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/*++
Module Name:
GzipDataWriter.h
Abstract:
Headers for the GzipDataWriter & related classes for the SNAP sequencer
Authors:
Ravi Pandya, Mar 2013
Environment:
User mode service.
Revision History:
--*/
#pragma once
#include "Compat.h"
#include "Read.h"
#include "Compat.h"
#include "DataWriter.h"
#include "VariableSizeVector.h"
#include "stdafx.h"
#include "zlib.h"
#include "Error.h"
using std::pair;
class GzipWriterFilterSupplier : public DataWriter::FilterSupplier
{
public:
GzipWriterFilterSupplier(bool i_bamFormat, size_t i_chunkSize, int i_numThreads, bool i_bindToProcessors, bool i_multiThreaded)
:
FilterSupplier(DataWriter::ResizeFilter),
bamFormat(i_bamFormat),
chunkSize(i_chunkSize),
numThreads(i_numThreads),
bindToProcessors(i_bindToProcessors),
multiThreaded(i_multiThreaded),
closing(false)
{
InitializeExclusiveLock(&lock);
}
virtual ~GzipWriterFilterSupplier()
{
DestroyExclusiveLock(&lock);
}
const bool multiThreaded;
virtual DataWriter::Filter* getFilter();
virtual void onClosing(DataWriterSupplier* supplier);
virtual void onClosed(DataWriterSupplier* supplier) {}
void addTranslations(VariableSizeVector< pair<_uint64,_uint64> >* translation);
bool translate(_uint64 logical, _uint64* o_physical, _uint64* delta);
// translate to BAM virtual offset format
_uint64 toVirtualOffset(_uint64 logical)
{
_uint64 physical, delta;
if (logical != UINT64_MAX && translate(logical, &physical, &delta)) {
if (delta < 65536 && physical < ((_uint64) 1 << 48)) {
return (physical << 16) | delta;
}
WriteErrorMessage( "Invalid virtual file offset, logical=%llu, start=%llu, delta=%llu\n", logical, physical, delta);
}
return 0;
}
private:
friend class GzipWriterFilter;
friend class GzipCompressWorkerManager;
void addTranslation(_uint64 logical, _uint64 physical)
{
AcquireExclusiveLock(&lock);
translation.push_back(pair<_uint64,_uint64>(logical, physical));
ReleaseExclusiveLock(&lock);
}
static bool translationComparator(const pair<_uint64,_uint64>& a, const pair<_uint64,_uint64>& b);
const bool bamFormat;
const size_t chunkSize;
const int numThreads;
const bool bindToProcessors;
ExclusiveLock lock;
VariableSizeVector< pair<_uint64,_uint64> > translation;
bool closing;
};
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