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// Copyright 2010 Martin C. Frith
#ifndef MCF_TANTAN_OPTIONS_HH
#define MCF_TANTAN_OPTIONS_HH
namespace mcf {
struct TantanOptions {
TantanOptions();
void fromArgs(int argc, char** argv);
bool isProtein;
char maskSymbol;
bool isPreserveLowercase;
const char *scoreMatrixFileName;
double repeatProb;
double repeatEndProb;
int maxCycleLength;
double repeatOffsetProbDecay;
int matchScore;
int mismatchCost;
int gapExistenceCost;
int gapExtensionCost;
double minMaskProb;
double minCopyNumber;
enum OutputType { maskOut, probOut, countOut, bedOut, repOut } outputType;
int indexOfFirstNonOptionArgument;
};
}
#endif
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