From 7a9a3327f5a929686af2263468190a94fdea49ed Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 31 Mar 2022 10:34:56 -0500
Subject: [PATCH] Update dependencies

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
---
 Manifest.toml | 428 ++++++++++++++++++++++++++++++++++----------------
 Project.toml  |  35 ++++-
 README.md     |  78 ++++-----
 3 files changed, 369 insertions(+), 172 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index 2c6c9c4..815d9a3 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -28,21 +28,21 @@ version = "0.1.0"
 
 [[Arpack]]
 deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"]
-git-tree-sha1 = "288d58589d4249a63095f3f41ece91bf34c32c19"
+git-tree-sha1 = "91ca22c4b8437da89b030f08d71db55a379ce958"
 uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
-version = "0.5.0"
+version = "0.5.3"
 
 [[Arpack_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"]
-git-tree-sha1 = "4c31b0101997beb213a9e6c39116b052e73ca38c"
+deps = ["Libdl", "OpenBLAS_jll", "Pkg"]
+git-tree-sha1 = "e214a9b9bd1b4e1b4f15b22c0994862b66af7ff7"
 uuid = "68821587-b530-5797-8361-c406ea357684"
-version = "3.8.0+0"
+version = "3.5.0+3"
 
 [[ArrayInterface]]
 deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"]
-git-tree-sha1 = "1ee88c4c76caa995a885dc2f22a5d548dfbbc0ba"
+git-tree-sha1 = "6e8fada11bb015ecf9263f64b156f98b546918c7"
 uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
-version = "3.2.2"
+version = "5.0.5"
 
 [[ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra", "SparseArrays"]
@@ -59,17 +59,17 @@ git-tree-sha1 = "b25e88db7944f98789130d7b503276bc34bc098e"
 uuid = "bf4720bc-e11a-5d0c-854e-bdca1663c893"
 version = "0.1.0"
 
-[[AutoGrad]]
-deps = ["Libdl", "LinearAlgebra", "SpecialFunctions", "Statistics", "TimerOutputs"]
-git-tree-sha1 = "0f97c20e513d18e9c0d8f58e1b6eb0e288249832"
-uuid = "6710c13c-97f1-543f-91c5-74e8f7d95b35"
-version = "1.2.5"
-
 [[AutoHashEquals]]
 git-tree-sha1 = "45bb6705d93be619b81451bb2006b7ee5d4e4453"
 uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f"
 version = "0.2.0"
 
+[[Automa]]
+deps = ["Printf", "ScanByte", "TranscodingStreams"]
+git-tree-sha1 = "d50976f217489ce799e366d9561d56a98a30d7fe"
+uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
+version = "0.8.2"
+
 [[AxisAlgorithms]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"]
 git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7"
@@ -82,16 +82,23 @@ git-tree-sha1 = "d127d5e4d86c7680b20c35d40b503c74b9a39b5e"
 uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
 version = "0.4.4"
 
-[[BFloat16s]]
-deps = ["LinearAlgebra", "Printf", "Random", "Test"]
-git-tree-sha1 = "a598ecb0d717092b5539dbbe890c98bac842b072"
-uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b"
-version = "0.2.0"
+[[BBI]]
+deps = ["BioCore", "Libz"]
+git-tree-sha1 = "1dc447cec8b0e52d307a1bdd398c9dcd4aeba0e2"
+uuid = "19670fab-07f0-5a41-99c5-c090d774ee27"
+version = "0.2.1"
 
-[[BSON]]
-git-tree-sha1 = "306bb5574b0c1c56d7e1207581516c557d105cad"
-uuid = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
-version = "0.3.5"
+[[BED]]
+deps = ["Automa", "BGZFStreams", "BioGenerics", "ColorTypes", "FixedPointNumbers", "GenomicFeatures", "Indexes", "TranscodingStreams"]
+git-tree-sha1 = "b353d994d389c3b2dc64ce83a5e8f5213f1e19e5"
+uuid = "8e4a8c10-cb6b-11e8-08d2-83478d609d67"
+version = "0.2.1"
+
+[[BGZFStreams]]
+deps = ["CodecZlib"]
+git-tree-sha1 = "a9c80401403c068c02784cd53d417d3a82e2d2bd"
+uuid = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
+version = "0.3.1"
 
 [[BandedMatrices]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"]
@@ -108,6 +115,56 @@ git-tree-sha1 = "4c10eee4af024676200bc7752e536f858c6b8f93"
 uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 version = "1.3.1"
 
