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/*++
Module Name:
AlignerContext.h
Abstract:
Common parameters for running single & paired alignment.
Authors:
Ravi Pandya, May, 2012
Environment:
User mode service.
Revision History:
Integrated from SingleAligner.cpp & PairedAligner.cpp
--*/
#pragma once
#include "stdafx.h"
#include "Genome.h"
#include "RangeSplitter.h"
#include "AlignerOptions.h"
#include "AlignerStats.h"
#include "ParallelTask.h"
#include "GenomeIndex.h"
class AlignerExtension;
/*++
Common context state shared across threads during alignment process
--*/
class AlignerContext : public TaskContextBase
{
public:
AlignerContext(int i_argc, const char **i_argv, const char *i_version, AlignerExtension* i_extension = NULL);
~AlignerContext();
// running alignment
void runAlignment(int argc, const char **argv, const char *version, unsigned *nArgsConsumed);
// ParallelTask template
void initializeThread();
void runThread();
void finishThread(AlignerContext* common);
void printStats();
void beginIteration();
void finishIteration();
// advance to next iteration in range, return false when past end
bool nextIteration();
// overrideable by concrete single/paired alignment subclasses
// parse options from the command line
AlignerOptions* parseOptions(int argc, const char **argv, const char *version, unsigned *argsConsumed, bool paired);
// initialize from options
virtual bool initialize();
// new stats object
virtual AlignerStats* newStats() = 0;
// instantiate and run a parallel task
virtual void runTask() = 0;
// run single thread within single iteration
virtual void runIterationThread() = 0;
virtual void typeSpecificBeginIteration() = 0;
virtual void typeSpecificNextIteration() = 0;
virtual bool isPaired() = 0;
friend class AlignerContext2;
// common state across all threads
GenomeIndex *index;
ReadWriterSupplier *writerSupplier;
ReaderContext readerContext;
_int64 alignStart;
_int64 alignTime;
AlignerOptions *options;
AlignerStats *stats;
AlignerExtension *extension;
unsigned maxDist;
unsigned numSeedsFromCommandLine;
double seedCoverage;
unsigned minWeightToCheck;
int maxHits;
bool detailedStats;
ReadClippingType clipping;
unsigned extraSearchDepth;
int argc;
const char **argv;
const char *version;
FILE *perfFile;
bool noUkkonen;
bool noOrderedEvaluation;
bool noTruncation;
bool useAffineGap;
bool ignoreAlignmentAdjustmentForOm;
bool altAwareness;
bool emitALTAlignments;
int maxSecondaryAlignmentAdditionalEditDistance;
int maxSecondaryAlignments;
int maxSecondaryAlignmentsPerContig;
int maxScoreGapToPreferNonALTAlignment;
unsigned minReadLength;
unsigned matchReward;
unsigned subPenalty;
unsigned gapOpenPenalty;
unsigned gapExtendPenalty;
unsigned minAGScore;
// iteration variables
int maxHits_;
int maxDist_;
// Per-thread context state used during alignment process
ReadWriter *readWriter;
};
// abstract class for extending base context
class AlignerExtension
{
public:
virtual ~AlignerExtension() {}
virtual AbstractOptions* extraOptions() { return NULL; }
virtual AbstractStats* extraStats() { return NULL; }
virtual bool skipAlignment() { return false; }
virtual void initialize() {}
virtual void beginIteration() {}
virtual AlignerExtension* copy() { return new AlignerExtension(); }
virtual void beginThread() {}
virtual bool runIterationThread(PairedReadSupplier* supplier, AlignerContext* threadContext) { return false; }
virtual bool runIterationThread(ReadSupplier* supplier, AlignerContext* threadContext) { return false; }
virtual void writeRead(Read* read, SingleAlignmentResult* result) {}
virtual void writePair(Read* read0, Read* read1, PairedAlignmentResult* result) {}
virtual void finishThread() {}
virtual void finishIteration() {}
virtual void printStats() {}
virtual void finishAlignment() {}
};
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