From a3cbfcaaeeb6731dec8069fb2438b187c6ccbaa7 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Sat, 19 Nov 2022 15:32:40 -0600
Subject: [PATCH] Update to BioAlignments v3

---
 Manifest.toml | 684 ++++++++++++++++++++++++--------------------------
 Project.toml  |   4 -
 README.md     |   8 +-
 3 files changed, 328 insertions(+), 368 deletions(-)

diff --git a/Manifest.toml b/Manifest.toml
index 8833606..26f5940 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -7,9 +7,9 @@ uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
 version = "1.2.1"
 
 [[AbstractTrees]]
-git-tree-sha1 = "5c0b629df8a5566a06f5fef5100b53ea56e465a0"
+git-tree-sha1 = "52b3b436f8f73133d7bc3a6c71ee7ed6ab2ab754"
 uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-version = "0.4.2"
+version = "0.4.3"
 
 [[Adapt]]
 deps = ["LinearAlgebra"]
@@ -34,9 +34,9 @@ version = "0.1.0"
 
 [[Arpack]]
 deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"]
-git-tree-sha1 = "91ca22c4b8437da89b030f08d71db55a379ce958"
+git-tree-sha1 = "9b9b347613394885fd1c8c7729bfc60528faa436"
 uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97"
-version = "0.5.3"
+version = "0.5.4"
 
 [[Arpack_jll]]
 deps = ["Libdl", "OpenBLAS_jll", "Pkg"]
@@ -52,21 +52,21 @@ version = "6.0.23"
 
 [[ArrayInterfaceCore]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "5bb0f8292405a516880a3809954cb832ae7a31c5"
+git-tree-sha1 = "c46fb7dd1d8ca1d213ba25848a5ec4e47a1a1b08"
 uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2"
-version = "0.1.20"
+version = "0.1.26"
 
 [[ArrayInterfaceGPUArrays]]
 deps = ["Adapt", "ArrayInterfaceCore", "GPUArraysCore", "LinearAlgebra"]
-git-tree-sha1 = "febba7add2873aecc0b6620b55969e73ec875bce"
+git-tree-sha1 = "fc114f550b93d4c79632c2ada2924635aabfa5ed"
 uuid = "6ba088a2-8465-4c0a-af30-387133b534db"
-version = "0.2.1"
+version = "0.2.2"
 
 [[ArrayInterfaceOffsetArrays]]
 deps = ["ArrayInterface", "OffsetArrays", "Static"]
-git-tree-sha1 = "c49f6bad95a30defff7c637731f00934c7289c50"
+git-tree-sha1 = "3d1a9a01976971063b3930d1aed1d9c4af0817f8"
 uuid = "015c0d05-e682-4f19-8f0a-679ce4c54826"
-version = "0.1.6"
+version = "0.1.7"
 
 [[ArrayInterfaceStaticArrays]]
 deps = ["Adapt", "ArrayInterface", "ArrayInterfaceStaticArraysCore", "LinearAlgebra", "Static", "StaticArrays"]
@@ -76,15 +76,15 @@ version = "0.1.4"
 
 [[ArrayInterfaceStaticArraysCore]]
 deps = ["Adapt", "ArrayInterfaceCore", "LinearAlgebra", "StaticArraysCore"]
-git-tree-sha1 = "a1e2cf6ced6505cbad2490532388683f1e88c3ed"
+git-tree-sha1 = "93c8ba53d8d26e124a5a8d4ec914c3a16e6a0970"
 uuid = "dd5226c6-a4d4-4bc7-8575-46859f9c95b9"
-version = "0.1.0"
+version = "0.1.3"
 
 [[ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "ac5cc6021f32a272ee572dd2a325049a1fa0d034"
+git-tree-sha1 = "7c3a0ce8d64ad84438b1bf60eca4f003a84e33e1"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
-version = "0.8.11"
+version = "0.8.14"
 
 [[Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -137,19 +137,19 @@ uuid = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
 version = "0.3.1"
 
 [[BandedMatrices]]
-deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "2495db5e036dd9f16538250cf3e51bc82d0326db"
+deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "SparseArrays"]
+git-tree-sha1 = "45fc0722d59676040e356e7c059d6e51c2b24382"
 uuid = "aae01518-5342-5314-be14-df237901396f"
-version = "0.17.6"
+version = "0.17.8"
 
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
 [[BenchmarkTools]]
 deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"]
-git-tree-sha1 = "4c10eee4af024676200bc7752e536f858c6b8f93"
+git-tree-sha1 = "d9a9701b899b30332bbcb3e1679c41cce81fb0e8"
 uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-version = "1.3.1"
+version = "1.3.2"
 
 [[BigWig]]
 deps = ["BBI", "BioCore", "BufferedStreams", "GenomicFeatures", "Libz"]
@@ -159,11 +159,9 @@ version = "0.1.0"
 