+[[BigWig]]
+deps = ["BBI", "BioCore", "BufferedStreams", "GenomicFeatures", "Libz"]
+git-tree-sha1 = "b83f8ab279139bdd68b593bee5862fdb0b855b98"
+uuid = "9d649c22-cb6b-11e8-1fa9-f3896fced444"
+version = "0.1.0"
+
+[[BioAlignments]]
+deps = ["BioGenerics", "BioSequences", "BioSymbols", "IntervalTrees", "LinearAlgebra"]
+git-tree-sha1 = "fcc3ec5fbdeeba2a05b2ca15cb518d31f3f308dc"
+repo-rev = "operations-fix"
+repo-url = "https://github.com/MillironX/BioAlignments.jl"
+uuid = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
+version = "2.0.0"
+
+[[BioCore]]
+deps = ["Automa", "BufferedStreams", "YAML"]
+git-tree-sha1 = "476edbf4ef94594fff430a84ca96f86cb2327a71"
+uuid = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
+version = "2.0.5"
+
+[[BioGenerics]]
+deps = ["TranscodingStreams"]
+git-tree-sha1 = "6d3f3b474b3df2e83dc67ad12ec63aee4eb5241b"
+uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea"
+version = "0.1.1"
+
+[[BioSequences]]
+deps = ["BioGenerics", "BioSymbols", "Combinatorics", "IndexableBitVectors", "Printf", "Random", "StableRNGs", "Twiddle"]
+git-tree-sha1 = "093ccb9211bdc71924abf8e74a0790af11da35a7"
+uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+version = "2.0.5"
+
+[[BioServices]]
+deps = ["Dates", "Gumbo", "HTTP", "JSON", "XMLDict"]
+git-tree-sha1 = "0e95f5b4a48df7cc9bbb7cf0b407577cb0aea17e"
+uuid = "a0d4ced5-b29c-5395-b614-ca030a679c4b"
+version = "0.4.0"
+
+[[BioStructures]]
+deps = ["BioAlignments", "BioCore", "BioGenerics", "BioSequences", "BioSymbols", "CodecZlib", "DataFrames", "Downloads", "Format", "Graphs", "LinearAlgebra", "MMTF", "MetaGraphs", "RecipesBase", "Statistics"]
+git-tree-sha1 = "2153767a968c8e2028cefcd6e221fc66c008951a"
+uuid = "de9282ab-8554-53be-b2d6-f6c222edabfc"
+version = "1.2.1"
+
+[[BioSymbols]]
+deps = ["Automa"]
+git-tree-sha1 = "ec77888ac3e78f9d372c2b533bdb52668f9e2b09"
+uuid = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
+version = "4.0.4"
+
 [[BitTwiddlingConvenienceFunctions]]
 deps = ["Static"]
 git-tree-sha1 = "28bbdbf0354959db89358d1d79d421ff31ef0b5e"
@@ -157,15 +214,9 @@ version = "0.1.1"
 
 [[CSV]]
 deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"]
-git-tree-sha1 = "9310d9495c1eb2e4fa1955dd478660e2ecab1fbb"
+git-tree-sha1 = "49f14b6c56a2da47608fe30aed711b5882264d7a"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-version = "0.10.3"
-
-[[CUDA]]
-deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"]
-git-tree-sha1 = "a28686d7c83026069cc2505016269cca77506ed3"
-uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
-version = "3.8.5"
+version = "0.9.11"
 
 [[Cairo_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
@@ -221,18 +272,42 @@ git-tree-sha1 = "9fb640864691a0936f94f89150711c36072b0e8f"
 uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
 version = "1.0.8"
 
+[[CodecBase]]
+deps = ["TranscodingStreams"]
+git-tree-sha1 = "744128fbfc6fe0739085d995b1756f1856964d4c"
+uuid = "6c391c72-fb7b-5838-ba82-7cfb1bcfecbf"
+version = "0.3.0"
+
 [[CodecBzip2]]
 deps = ["Bzip2_jll", "Libdl", "TranscodingStreams"]
 git-tree-sha1 = "2e62a725210ce3c3c2e1a3080190e7ca491f18d7"
 uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
 version = "0.7.2"
 
+[[CodecLz4]]
+deps = ["Lz4_jll", "TranscodingStreams"]
+git-tree-sha1 = "59fe0cb37784288d6b9f1baebddbf75457395d40"
+uuid = "5ba52731-8f18-5e0d-9241-30f10d1ec561"
+version = "0.4.0"
+
+[[CodecXz]]
+deps = ["Libdl", "TranscodingStreams", "XZ_jll"]
+git-tree-sha1 = "82c4c000edf64b6bda6766377e69a1028f3549ee"
+uuid = "ba30903b-d9e8-5048-a5ec-d1f5b0d4b47b"
+version = "0.7.0"
+
 [[CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
 git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da"
 uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
 version = "0.7.0"
 
+[[CodecZstd]]
+deps = ["CEnum", "TranscodingStreams", "Zstd_jll"]
+git-tree-sha1 = "849470b337d0fa8449c21061de922386f32949d9"
+uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2"
+version = "0.7.2"
+
 [[ColorBrewer]]
 deps = ["Colors", "JSON", "Test"]
 git-tree-sha1 = "61c5334f33d91e570e1d0c3eb5465835242582c4"
@@ -396,9 +471,9 @@ version = "0.4.0"
 
 [[DiffEqBase]]
 deps = ["ArrayInterface", "ChainRulesCore", "DEDataArrays", "DataStructures", "Distributions", "DocStringExtensions", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "IterativeSolvers", "LabelledArrays", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "StaticArrays", "Statistics", "SuiteSparse", "ZygoteRules"]
-git-tree-sha1 = "caada727813396d9402c26e5175a01def8fd89ce"
+git-tree-sha1 = "d1c8d8b645500d7dffec3355d29af6c4f8bfa6df"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.82.2"
+version = "6.82.3"
 
 [[DiffEqCallbacks]]
 deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "NLsolve", "OrdinaryDiffEq", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArrays"]
@@ -498,17 +573,18 @@ git-tree-sha1 = "b026981973ccbe38682fbb4ccb0732fd6b1e1207"
 uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18"
 version = "1.13.0"
 
-[[ExprTools]]
-git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d"
-uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
-version = "0.1.8"
-
 [[EzXML]]
 deps = ["Printf", "XML2_jll"]
 git-tree-sha1 = "0fa3b52a04a4e210aeb1626def9c90df3ae65268"
 uuid = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
 version = "1.1.0"
 
