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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 "Genome.h"
#include "Read.h"
#define INSTRUMENTATION_FOR_PAPER 0 // Turn this on to generate raw data about hit sets and their intersections for the paper
#if INSTRUMENTATION_FOR_PAPER
#define MAX_HIT_SIZE_LOG_2 15 // This is for the instrumentation
extern _int64 g_alignmentTimeByHitCountsOfEachSeed[MAX_HIT_SIZE_LOG_2+1][MAX_HIT_SIZE_LOG_2+1]; // In the paired-end aligner, if you have seeds A and B with hit set sizes |A| and |B| then the total time in ns gets added into g_alignmentTimeByHitCountsOfEachSeed[log2(|A|)][log2(|B|)]
extern _int64 g_alignmentCountByHitCountsOfEachSeed[MAX_HIT_SIZE_LOG_2 + 1][MAX_HIT_SIZE_LOG_2 + 1]; // Same as above, but just add one per time.
#endif // INSTRUMENTATION_FOR_PAPER
#define MAPQ_LIMIT_FOR_SINGLE_HIT 10
struct AbstractOptions
{
virtual void usageMessage() = 0;
virtual bool parse(const char** argv, int argc, int& n, bool *done) = 0;
};
enum FileType {UnknownFileType, SAMFile, FASTQFile, BAMFile, InterleavedFASTQFile, CRAMFile}; // Add more as needed
struct SNAPFile {
SNAPFile() : fileName(NULL), secondFileName(NULL), fileType(UnknownFileType), isStdio(false), omitSQLines(false) {}
const char *fileName;
const char *secondFileName;
FileType fileType;
bool isCompressed;
bool isStdio; // Only applies to the first file for two-file inputs
bool omitSQLines; // Special (formerly) undocumented option for Charles Chiu's group. Mostly a bad idea.
PairedReadSupplierGenerator *createPairedReadSupplierGenerator(int numThreads, bool quicklyDropUnpairedReads, const ReaderContext& context);
ReadSupplierGenerator *createReadSupplierGenerator(int numThreads, const ReaderContext& context);
static bool generateFromCommandLine(const char **args, int nArgs, int *argsConsumed, SNAPFile *snapFile, bool paired, bool isInput);
};
struct AlignerOptions : public AbstractOptions
{
AlignerOptions(const char* i_commandLine, bool forPairedEnd = false);
const char *commandLine;
const char *indexDir;
const char *similarityMapFile;
int numThreads;
unsigned maxDist;
float maxDistFraction;
unsigned numSeedsFromCommandLine;
double seedCoverage; // Exclusive with numSeeds; this is readSize/seedSize
bool seedCountSpecified; // Has either -n or -sc been specified? This bool is used to make sure they're not both specified on the command line
unsigned maxHits;
int minWeightToCheck;
bool bindToProcessors;
bool ignoreMismatchedIDs;
SNAPFile outputFile;
int nInputs;
SNAPFile *inputs;
ReadClippingType clipping;
bool sortOutput;
bool noIndex;
bool noDuplicateMarking;
bool noQualityCalibration; // This doesn't appear to be used.
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
AbstractOptions *extra; // extra options
const char *rgLineContents;
const char *perfFileName;
bool useTimingBarrier;
unsigned extraSearchDepth;
const char *defaultReadGroup; // if not specified in input
bool ignoreSecondaryAlignments; // on input, default true
int maxSecondaryAlignmentAdditionalEditDistance;
int maxSecondaryAlignments;
int maxSecondaryAlignmentsPerContig;
bool preserveClipping;
float expansionFactor;
bool noUkkonen;
bool noOrderedEvaluation;
bool noTruncation;
bool useAffineGap;
unsigned matchReward;
unsigned subPenalty;
unsigned gapOpenPenalty;
unsigned gapExtendPenalty;
unsigned minReadLength;
bool mapIndex;
bool prefetchIndex;
size_t writeBufferSize;
bool dropIndexBeforeSort;
bool killIfTooSlow;
const char * sortIntermediateDirectory;
bool profile;
bool profileAffineGap;
bool ignoreAlignmentAdjustmentsForOm;
bool emitInternalScore;
char internalScoreTag[3];
bool altAwareness;
int maxScoreGapToPreferNonALTAlignment;
bool emitALTAlignments;
static bool useHadoopErrorMessages; // This is static because it's global (and I didn't want to push the options object to every place in the code)
static bool outputToStdout; // Likewise
void usage();
virtual void usageMessage();
virtual bool parse(const char** argv, int argc, int& n, bool *done);
enum FilterFlags
{
FilterUnaligned = 0x0001,
FilterSingleHit = 0x0002,
FilterMultipleHits = 0x0004,
FilterBothMatesMatch = 0x0008,
FilterTooShort = 0x0010
};
bool passFilter(Read* read, AlignmentResult result, bool tooShort, bool secondaryAlignment);
virtual bool isPaired() { return false; }
};
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