New Branch V2

Manifest.toml

@@ -0,0 +1,324 @@
+# This file is machine-generated - editing it directly is not advised
+
+[[Artifacts]]
+deps = ["Pkg"]
+git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+version = "1.3.0"
+
+[[Base64]]
+uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
+
+[[CSV]]
+deps = ["Dates", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode"]
+git-tree-sha1 = "6d4242ef4cb1539e7ede8e01a47a32365e0a34cd"
+uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+version = "0.8.4"
+
+[[CategoricalArrays]]
+deps = ["DataAPI", "Future", "JSON", "Missings", "Printf", "Statistics", "StructTypes", "Unicode"]
+git-tree-sha1 = "f713d583d10fc036252fd826feebc6c173c522a8"
+uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
+version = "0.9.5"
+
+[[ChainRulesCore]]
+deps = ["Compat", "LinearAlgebra", "SparseArrays"]
+git-tree-sha1 = "44e9f638aa9ed1ad58885defc568c133010140aa"
+uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+version = "0.9.37"
+
+[[Compat]]
+deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
+git-tree-sha1 = "ac4132ad78082518ec2037ae5770b6e796f7f956"
+uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
+version = "3.27.0"
+
+[[CompilerSupportLibraries_jll]]
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+uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
+version = "0.3.4+0"
+
+[[Crayons]]
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+uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
+version = "4.0.4"
+
+[[DataAPI]]
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+uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
+version = "1.6.0"
+
+[[DataFrames]]
+deps = ["CategoricalArrays", "Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
+git-tree-sha1 = "d50972453ef464ddcebdf489d11885468b7b83a3"
+uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+version = "0.22.7"
+
+[[DataStructures]]
+deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
+git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677"
+uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+version = "0.18.9"
+
+[[DataValueInterfaces]]
+git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
+uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
+version = "1.0.0"
+
+[[Dates]]
+deps = ["Printf"]
+uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
+
+[[DelimitedFiles]]
+deps = ["Mmap"]
+uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+
+[[Distributed]]
+deps = ["Random", "Serialization", "Sockets"]
+uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
+
+[[Distributions]]
+deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"]
+git-tree-sha1 = "e64debe8cd174cc52d7dd617ebc5492c6f8b698c"
+uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
+version = "0.24.15"
+
+[[FillArrays]]
+deps = ["LinearAlgebra", "Random", "SparseArrays"]
+git-tree-sha1 = "31939159aeb8ffad1d4d8ee44d07f8558273120a"
+uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
+version = "0.11.7"
+
+[[Formatting]]
+deps = ["Printf"]
+git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8"
+uuid = "59287772-0a20-5a39-b81b-1366585eb4c0"
+version = "0.4.2"
+
+[[Future]]
+deps = ["Random"]
+uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
+
+[[InteractiveUtils]]
+deps = ["Markdown"]
+uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+
+[[InvertedIndices]]
+deps = ["Test"]
+git-tree-sha1 = "15732c475062348b0165684ffe28e85ea8396afc"
+uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
+version = "1.0.0"
+
+[[IteratorInterfaceExtensions]]
+git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
+uuid = "82899510-4779-5014-852e-03e436cf321d"
+version = "1.0.0"
+
+[[JLLWrappers]]
+git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0"
+uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
+version = "1.2.0"
+
+[[JSON]]
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "81690084b6198a2e1da36fcfda16eeca9f9f24e4"
+uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+version = "0.21.1"
+
+[[JWAS]]
+deps = ["CSV", "DataFrames", "DelimitedFiles", "Distributions", "InteractiveUtils", "LinearAlgebra", "Printf", "ProgressMeter", "Random", "SparseArrays", "StatsBase", "Test"]
+git-tree-sha1 = "cadc230450e5af65441a85a34f63d916de1c99b3"
+uuid = "c9a035f4-d403-5e6b-8649-6be755bc4798"
+version = "0.12.0"
+
+[[LibGit2]]
+deps = ["Printf"]
+uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
+
+[[Libdl]]
+uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
+
+[[LinearAlgebra]]
+deps = ["Libdl"]
+uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+
+[[Logging]]
+uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
+
+[[Markdown]]
+deps = ["Base64"]
+uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
+
+[[Missings]]
+deps = ["DataAPI"]
+git-tree-sha1 = "f8c673ccc215eb50fcadb285f522420e29e69e1c"
+uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
+version = "0.4.5"
+
+[[Mmap]]
+uuid = "a63ad114-7e13-5084-954f-fe012c677804"
+
+[[OpenSpecFun_jll]]
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "9db77584158d0ab52307f8c04f8e7c08ca76b5b3"
+uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
+version = "0.5.3+4"
+
+[[OrderedCollections]]
+git-tree-sha1 = "4fa2ba51070ec13fcc7517db714445b4ab986bdf"
+uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+version = "1.4.0"
+
+[[PDMats]]
+deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
+git-tree-sha1 = "f82a0e71f222199de8e9eb9a09977bd0767d52a0"
+uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
+version = "0.11.0"
+
+[[Parsers]]
+deps = ["Dates"]
+git-tree-sha1 = "c8abc88faa3f7a3950832ac5d6e690881590d6dc"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "1.1.0"
+
+[[Pkg]]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
+uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+
+[[PooledArrays]]
+deps = ["DataAPI", "Future"]
+git-tree-sha1 = "cde4ce9d6f33219465b55162811d8de8139c0414"
+uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
+version = "1.2.1"
+
+[[PrettyTables]]
+deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"]
+git-tree-sha1 = "574a6b3ea95f04e8757c0280bb9c29f1a5e35138"
+uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
+version = "0.11.1"
+
+[[Printf]]
+deps = ["Unicode"]
+uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+
+[[ProgressMeter]]
+deps = ["Distributed", "Printf"]
+git-tree-sha1 = "6e9c89cba09f6ef134b00e10625590746ba1e036"
+uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
+version = "1.5.0"
+
+[[QuadGK]]
+deps = ["DataStructures", "LinearAlgebra"]
+git-tree-sha1 = "12fbe86da16df6679be7521dfb39fbc861e1dc7b"
+uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
+version = "2.4.1"
+
+[[REPL]]
+deps = ["InteractiveUtils", "Markdown", "Sockets"]
+uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
+
+[[Random]]
+deps = ["Serialization"]
+uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[[Reexport]]
+git-tree-sha1 = "57d8440b0c7d98fc4f889e478e80f268d534c9d5"
+uuid = "189a3867-3050-52da-a836-e630ba90ab69"
+version = "1.0.0"
+
+[[Rmath]]
+deps = ["Random", "Rmath_jll"]
+git-tree-sha1 = "86c5647b565873641538d8f812c04e4c9dbeb370"
+uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa"
+version = "0.6.1"
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+[[Rmath_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "1b7bf41258f6c5c9c31df8c1ba34c1fc88674957"
+uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
+version = "0.2.2+2"
+
+[[SHA]]
+uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
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+[[SentinelArrays]]
+deps = ["Dates", "Random"]
+git-tree-sha1 = "6ccde405cf0759eba835eb613130723cb8f10ff9"
+uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
+version = "1.2.16"
+
+[[Serialization]]
+uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
+
+[[SharedArrays]]
+deps = ["Distributed", "Mmap", "Random", "Serialization"]
+uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
+
+[[Sockets]]
+uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
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+[[SortingAlgorithms]]
+deps = ["DataStructures", "Random", "Test"]
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+uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
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+
+[[SparseArrays]]
+deps = ["LinearAlgebra", "Random"]
+uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+[[SpecialFunctions]]
+deps = ["ChainRulesCore", "OpenSpecFun_jll"]
+git-tree-sha1 = "5919936c0e92cff40e57d0ddf0ceb667d42e5902"
+uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
+version = "1.3.0"
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+[[Statistics]]
+deps = ["LinearAlgebra", "SparseArrays"]
+uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
+[[StatsBase]]
+deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"]
+git-tree-sha1 = "4d8ca45223d7a28839e775d73a6f6b6b2ac64fd1"
+uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
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+[[StatsFuns]]
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+git-tree-sha1 = "ced55fd4bae008a8ea12508314e725df61f0ba45"
+uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
+version = "0.9.7"
+
+[[StructTypes]]
+deps = ["Dates", "UUIDs"]
+git-tree-sha1 = "63fbaf8345b590161cd0c35b927f88d3f7b2cf75"
+uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
+version = "1.6.0"
+
+[[SuiteSparse]]
+deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
+uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
+
+[[TableTraits]]
+deps = ["IteratorInterfaceExtensions"]
+git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
+uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
+version = "1.0.1"
+
+[[Tables]]
+deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
+git-tree-sha1 = "c9d2d262e9a327be1f35844df25fe4561d258dc9"
+uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
+version = "1.4.2"
+
+[[Test]]
+deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
+uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[[UUIDs]]
+deps = ["Random", "SHA"]
+uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
+
+[[Unicode]]
+uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