+[[FASTX]]
+deps = ["Automa", "BioGenerics", "BioSequences", "BioSymbols", "TranscodingStreams"]
+git-tree-sha1 = "6582055aa8f890663f63cbf9bc748b0a537b5fd3"
+uuid = "c2308a5c-f048-11e8-3e8a-31650f418d12"
+version = "1.2.0"
+
 [[FFMPEG]]
 deps = ["FFMPEG_jll"]
 git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8"
@@ -583,18 +659,17 @@ git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc"
 uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 version = "0.8.4"
 
-[[Flux]]
-deps = ["AbstractTrees", "Adapt", "ArrayInterface", "CUDA", "CodecZlib", "Colors", "DelimitedFiles", "Functors", "Juno", "LinearAlgebra", "MacroTools", "NNlib", "NNlibCUDA", "Pkg", "Printf", "Random", "Reexport", "SHA", "SparseArrays", "Statistics", "StatsBase", "Test", "ZipFile", "Zygote"]
-git-tree-sha1 = "983271b47332fd3d9488d6f2d724570290971794"
-uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c"
-version = "0.12.9"
-
 [[Fontconfig_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"]
 git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03"
 uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
 version = "2.13.93+0"
 
+[[Format]]
+git-tree-sha1 = "03bcdf8ab1a5b9e6455ccb45c30910d282aa09f4"
+uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
+version = "1.3.2"
+
 [[Formatting]]
 deps = ["Printf"]
 git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8"
@@ -642,11 +717,6 @@ git-tree-sha1 = "04cb9cfaa6ba5311973994fe3496ddec19b6292a"
 uuid = "de31a74c-ac4f-5751-b3fd-e18cd04993ca"
 version = "0.5.0"
 
-[[Functors]]
-git-tree-sha1 = "223fffa49ca0ff9ce4f875be001ffe173b2b7de4"
-uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
-version = "0.2.8"
-
 [[Future]]
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
@@ -667,29 +737,35 @@ version = "1.6.1"
 deps = ["Artifacts", "Libdl"]
 uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d"
 
-[[GPUArrays]]
-deps = ["Adapt", "LLVM", "LinearAlgebra", "Printf", "Random", "Serialization", "Statistics"]
-git-tree-sha1 = "9010083c218098a3695653773695a9949e7e8f0d"
-uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "8.3.1"
-
-[[GPUCompiler]]
-deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"]
-git-tree-sha1 = "647a54f196b5ffb7c3bc2fec5c9a57fa273354cc"
-uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
-version = "0.13.14"
-
 [[GR]]
 deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"]
-git-tree-sha1 = "df5f5b0450c489fe6ed59a6c0a9804159c22684d"
+git-tree-sha1 = "af237c08bda486b74318c8070adb96efa6952530"
 uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
-version = "0.64.1"
+version = "0.64.2"
 
 [[GR_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"]
-git-tree-sha1 = "83578392343a7885147726712523c39edc714956"
+git-tree-sha1 = "cd6efcf9dc746b06709df14e462f0a3fe0786b1e"
 uuid = "d2c73de3-f751-5644-a686-071e5b155ba9"
-version = "0.64.1+0"
+version = "0.64.2+0"
+
+[[GenomeGraphs]]
+deps = ["BioSequences", "FASTX", "ReadDatastores"]
+git-tree-sha1 = "901468d589c1432556e5b982d1a9618617e25c36"
+uuid = "3aa97884-90e5-11e8-2134-af657ec4f203"
+version = "0.2.0"
+
+[[GenomicAnnotations]]
+deps = ["BioGenerics", "BioSequences", "CodecZlib", "DataFrames", "TranscodingStreams"]
+git-tree-sha1 = "e0b5e58635c60590aaa3425f0b24ba37c698776b"
+uuid = "4f8a0a0a-376d-5ac0-ab14-e88793df67f0"
+version = "0.3.1"
+
+[[GenomicFeatures]]
+deps = ["BioGenerics", "DataStructures", "IntervalTrees"]
+git-tree-sha1 = "881bda64be17d6eefdb6dfccc329fdb904fa596e"
+uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446"
+version = "2.0.5"
 
 [[GeometryBasics]]
 deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
@@ -732,6 +808,18 @@ git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
 uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
 version = "1.0.2"
 
+[[Gumbo]]
+deps = ["AbstractTrees", "Gumbo_jll", "Libdl"]
+git-tree-sha1 = "e711d08d896018037d6ff0ad4ebe675ca67119d4"
+uuid = "708ec375-b3d6-5a57-a7ce-8257bf98657a"
+version = "0.8.0"
+
+[[Gumbo_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "29070dee9df18d9565276d68a596854b1764aa38"
+uuid = "528830af-5a63-567c-a44a-034ed33b8444"
+version = "0.10.2+0"
+
 [[HTTP]]
 deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets"]
 git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508"
@@ -893,6 +981,18 @@ git-tree-sha1 = "87f7662e03a649cffa2e05bf19c303e168732d3e"
 uuid = "905a6f67-0a94-5f89-b386-d35d92009cd1"
 version = "3.1.2+0"
 
