added a bunch of unit tests

.gitignore

@@ -49,3 +49,7 @@ docs/src/man/*.jlso
 data/1000_genome_phase3_v5/filtered/error.png
 
 data/1000_genome_phase3_v5/filtered/mendel.chr20.imputed.sample.error
+
+data/HRC/snpscores.txt
+
+data/HRC/mendel.chr10.imputed.target.sample.error

Manifest.toml

@@ -24,6 +24,12 @@ git-tree-sha1 = "d6f1ecde467019346f7601fb2ee58cb2bc60d121"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
 version = "0.4.8"
 
+[[Artifacts]]
+deps = ["Pkg"]
+git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
+uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
+version = "1.3.0"
+
 [[Automa]]
 deps = ["DataStructures", "Printf", "Test", "TranscodingStreams"]
 git-tree-sha1 = "1b1defa8b36d44dd22c715b5c884c8f795eea7fe"
@@ -81,10 +87,10 @@ uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
 version = "1.0.0"
 
 [[Bzip2_jll]]
-deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "03a44490020826950c68005cafb336e5ba08b7e8"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e"
 uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0"
-version = "1.0.6+4"
+version = "1.0.6+5"
 
 [[CSV]]
 deps = ["CategoricalArrays", "DataFrames", "Dates", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode"]
@@ -288,9 +294,14 @@ version = "1.0.0"
 
 [[JLD2]]
 deps = ["CodecZlib", "DataStructures", "MacroTools", "Mmap", "Pkg", "Printf", "Requires", "UUIDs"]
-git-tree-sha1 = "d2c0db66530ff444846d6e84bcf948a74ce31635"
+git-tree-sha1 = "1b8168c14939e43c7c4d2c9e8f0ddd8718965430"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.2.0"
+version = "0.2.4"
+
+[[JLLWrappers]]
+git-tree-sha1 = "7cec881362e5b4e367ff0279dd99a06526d51a55"
+uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
+version = "1.1.2"
 
 [[JLSO]]
 deps = ["BSON", "CodecZlib", "FilePathsBase", "Memento", "Pkg", "Serialization"]
@@ -318,10 +329,10 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
 [[Libiconv_jll]]
-deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "7c36dfe7971e55da03d8f54b67d4b3fb8ee01d63"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "8e924324b2e9275a51407a4e06deb3455b1e359f"
 uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
-version = "1.16.0+6"
+version = "1.16.0+7"
 
 [[LinearAlgebra]]
 deps = ["Libdl"]
@@ -639,10 +650,10 @@ uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
 version = "0.12.33"
 
 [[XML2_jll]]
-deps = ["Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "ecff6bff03b35d482ad5eb51276d6fc4c823cd39"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
+git-tree-sha1 = "be0db24f70aae7e2b89f2f3092e93b8606d659a6"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
-version = "2.9.10+2"
+version = "2.9.10+3"
 
 [[XZ_jll]]
 deps = ["Libdl", "Pkg"]
@@ -657,13 +668,13 @@ uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 version = "0.4.2"
 
 [[Zlib_jll]]
-deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "fdd89e5ab270ea0f2a0174bd9093e557d06d4bfa"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "320228915c8debb12cb434c59057290f0834dbf6"
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.11+16"
+version = "1.2.11+18"
 
 [[Zstd_jll]]
-deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "4de91f4313d9e88162d461e282fe3066ab3a3c09"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "6f1abcb0c44f184690912aa4b0ba861dd64f11b9"
 uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
-version = "1.4.5+1"
+version = "1.4.5+2"

Project.toml

@@ -5,7 +5,6 @@ authors = ["Benjamin Chu <[email protected]>", "Eric Sobel <[email protected]>", "
 version = "0.0.0"
 
 [deps]
-CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
@@ -14,7 +13,6 @@ GroupSlices = "d853e229-7c7c-56e9-b6be-9a1acc5f13d9"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JLSO = "9da8a3cd-07a3-59c0-a743-3fdc52c30d11"
 LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02"
-Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -27,7 +25,10 @@ VCFTools = "a620830f-fdd7-5ebc-8d26-3621ab35fbfe"
 Documenter = ">=0.20"
 
 [extras]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test", "CSV", "BenchmarkTools", "Statistics"]