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/*++
Module Name:
RangeSplitter.h
Abstract:
Headers for code to split a range into pieces for multiple cores to process. It's designed
to handle cores that proceed at varying rates.
Authors:
Bill Bolosky, 2011
Environment:
User mode service.
Revision History:
Pulled out of cSNAP.cpp to make it useful for various versions of the aligner
Generalized from FileSplitter to ranges, e.g. for scanning the genome /ravip/5/2012/
--*/
#pragma once
#include "Compat.h"
#include "Read.h"
#include "Genome.h"
#include "AlignerOptions.h"
//
// Utility class for letting multiple threads split chunks of a range to process.
// This is used by the parallel versions of the aligners.
//
class RangeSplitter
{
public:
RangeSplitter(_int64 rangeEnd_, int numThreads_, unsigned divisonSize_ = 5, _int64 rangeBegin_ = 0, unsigned minMillis_ = 200, unsigned minRangeSize_ = 32768);
// Get the next range for a thread to process, or return false if the whole range is done.
bool getNextRange(_int64 *rangeStart, _int64 *rangeLength);
private:
int numThreads;
_int64 rangeBegin;
_int64 rangeEnd;
unsigned divisionSize;
unsigned minMillis;
unsigned minRangeSize;
volatile _int64 position;
volatile _int64 startTime;
};
class RangeSplittingReadSupplier : public ReadSupplier {
public:
RangeSplittingReadSupplier(RangeSplitter *i_splitter, ReadReader *i_underlyingReader) :
splitter(i_splitter), underlyingReader(i_underlyingReader), read() {}
virtual ~RangeSplittingReadSupplier();
Read *getNextRead();
virtual void holdBatch(DataBatch batch)
{ underlyingReader->holdBatch(batch); }
virtual bool releaseBatch(DataBatch batch)
{ return underlyingReader->releaseBatch(batch); }
private:
RangeSplitter *splitter;
ReadReader *underlyingReader;
Read read;
};
class RangeSplittingReadSupplierGenerator: public ReadSupplierGenerator {
public:
RangeSplittingReadSupplierGenerator(const char *i_fileName, bool i_isSAM, unsigned numThreads, const ReaderContext& context);
~RangeSplittingReadSupplierGenerator() {delete splitter; delete [] fileName;}
ReadSupplier *generateNewReadSupplier();
ReaderContext* getContext() { return &context; }
private:
RangeSplitter *splitter;
char *fileName;
const bool isSAM;
const int numThreads;
ReaderContext context;
};
class RangeSplittingPairedReadSupplier : public PairedReadSupplier {
public:
RangeSplittingPairedReadSupplier(RangeSplitter *i_splitter, PairedReadReader *i_underlyingReader) : splitter(i_splitter), underlyingReader(i_underlyingReader) {}
virtual ~RangeSplittingPairedReadSupplier();
virtual bool getNextReadPair(Read **read1, Read **read2);
virtual void holdBatch(DataBatch batch)
{ underlyingReader->releaseBatch(batch); }
virtual bool releaseBatch(DataBatch batch)
{ return underlyingReader->releaseBatch(batch); }
private:
PairedReadReader *underlyingReader;
RangeSplitter *splitter;
Read internalRead1;
Read internalRead2;
};
class RangeSplittingPairedReadSupplierGenerator: public PairedReadSupplierGenerator {
public:
RangeSplittingPairedReadSupplierGenerator(const char *i_fileName1, const char *i_fileName2, enum FileType i_fileType, unsigned numThreads, bool i_quicklyDropUnpairedReads, const ReaderContext& context);
~RangeSplittingPairedReadSupplierGenerator();
PairedReadSupplier *generateNewPairedReadSupplier();
ReaderContext* getContext() { return &context; }
private:
RangeSplitter *splitter;
char *fileName1;
char *fileName2;
const int numThreads;
enum FileType fileType;
ReaderContext context;
bool quicklyDropUnpairedReads;
};
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