+[[IndexableBitVectors]]
+deps = ["Random", "Test"]
+git-tree-sha1 = "b7f5e42dc867b8a8654a5f899064632dac05bc82"
+uuid = "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d"
+version = "1.0.0"
+
+[[Indexes]]
+deps = ["BGZFStreams", "BioGenerics", "GenomicFeatures", "TranscodingStreams"]
+git-tree-sha1 = "275bce824b40fd2e70358e0a652ba1b34172f240"
+uuid = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
+version = "0.1.3"
+
 [[IndirectArrays]]
 git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f"
 uuid = "9b13fd28-a010-5f03-acff-a1bbcff69959"
@@ -959,6 +1059,12 @@ git-tree-sha1 = "bcf640979ee55b652f3b01650444eb7bbe3ea837"
 uuid = "8197267c-284f-5f27-9208-e0e47529a953"
 version = "0.5.4"
 
+[[IntervalTrees]]
+deps = ["InteractiveUtils", "Profile", "Random", "Test"]
+git-tree-sha1 = "6c9fcd87677231ae293f6806fad928c216ab6658"
+uuid = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
+version = "1.0.0"
+
 [[InverseFunctions]]
 deps = ["Test"]
 git-tree-sha1 = "91b5dcf362c5add98049e6c29ee756910b03051d"
@@ -1057,12 +1163,6 @@ git-tree-sha1 = "b791e85f20aa441fb0602dcbcef59f27281365cc"
 uuid = "480116ec-64ea-5dec-baca-db6b11e96e37"
 version = "0.6.2"
 
-[[Juno]]
-deps = ["Base64", "Logging", "Media", "Profile"]
-git-tree-sha1 = "07cb43290a840908a771552911a6274bc6c072c7"
-uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d"
-version = "0.8.4"
-
 [[KLU]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"]
 git-tree-sha1 = "cae5e3dfd89b209e01bcd65b3a25e74462c67ee0"
@@ -1075,11 +1175,11 @@ git-tree-sha1 = "591e8dc09ad18386189610acafb970032c519707"
 uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
 version = "0.6.3"
 
-[[Knet]]
-deps = ["AutoGrad", "CUDA", "FileIO", "ImageCore", "ImageMagick", "JLD2", "Libdl", "LinearAlgebra", "NNlib", "Pkg", "Printf", "Random", "Serialization", "SpecialFunctions", "Statistics"]
-git-tree-sha1 = "b1874af1797705ae47773c2c7aa1ad4aad76dd1e"
-uuid = "1902f260-5fb4-5aff-8c31-6271790ab950"
-version = "1.4.10"
+[[KmerAnalysis]]
+deps = ["BioSequences", "Distributed", "ReadDatastores"]
+git-tree-sha1 = "9d62f1e2b9a7f63e5784905be6de9b52c7643a2b"
+uuid = "a20136b7-8e32-4c10-91d3-7060c0bd8ec7"
+version = "0.4.4"
 
 [[Knockout]]
 deps = ["JSExpr", "JSON", "Observables", "Test", "WebIO"]
@@ -1111,18 +1211,6 @@ git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434"
 uuid = "88015f11-f218-50d7-93a8-a6af411a945d"
 version = "3.0.0+1"
 
-[[LLVM]]
-deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"]
-git-tree-sha1 = "c9b86064be5ae0f63e50816a5a90b08c474507ae"
-uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "4.9.1"
-
-[[LLVMExtra_jll]]
-deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
-git-tree-sha1 = "5558ad3c8972d602451efe9d81c78ec14ef4f5ef"
-uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab"
-version = "0.0.14+2"
-
 [[LZO_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6"
@@ -1284,6 +1372,12 @@ git-tree-sha1 = "077c7c9d746cbe30ac5f001ea4c1277f64cc5dad"
 uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
 version = "0.12.103"
 
+[[Lz4_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "5d494bc6e85c4c9b626ee0cab05daa4085486ab1"
+uuid = "5ced341a-0733-55b8-9ab6-a4889d929147"
+version = "1.9.3+0"
+
 [[MKL_jll]]
 deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
 git-tree-sha1 = "e595b205efd49508358f7dc670a940c790204629"
@@ -1296,6 +1390,12 @@ git-tree-sha1 = "3bd9fd4baf19dfc1edf344bc578da7f565da2e18"
 uuid = "f0e99cf1-93fa-52ec-9ecc-5026115318e0"
 version = "0.9.0"
 
+[[MMTF]]
+deps = ["CodecZlib", "Downloads", "MsgPack"]
+git-tree-sha1 = "2af5e4051f50bd99755b84d8bf3547db073992f3"
+uuid = "259c3a9c-12c3-507f-b21f-68ecc40fcda4"
+version = "1.0.0"
+
 [[MacroTools]]
 deps = ["Markdown", "Random"]
 git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf"
@@ -1324,9 +1424,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[MathOptInterface]]
 deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "JSON", "LinearAlgebra", "MutableArithmetics", "OrderedCollections", "Printf", "SparseArrays", "Test", "Unicode"]
-git-tree-sha1 = "09be99195f42c601f55317bd89f3c6bbaec227dc"
+git-tree-sha1 = "779ad2ee78c4a24383887fdba177e9e5034ce207"
 uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
-version = "1.1.1"
+version = "1.1.2"
 
 [[MathProgBase]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -1349,24 +1449,12 @@ git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f"
 uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
 version = "0.3.1"
 
-[[Media]]
-deps = ["MacroTools", "Test"]
-git-tree-sha1 = "75a54abd10709c01f1b86b84ec225d26e840ed58"
-uuid = "e89f7d12-3494-54d1-8411-f7d8b9ae1f27"
-version = "0.5.0"
-
 [[MetaGraphs]]
 deps = ["Graphs", "JLD2", "Random"]
 git-tree-sha1 = "2af69ff3c024d13bde52b34a2a7d6887d4e7b438"
 uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 version = "0.7.1"
 
