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Commit d19ba5b9 authored by Romain Feron's avatar Romain Feron
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Formatting

parent c889dcb2
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src/radsex.h
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......@@ -24,29 +24,65 @@ class RadSex {
Parameters parameters;
// Define all analyses
std::map<std::string, Analysis> analyses { {"sex_distribution", Analysis("sex_distribution", "Compute a matrix of sequences distribution between sexes",
std::vector<std::string> {"input_file_path", "output_file_path", "popmap_file_path", "min_cov"},
sex_distribution)},
{"process_reads", Analysis("process_reads", "Compute a matrix of coverage from a set of demultiplexed reads files",
std::vector<std::string> {"input_dir_path", "output_file_path", "n_threads", "min_cov"},
process_reads)},
{"subset", Analysis("subset", "Extract a subset of the coverage matrix",
std::vector<std::string> {"input_file_path", "output_file_path", "popmap_file_path", "min_cov",
"min_males", "min_females", "max_males", "max_females", "min_individuals", "max_individuals"},
subset)},
{"frequencies", Analysis("frequencies", "Calculate the frequency of markers in the population",
std::vector<std::string> {"input_file_path", "output_file_path", "min_cov"},
frequencies)},
std::map<std::string, Analysis> analyses { {"sex_distribution",
Analysis("sex_distribution",
"Compute a matrix of sequences distribution between sexes",
std::vector<std::string> {"input_file_path",
"output_file_path",
"popmap_file_path",
"min_cov",
"output_matrix"},
sex_distribution)},
{"process_reads",
Analysis("process_reads",
"Compute a matrix of coverage from a set of demultiplexed reads files",
std::vector<std::string> {"input_dir_path",
"output_file_path",
"n_threads",
"min_cov"},
process_reads)},
{"subset",
Analysis("subset",
"Extract a subset of the coverage matrix",
std::vector<std::string> {"input_file_path",
"output_file_path",
"popmap_file_path",
"min_cov",
"min_males",
"min_females",
"max_males",
"max_females",
"min_individuals",
"max_individuals"},
subset)},
{"frequencies",
Analysis("frequencies",
"Calculate the frequency of markers in the population",
std::vector<std::string> {"input_file_path",
"output_file_path",
"min_cov"},
frequencies)},
{"group_loci",
Analysis("group_loci",
"Recreate polymorphic loci from a subset of coverage matrix",
std::vector<std::string> {"input_file_path",
"coverage_matrix_path",
"output_file_path",
"max_distance",
"n_threads",
"min_cov"},
group_loci)},
{"significant_sequences",
Analysis("significant_sequences",
"Extract sequences significantly associated with sex from the coverage matrix.",
std::vector<std::string> {"input_file_path",
"output_file_path",
"popmap_file_path",
"min_cov"},
significant_sequences)},
// {"demultiplexing", Analysis("demultiplexing", "Demultiplexes a set of reads files",
// std::vector<std::string> {"input_file_path", "output_dir_path", "barcodes_file_path", "min_cov"},
// demultiplexing)},
{"group_loci", Analysis("group_loci", "Recreate polymorphic loci from a subset of coverage matrix",
std::vector<std::string> {"input_file_path", "coverage_matrix_path", "output_file_path",
"max_distance", "n_threads", "min_cov"},
group_loci)},
{"significant_sequences", Analysis("significant_sequences", "Extract sequences significantly associated with sex from the coverage matrix.",
std::vector<std::string> {"input_file_path", "output_file_path", "popmap_file_path", "min_cov"},
significant_sequences)},
};
// In the constructor, the type of analysis is detected and all analysis objects are initialized
......
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