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AlignerOptions.h
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AlignerOptions.h
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/*++
Module Name:
AlignerOptions.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 "options.h"
#include "Range.h"
#include "Genome.h"
#include "SAM.h"
#include "RangeSplitter.h"
struct AbstractOptions
{
virtual void usageMessage() = 0;
virtual bool parse(const char** argv, int argc, int& n) = 0;
};
struct AlignerOptions : public AbstractOptions
{
AlignerOptions(const char* i_commandLine, bool forPairedEnd = false);
const char *commandLine;
const char *indexDir;
int numThreads;
Range maxDist;
Range numSeeds;
Range maxHits;
Range confDiff;
Range adaptiveConfDiff;
bool computeError;
bool bindToProcessors;
bool ignoreMismatchedIDs;
unsigned selectivity;
const char *samFileTemplate;
bool doAlignerPrefetch;
const char *inputFilename;
bool inputFileIsFASTQ; // Else SAM
ReadClippingType clipping;
bool sortOutput;
unsigned sortMemory; // total output sorting buffer size in Gb
unsigned filterFlags;
bool explorePopularSeeds;
bool stopOnFirstHit;
bool useM; // Should we generate CIGAR strings using = and X, or using the old-style M?
unsigned gapPenalty; // if non-zero use gap penalty aligner
unsigned misalignThreshold; // For error reporting: min distance from real location to mark a read as misaligned
AbstractOptions *extra; // extra options
const char *rgLineContents;
void usage();
virtual void usageMessage();
virtual bool parse(const char** argv, int argc, int& n);
enum FilterFlags
{
FilterUnaligned = 0x0001,
FilterSingleHit = 0x0002,
FilterMultipleHits = 0x0004,
};
bool passFilter(Read* read, AlignmentResult result);
};