-[[Metalhead]]
-deps = ["Artifacts", "BSON", "Flux", "Functors", "LazyArtifacts"]
-git-tree-sha1 = "34f54f87a4ab86d6fbffd34b578d6c8b8cdea1d9"
-uuid = "dbeba491-748d-5e0e-a39e-b530a07fa0cc"
-version = "0.6.1"
-
 [[Missings]]
 deps = ["DataAPI"]
 git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f"
@@ -1385,11 +1473,23 @@ version = "0.3.3"
 [[MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 
+[[MsgPack]]
+deps = ["Serialization"]
+git-tree-sha1 = "a8cbf066b54d793b9a48c5daa5d586cf2b5bd43d"
+uuid = "99f44e22-a591-53d1-9472-aa23ef4bd671"
+version = "1.1.0"
+
 [[MuladdMacro]]
 git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68"
 uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 version = "0.2.2"
 
+[[MultipleTesting]]
+deps = ["Distributions", "SpecialFunctions", "StatsBase"]
+git-tree-sha1 = "7e97fc2e370b0a1c18dca532c23af214b2148cdd"
+uuid = "f8716d33-7c4a-5097-896f-ce0ecbd3ef6b"
+version = "0.5.0"
+
 [[MultivariateStats]]
 deps = ["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"]
 git-tree-sha1 = "7008a3412d823e29d370ddc77411d593bd8a3d03"
@@ -1426,18 +1526,6 @@ git-tree-sha1 = "019f12e9a1a7880459d0173c182e6a99365d7ac1"
 uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 version = "4.5.1"
 
-[[NNlib]]
-deps = ["Adapt", "ChainRulesCore", "Compat", "LinearAlgebra", "Pkg", "Requires", "Statistics"]
-git-tree-sha1 = "a59a614b8b4ea6dc1dcec8c6514e251f13ccbe10"
-uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
-version = "0.8.4"
-
-[[NNlibCUDA]]
-deps = ["CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"]
-git-tree-sha1 = "0d18b4c80a92a00d3d96e8f9677511a7422a946e"
-uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d"
-version = "0.2.2"
-
 [[NaNMath]]
 git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
@@ -1610,9 +1698,9 @@ version = "2.1.0"
 
 [[Parsers]]
 deps = ["Dates"]
-git-tree-sha1 = "85b5da0fa43588c75bb1ff986493443f821c70b7"
+git-tree-sha1 = "621f4f3b4977325b9128d5fae7a8b4829a0c2222"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.2.3"
+version = "2.2.4"
 
 [[Pidfile]]
 deps = ["FileWatching", "Test"]
@@ -1684,11 +1772,23 @@ git-tree-sha1 = "28ef6c7ce353f0b35d0df0d5930e0d072c1f5b9b"
 uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.4.1"
 
+[[PopGen]]
+deps = ["DataFrames", "Distributions", "MultipleTesting", "PooledArrays", "PopGenCore", "ProgressMeter", "Random", "Reexport", "StatsBase"]
+git-tree-sha1 = "2b2cfa0d7a8659e8f0b1c2ef5be8d5ccc8b88986"
+uuid = "af524d12-c74b-11e9-22a8-3b091653023f"
+version = "0.7.1"
+
+[[PopGenCore]]
+deps = ["CSV", "CodecZlib", "DataFrames", "PooledArrays", "Random", "StaticArrays", "StatsBase", "VariantCallFormat"]
+git-tree-sha1 = "e107a2412c47098cfe23d0726962d03c3ed64495"
+uuid = "45b36091-5ef7-4b08-b448-aaf24c763a14"
+version = "0.5.1"
+
 [[Poppler_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "Pkg", "libpng_jll"]
-git-tree-sha1 = "02148a0cb2532f22c0589ceb75c110e168fb3d1f"
+git-tree-sha1 = "e11443687ac151ac6ef6699eb75f964bed8e1faa"
 uuid = "9c32591e-4766-534b-9725-b71a8799265b"
-version = "21.9.0+0"
+version = "0.87.0+2"
 
 [[PositiveFactorizations]]
 deps = ["LinearAlgebra"]
@@ -1801,6 +1901,12 @@ git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734"
 uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439"
 version = "0.4.3"
 
+[[ReadDatastores]]
+deps = ["BioSequences", "FASTX"]
+git-tree-sha1 = "72f9df4854d3ee73097ce9f89871557848692541"
+uuid = "70a005b8-9d8a-11e9-0d98-c909fa2e52d2"
+version = "0.4.0"
+
 [[RealDot]]
 deps = ["LinearAlgebra"]
 git-tree-sha1 = "9f0a1b71baaf7650f4fa8a1d168c7fb6ee41f0c9"
@@ -1886,6 +1992,11 @@ version = "1.3.0"
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
+[[SIMD]]
+git-tree-sha1 = "7dbc15af7ed5f751a82bf3ed37757adf76c32402"
+uuid = "fdea26ae-647d-5447-a871-4b548cad5224"
+version = "3.4.1"
+
 [[SIMDDualNumbers]]
 deps = ["ForwardDiff", "IfElse", "SLEEFPirates", "VectorizationBase"]
 git-tree-sha1 = "62c2da6eb66de8bb88081d20528647140d4daa0e"
@@ -1903,6 +2014,12 @@ git-tree-sha1 = "d4c366b135fc2e1af7a000473e08edc5afd94819"
 uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa"
 version = "0.6.31"
 
