Commit b6dc2d5a authored by RomainFeron's avatar RomainFeron
Browse files

Tentative fix for osx uint error

parent 08770968
......@@ -50,24 +50,24 @@ struct Parameters {
std::string group2 = ""; ///< Name of the secondfirst group for analysis comparing two groups
// Common analyses parameters
uint n_threads = 1; ///< Number of threads to use for "process"
uint min_depth = 1; ///< Minimum depth to consider a marker present in an individual
unsigned int n_threads = 1; ///< Number of threads to use for "process"
unsigned int min_depth = 1; ///< Minimum depth to consider a marker present in an individual
float signif_threshold = static_cast<float>(0.05); ///< P-value threshold to consider a marker significantly associated with group
bool disable_correction = false; ///< If true, Bonferroni correction will NOT be applied when estimating significance of association with group
// "subset" specific parameters
uint subset_min_group1 = 0; ///< Minimum number of individuals from the first group in which a marker is present to retain a marker
uint subset_min_group2 = 0; ///< Minimum number of individuals from the second group in which a marker is present to retain a marker
uint subset_max_group1 = 9999; ///< Maximum number of individuals from the first group in which a marker is present to retain a marker
uint subset_max_group2 = 9999; ///< Maximum number of individuals from the second group in which a marker is present to retain a marker
uint subset_min_individuals = 0; ///< Minimum number of individuals from the entire dataset in which a marker is present to retain a marker
uint subset_max_individuals = 9999; ///< Maximum number of individuals from the entire dataset in which a marker is present to retain a marker
unsigned int subset_min_group1 = 0; ///< Minimum number of individuals from the first group in which a marker is present to retain a marker
unsigned int subset_min_group2 = 0; ///< Minimum number of individuals from the second group in which a marker is present to retain a marker
unsigned int subset_max_group1 = 9999; ///< Maximum number of individuals from the first group in which a marker is present to retain a marker
unsigned int subset_max_group2 = 9999; ///< Maximum number of individuals from the second group in which a marker is present to retain a marker
unsigned int subset_min_individuals = 0; ///< Minimum number of individuals from the entire dataset in which a marker is present to retain a marker
unsigned int subset_max_individuals = 9999; ///< Maximum number of individuals from the entire dataset in which a marker is present to retain a marker
bool set_max_group1 = true; ///< If true, set subset_max_group1 to the number of group1 individuals in the popmap (i.e. it was not specified by the user)
bool set_max_group2 = true; ///< If true, set subset_max_group2 to the number of group1 individuals in the popmap (i.e. it was not specified by the user)
bool set_max_individuals = true; ///< If true, set subset_max_individuals to the number of group1 individuals in the popmap (i.e. it was not specified by the user)
// "map" specific parameters
uint map_min_quality = 20; ///< Minimum mapping quality to retained an aligned marker
unsigned int map_min_quality = 20; ///< Minimum mapping quality to retained an aligned marker
float map_min_frequency = static_cast<float>(0.1); ///< Minimum frequency of a marker in the population to retain the marker
};
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