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/*++
Module Name:
PairedAligner.h
Abstract:
Header for the paired end aligner scaffolding
Authors:
Matei Zaharia, February, 2012
Environment:
User mode service.
Revision History:
Adapted from cSNAP, which was in turn adapted from the scala prototype
--*/
#pragma once
#include "stdafx.h"
#include "AlignerContext.h"
#include "ReadSupplierQueue.h"
struct PairedAlignerStats;
static const int DEFAULT_BATCH_SIZE_IS_ESTIMATION = 256 * 1024;
// Parameters from BWA-MEM
static const int OUTLIER_BOUND = 2;
static const int MAPPING_BOUND = 3;
static const int MAX_STDDEV = 4;
class PairedAlignerContext : public AlignerContext
{
public:
PairedAlignerContext(AlignerExtension* i_extension = NULL);
protected:
// AlignerContext
virtual bool initialize();
virtual AlignerStats* newStats();
virtual void runTask();
virtual void runIterationThread();
// for subclasses
virtual void updateStats(PairedAlignerStats* stats, Read* read0, Read* read1, PairedAlignmentResult* result, bool useful0, bool useful1);
bool isPaired() {return true;}
void computeSpacingDist(GenomeDistance* pairedEndSpacing, int* minSpacing, int* maxSpacing, double* avg, double* stddev);
protected:
virtual void typeSpecificBeginIteration();
virtual void typeSpecificNextIteration();
PairedReadSupplierGenerator *pairedReadSupplierGenerator;
int minSpacing;
int maxSpacing;
bool forceSpacing;
unsigned intersectingAlignerMaxHits;
unsigned maxCandidatePoolSize;
const char *fastqFile1;
bool ignoreMismatchedIDs;
bool quicklyDropUnpairedReads;
bool inferSpacing;
int maxSeedsSingleEnd;
int minScoreRealignment;
int minScoreGapRealignmentALT;
int minAGScoreImprovement;
GenomeDistance pairedEndSpacing[DEFAULT_BATCH_SIZE_IS_ESTIMATION]; // Spacing between reads aligned as FR pairs
static int compareBySpacing(const void *first_, const void *second_);
friend class AlignerContext2;
};
struct PairedAlignerOptions : public AlignerOptions
{
PairedAlignerOptions(const char* i_commandLine);
virtual void usageMessage();
virtual bool parse(const char** argv, int argc, int& n, bool *done);
virtual bool isPaired() { return true; }
int minSpacing;
int maxSpacing;
bool forceSpacing;
unsigned intersectingAlignerMaxHits;
unsigned maxCandidatePoolSize;
bool quicklyDropUnpairedReads;
bool inferSpacing;
int maxSeedsSingleEnd;
int minScoreRealignment;
int minScoreGapRealignmentALT;
int minAGScoreImprovement;
};
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