+[[ScanByte]]
+deps = ["Libdl", "SIMD"]
+git-tree-sha1 = "9cc2955f2a254b18be655a4ee70bc4031b2b189e"
+uuid = "7b38b023-a4d7-4c5e-8d43-3f3097f304eb"
+version = "0.3.0"
+
 [[SciMLBase]]
 deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "RecipesBase", "RecursiveArrayTools", "StaticArrays", "Statistics", "Tables", "TreeViews"]
 git-tree-sha1 = "61159e034c4cb36b76ad2926bb5bf8c28cc2fb12"
@@ -1994,6 +2111,12 @@ git-tree-sha1 = "cbf21db885f478e4bd73b286af6e67d1beeebe4c"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
 version = "1.8.4"
 
+[[StableRNGs]]
+deps = ["Random", "Test"]
+git-tree-sha1 = "b57c4216b6c163a3a9d674f6b9f7b99cdccdb959"
+uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
+version = "0.1.2"
+
 [[StackViews]]
 deps = ["OffsetArrays"]
 git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c"
@@ -2002,9 +2125,9 @@ version = "0.1.1"
 
 [[Static]]
 deps = ["IfElse"]
-git-tree-sha1 = "7f5a513baec6f122401abfc8e9c074fdac54f6c1"
+git-tree-sha1 = "87e9954dfa33fd145694e42337bdd3d5b07021a6"
 uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "0.4.1"
+version = "0.6.0"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
@@ -2082,6 +2205,12 @@ git-tree-sha1 = "d24a825a95a6d98c385001212dc9020d609f2d4f"
 uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4"
 version = "1.8.1"
 
+[[SubstitutionModels]]
+deps = ["BioSymbols", "LinearAlgebra", "StaticArrays"]
+git-tree-sha1 = "5e18123c57ff933efff915f4b44eb5d46a4089d1"
+uuid = "8365b1bb-bd83-58ee-a267-f2965fc81c73"
+version = "0.5.0"
+
 [[SuiteSparse]]
 deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
@@ -2128,6 +2257,12 @@ version = "1.7.0"
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
 
+[[Tectonic]]
+deps = ["Pkg"]
+git-tree-sha1 = "0b3881685ddb3ab066159b2ce294dc54fcf3b9ee"
+uuid = "9ac5f52a-99c6-489f-af81-462ef484790f"
+version = "0.8.0"
+
 [[TensorCore]]
 deps = ["LinearAlgebra"]
 git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6"
@@ -2151,10 +2286,10 @@ uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69"
 version = "0.5.4"
 
 [[TikzPictures]]
-deps = ["LaTeXStrings", "Poppler_jll"]
-git-tree-sha1 = "40d1559df48a5316eb66ad29ac734db6829e433d"
+deps = ["LaTeXStrings", "Poppler_jll", "Requires", "Tectonic"]
+git-tree-sha1 = "4e75374d207fefb21105074100034236fceed7cb"
 uuid = "37f6aa50-8035-52d0-81c2-5a1d08754b2d"
-version = "3.2.0"
+version = "3.4.2"
 
 [[TiledIteration]]
 deps = ["OffsetArrays"]
@@ -2162,12 +2297,6 @@ git-tree-sha1 = "5683455224ba92ef59db72d10690690f4a8dc297"
 uuid = "06e1c1a7-607b-532d-9fad-de7d9aa2abac"
 version = "0.3.1"
 
-[[TimerOutputs]]
-deps = ["ExprTools", "Printf"]
-git-tree-sha1 = "d60b0c96a16aaa42138d5d38ad386df672cb8bd8"
-uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
-version = "0.5.16"
-
 [[TranscodingStreams]]
 deps = ["Random", "Test"]
 git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c"
@@ -2186,6 +2315,17 @@ git-tree-sha1 = "b8d08f55b02625770c09615d96927b3a8396925e"
 uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf"
 version = "0.1.11"
 
+[[Twiddle]]
+git-tree-sha1 = "29509c4862bfb5da9e76eb6937125ab93986270a"
+uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795"
+version = "1.1.2"
+
+[[TwoBit]]
+deps = ["BioGenerics", "BioSequences"]
+git-tree-sha1 = "adea0d50015bad1698e08a7500185fff0795f638"
+uuid = "75842c30-9b2d-11e9-3f58-f17fe2b89951"
+version = "0.1.0"
+
 [[UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
@@ -2221,6 +2361,12 @@ git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670"
 uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d"
 version = "0.1.2"
 
+[[VariantCallFormat]]
+deps = ["Automa", "BGZFStreams", "BioCore", "BufferedStreams"]
+git-tree-sha1 = "3f459ba763786964d472558c4b223bd332e89f24"
+uuid = "28eba6e3-a997-4ad9-87c6-d933b8bca6c1"
+version = "0.5.3"
+
 [[VectorizationBase]]
 deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "Hwloc", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"]
 git-tree-sha1 = "a48484def839a98571683a8b5b942fc910329480"
@@ -2281,18 +2427,38 @@ git-tree-sha1 = "de67fa59e33ad156a590055375a30b23c40299d3"
 uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
 version = "0.5.5"
 
+[[XAM]]
+deps = ["Automa", "BGZFStreams", "BioAlignments", "BioGenerics", "BioSequences", "GenomicFeatures", "Indexes", "Printf", "TranscodingStreams"]
+git-tree-sha1 = "6689a68552e7b91078dd2022946477d68e8a4cf8"
+repo-rev = "operations-fix"
+repo-url = "https://github.com/MillironX/XAM.jl"
+uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
+version = "0.2.7"
+
 [[XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
 git-tree-sha1 = "1acf5bdf07aa0907e0a37d3718bb88d4b687b74a"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
 version = "2.9.12+0"
 
