deflatecontext.deflateB[objectid]->blockid * 2 + 1;
libmaus2::exception::LibMausException se;
se.getStream() << ex.what() << std::endl;
se.finish();
libmaus2::exception::LibMausException::unique_ptr_type tex(se.uclone());
deflatecontext.deflatepse = UNIQUE_PTR_MOVE(tex);
}
}
deflatecontext.deflatenextwriteid += 1;
deflatecontext.deflatewritequeue.setReadyFor(
BgzfThreadQueueElement(
libmaus2::lz::BgzfThreadOpBase::libmaus2_lz_bgzf_op_write_block,
objectid,
deflatecontext.deflatenextwriteid
),
&(deflatecontext.deflategloblist)
);
deflatecontext.deflatefreelist.enque(objectid);
break;
}
default:
{
break;
}
}
}
return 0;
}