Project.toml

@@ -1,20 +1,26 @@
 name = "XSim"
 uuid = "3d41126b-a46a-5bdb-b7a1-7ea6cc35a8ef"
-version = "0.5"
 authors = ["Hao Cheng <qtlcheng@ucdavis.edu>"]
+version = "0.5.0"
 
 [deps]
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 JWAS = "c9a035f4-d403-5e6b-8649-6be755bc4798"
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
+CSV = "0.5, 0.6, 0.7, 0.8"
 DataFrames = "0.19, 0.20, 0.21, 0.22"
 Distributions = "0.21, 0.22, 0.23, 0.24"
-CSV = "0.5, 0.6, 0.7, 0.8"
-JWAS  = "0.11, 0.12"
+JWAS = "0.11, 0.12"
 julia = "1"
+
+[extras]
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -20,7 +20,7 @@ using XSim
 chrLength= 0.1  #length of each chromosome 
 numChr   = 2    #number of chromosomes
 nLoci    = 10   #number of loci for each chromosome
-nQTL     = 1    #number of QTL for each chromosomefects,mutRate);
+nQTL     = 1    #number of QTL for each chromosomefects,rate_mutation);
 build_genome(numChr,chrLength,nLoci,nQTL) #this genome information will be used for subsequent computaions
 
 #generate founders