+[[XMLDict]]
+deps = ["EzXML", "IterTools", "OrderedCollections"]
+git-tree-sha1 = "d9a3faf078210e477b291c79117676fca54da9dd"
+uuid = "228000da-037f-5747-90a9-8195ccbf91a5"
+version = "0.4.1"
+
 [[XSLT_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"]
 git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a"
 uuid = "aed1982a-8fda-507f-9586-7b0439959a61"
 version = "1.1.34+0"
 
+[[XZ_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "a921669cd9a45c23031fd4eb904f5cc3d20de415"
+uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
+version = "5.2.5+2"
+
 [[Xorg_libX11_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
 git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527"
@@ -2437,12 +2603,6 @@ git-tree-sha1 = "fe5c65a526f066fb3000da137d5785d9649a8a47"
 uuid = "8f1865be-045e-5c20-9c9f-bfbfb0764568"
 version = "4.3.4+0"
 
-[[ZipFile]]
-deps = ["Libdl", "Printf", "Zlib_jll"]
-git-tree-sha1 = "3593e69e469d2111389a9bd06bac1f3d730ac6de"
-uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea"
-version = "0.9.4"
-
 [[Zlib_jll]]
 deps = ["Libdl"]
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
diff --git a/Project.toml b/Project.toml
index dc330ee..c72beaa 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,9 +1,25 @@
 [deps]
+Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
+BED = "8e4a8c10-cb6b-11e8-08d2-83478d609d67"
+BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+BigWig = "9d649c22-cb6b-11e8-1fa9-f3896fced444"
+BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
+BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+BioServices = "a0d4ced5-b29c-5395-b614-ca030a679c4b"
+BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"
+BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
 BusinessDays = "4f18b42c-503e-5345-9536-bb0f25fc7038"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
 Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
+CodecBase = "6c391c72-fb7b-5838-ba82-7cfb1bcfecbf"
+CodecBzip2 = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
+CodecLz4 = "5ba52731-8f18-5e0d-9241-30f10d1ec561"
+CodecXz = "ba30903b-d9e8-5048-a5ec-d1f5b0d4b47b"
+CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
+CodecZstd = "6b39b394-51ab-5f42-8807-6242bab2b4c2"
 DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
@@ -12,26 +28,31 @@ DecisionTree = "7806a523-6efd-50cb-b5f6-3fa6f1930dbb"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 EzXML = "8f5d6c58-4d21-5cfd-889c-e3ad7ee6a615"
-Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
+GenomeGraphs = "3aa97884-90e5-11e8-2134-af657ec4f203"
+GenomicAnnotations = "4f8a0a0a-376d-5ac0-ab14-e88793df67f0"
+GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
 ImageMagick = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
 Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
+Indexes = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
 Interact = "c601a237-2ae4-5e1e-952c-7a85b0c7eef1"
+IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
 JDBC = "6042db11-3c3d-5e84-8dba-9cbf74c9ba48"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 JuliaWebAPI = "480116ec-64ea-5dec-baca-db6b11e96e37"
 KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
-Knet = "1902f260-5fb4-5aff-8c31-6271790ab950"
+KmerAnalysis = "a20136b7-8e32-4c10-91d3-7060c0bd8ec7"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LightXML = "9c8b4983-aa76-5018-a973-4c85ecc9e179"
 MLBase = "f0e99cf1-93fa-52ec-9ecc-5026115318e0"
-Metalhead = "dbeba491-748d-5e0e-a39e-b530a07fa0cc"
+MMTF = "259c3a9c-12c3-507f-b21f-68ecc40fcda4"
 NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Nettle = "49dea1ee-f6fa-5aa6-9a11-8816cee7d4b9"
@@ -41,12 +62,20 @@ PGFPlots = "3b7a836e-365b-5785-a47d-02c71176b4aa"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 ParserCombinator = "fae87a5f-d1ad-5cf0-8f61-c941e1580b46"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+PopGen = "af524d12-c74b-11e9-22a8-3b091653023f"
+PopGenCore = "45b36091-5ef7-4b08-b448-aaf24c763a14"
 ProtoBuf = "3349acd9-ac6a-5e09-bcdb-63829b23a429"
 QuantEcon = "fcd29c91-0bd7-5a09-975d-7ac3f643a60c"
+ReadDatastores = "70a005b8-9d8a-11e9-0d98-c909fa2e52d2"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
+SubstitutionModels = "8365b1bb-bd83-58ee-a267-f2965fc81c73"
+TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
+TwoBit = "75842c30-9b2d-11e9-3f58-f17fe2b89951"
 UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
+VariantCallFormat = "28eba6e3-a997-4ad9-87c6-d933b8bca6c1"
+XAM = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
diff --git a/README.md b/README.md
index 34f922f..c266e02 100644
--- a/README.md
+++ b/README.md
@@ -30,59 +30,67 @@ on the rationale for this and examples, see
 
 ## Included Packages
 
-Everything from my [JuliaPro image], plus
+Everything from my [JuliaPro image], minus
+
+- [ ] ~~[Flux](https://github.com/FluxML/Flux.jl)~~
+- [ ] ~~[Metalhead](https://github.com/FluxML/Metalhead.jl)~~
+- [ ] ~~[Knet](https://github.com/denizyuret/Knet.jl)~~
+
+plus
 
