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No default MAF cutoff for EHH calculations, only IHS/XPEHH. #43

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No default MAF cutoff for EHH calculations, only IHS/XPEHH. #43

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2 changes: 1 addition & 1 deletion src/main-ehh.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ int main(int argc, char** argv)
Argument<const char*> hap('d', "hap", "Hap file", false, false, "");
Argument<const char*> map('m', "map", "Map file", false, false, "");
Argument<double> cutoff('c', "cutoff", "EHH cutoff value (default: 0.05)", false, false, 0.05);
Argument<double> minMAF('b', "minmaf", "Minimum allele frequency (default: 0.05)", false, false, 0.05);
Argument<double> minMAF('b', "minmaf", "Minimum allele frequency (default: 0.05)", false, false, 0.00);
Argument<unsigned long long> scale('s', "scale", "Gap scale parameter in bp, used to scale gaps > scale parameter as in Voight, et al.", false, false, 20000);
Argument<bool> binom('a', "binom", "Use binomial coefficients rather than frequency squared for EHH", true, false);
Argument<unsigned long long> maxExtend('e', "max-extend", "Maximum distance in bp to traverse when calculating EHH (default: 0 (disabled))", false, false, 0);
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