 ### Programming Libraries
 
-- [ ] [Automa](https://github.com/BioJulia/Automa.jl)
-- [ ] [BioGenerics](https://github.com/BioJulia/BioGenerics.jl)
-- [ ] [BioTools](https://github.com/BioJulia/BioTools.jl)
-- [ ] [PopGenCore](https://github.com/BioJulia/PopGenCore.jl)
+- [x] [Automa](https://github.com/BioJulia/Automa.jl)
+- [x] [BioGenerics](https://github.com/BioJulia/BioGenerics.jl)
+- [ ] ~~[BioTools](https://github.com/BioJulia/BioTools.jl)~~ (Dependent on
+  BioSequnces v1. Seriously?)
+- [x] [PopGenCore](https://github.com/BioJulia/PopGenCore.jl)
 
 ### Biological Types
 
-- [ ] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)
-- [ ] [BioSequences](https://github.com/BioJulia/BioSequences.jl)
-- [ ] [BioStructures](https://github.com/BioJulia/BioStructures.jl)
-- [ ] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)
-- [ ] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)
-- [ ] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)
-- [ ] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl)
+- [x] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)
+- [x] [BioSequences](https://github.com/BioJulia/BioSequences.jl)
+- [x] [BioStructures](https://github.com/BioJulia/BioStructures.jl)
+- [x] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)
+- [x] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)
+- [x] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)
+- [x] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl)
 
 ### File Formats
 
-- [ ] [BED](https://github.com/BioJulia/BED.jl)
-- [ ] [BigBed](https://github.com/BioJulia/BigBed.jl)
-- [ ] [BigWig](https://github.com/BioJulia/BigWig.jl)
-- [ ] [FASTX](https://github.com/BioJulia/FASTX.jl)
-- [ ] [GenomicAnnotations](https://github.com/BioJulia/GenomicAnnotations.jl)
-- [ ] [GenomicFeatures](https://github.com/BioJulia/GenomicFeatures.jl)
-- [ ] [MMTF](https://github.com/BioJulia/MMTF.jl)
-- [ ] [TwoBit](https://github.com/BioJulia/TwoBit.jl)
-- [ ] [VariantCallFormat](https://github.com/rasmushenningsson/VariantCallFormat.jl)
-- [ ] [XAM](https://github.com/MillironX/XAM.jl)
+- [x] [BED](https://github.com/BioJulia/BED.jl)
+- [ ] ~~[BigBed](https://github.com/BioJulia/BigBed.jl)~~ (Dependency mismatch
+  with PopGen)
+- [x] [BigWig](https://github.com/BioJulia/BigWig.jl)
+- [x] [FASTX](https://github.com/BioJulia/FASTX.jl)
+- [x] [GenomicAnnotations](https://github.com/BioJulia/GenomicAnnotations.jl)
+- [x] [GenomicFeatures](https://github.com/BioJulia/GenomicFeatures.jl)
+- [x] [MMTF](https://github.com/BioJulia/MMTF.jl)
+- [x] [TwoBit](https://github.com/BioJulia/TwoBit.jl)
+- [x] [VariantCallFormat](https://github.com/rasmushenningsson/VariantCallFormat.jl)
+- [x] [XAM](https://github.com/MillironX/XAM.jl)
 
 ### Analyses
 
-- [ ] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)
-- [ ] [PopGen](https://github.com/BioJulia/PopGen.jl.git)
+- [x] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)
+- [x] [PopGen](https://github.com/BioJulia/PopGen.jl.git)
 
 ### Compression Codecs and File Processing
 
-- [ ] [BGZFStreams](https://github.com/BioJulia/BGZFStreams.jl)
-- [ ] [CodecBase](https://github.com/bicycle1885/CodecBase.jl)
-- [ ] [CodecBzip2](https://github.com/bicycle1885/CodecBzip2.jl)
-- [ ] [CodecLz4](https://github.com/invenia/CodecLz4.jl)
-- [ ] [CodecXz](https://github.com/bicycle1885/CodecXz.jl)
-- [ ] [CodecZlib](https://github.com/bicycle1885/CodecZlib.jl)
-- [ ] [CodecZstd](https://github.com/bicycle1885/CodecZstd.jl)
-- [ ] [Indexes](https://github.com/BioJulia/Indexes.jl)
-- [ ] [TranscodingStreams](https://github.com/JuliaIO/TranscodingStreams.jl)
+- [x] [BGZFStreams](https://github.com/BioJulia/BGZFStreams.jl)
+- [x] [CodecBase](https://github.com/bicycle1885/CodecBase.jl)
+- [x] [CodecBzip2](https://github.com/bicycle1885/CodecBzip2.jl)
+- [x] [CodecLz4](https://github.com/invenia/CodecLz4.jl)
+- [x] [CodecXz](https://github.com/bicycle1885/CodecXz.jl)
+- [x] [CodecZlib](https://github.com/bicycle1885/CodecZlib.jl)
+- [x] [CodecZstd](https://github.com/bicycle1885/CodecZstd.jl)
+- [x] [Indexes](https://github.com/BioJulia/Indexes.jl)
+- [x] [TranscodingStreams](https://github.com/JuliaIO/TranscodingStreams.jl)
 
 ### Data Storage and Retrieval
 
-- [ ] [BioServices](https://github.com/BioJulia/BioServices.jl)
-- [ ] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)
+- [x] [BioServices](https://github.com/BioJulia/BioServices.jl)
+- [x] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)
 
 [`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
 [biojulia]: https://biojulia.net