 [[BioAlignments]]
 deps = ["BioGenerics", "BioSequences", "BioSymbols", "IntervalTrees", "LinearAlgebra"]
-git-tree-sha1 = "29e735a07a5f03e76f0ce99f2293cecd946c3729"
-repo-rev = "operations-fix"
-repo-url = "https://github.com/MillironX/BioAlignments.jl"
+git-tree-sha1 = "707e7e02cfb91a2b09e8f89df0204603b026df88"
 uuid = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
-version = "2.1.0"
+version = "3.0.0"
 
 [[BioCore]]
 deps = ["Automa", "BufferedStreams", "YAML"]
@@ -178,10 +176,10 @@ uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 version = "0.1.2"
 
 [[BioSequences]]
-deps = ["BioGenerics", "BioSymbols", "Combinatorics", "IndexableBitVectors", "Printf", "Random", "StableRNGs", "Twiddle"]
-git-tree-sha1 = "093ccb9211bdc71924abf8e74a0790af11da35a7"
+deps = ["BioSymbols", "Random", "SnoopPrecompile", "Twiddle"]
+git-tree-sha1 = "90d2f278c4a20d43a885feb4847b8694d1ba4a60"
 uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-version = "2.0.5"
+version = "3.1.1"
 
 [[BioServices]]
 deps = ["Dates", "Gumbo", "HTTP", "JSON", "XMLDict"]
@@ -189,29 +187,23 @@ 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"
+deps = ["SnoopPrecompile"]
+git-tree-sha1 = "2052c3ec7c41b69efa0e9ff7e2734aa6658d4c40"
 uuid = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
-version = "4.0.4"
+version = "5.1.2"
 
 [[BitTwiddlingConvenienceFunctions]]
 deps = ["Static"]
-git-tree-sha1 = "eaee37f76339077f86679787a71990c4e465477f"
+git-tree-sha1 = "0c5f81f47bbbcf4aea7b2959135713459170798b"
 uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b"
-version = "0.1.4"
+version = "0.1.5"
 
 [[BoundaryValueDiffEq]]
 deps = ["BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase", "SparseArrays"]
-git-tree-sha1 = "2f80b70bd3ddd9aa3ec2d77604c1121bd115650e"
+git-tree-sha1 = "d4d28a2ac12b6252e6b09a6eebf71f6f8795de49"
 uuid = "764a87c0-6b3e-53db-9096-fe964310641d"
-version = "2.9.0"
+version = "2.10.0"
 
 [[BufferedStreams]]
 git-tree-sha1 = "bb065b14d7f941b8617bc323063dbe79f55d16ea"
@@ -220,9 +212,9 @@ version = "1.1.0"
 
 [[BusinessDays]]
 deps = ["Dates"]
-git-tree-sha1 = "0fa16b8e9abf893a5009008752e292f599c4f9b5"
+git-tree-sha1 = "4e387fb96795b71276b429eee6e4abd7e4aeea77"
 uuid = "4f18b42c-503e-5345-9536-bb0f25fc7038"
-version = "0.9.18"
+version = "0.9.19"
 
 [[Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -237,9 +229,9 @@ version = "0.4.2"
 
 [[CPUSummary]]
 deps = ["CpuId", "IfElse", "Static"]
-git-tree-sha1 = "9bdd5aceea9fa109073ace6b430a24839d79315e"
+git-tree-sha1 = "a7157ab6bcda173f533db4c93fc8a27a48843757"
 uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
-version = "0.1.27"
+version = "0.1.30"
 
 [[CSSUtil]]
 deps = ["Colors", "JSON", "Markdown", "Measures", "WebIO"]
@@ -249,9 +241,9 @@ version = "0.1.1"
 
 [[CSV]]
 deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"]
-git-tree-sha1 = "873fb188a4b9d76549b81465b1f75c82aaf59238"
+git-tree-sha1 = "c5fd7cd27ac4aed0acf4b73948f0110ff2a854b2"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-version = "0.10.4"
+version = "0.10.7"
 
 [[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"]
@@ -273,15 +265,15 @@ version = "0.2.2"
 
 [[ChainRules]]
 deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"]
-git-tree-sha1 = "a5fd229d3569a6600ae47abe8cd48cbeb972e173"
+git-tree-sha1 = "0c8c8887763f42583e1206ee35413a43c91e2623"
 uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
-version = "1.44.6"
+version = "1.45.0"
 
 [[ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "dc4405cee4b2fe9e1108caec2d760b7ea758eca2"
+git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.15.5"
+version = "1.15.6"
 
 [[ChangesOfVariables]]
 deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
@@ -296,16 +288,16 @@ uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9"
 version = "0.1.10"
 
 [[Clustering]]
-deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "SparseArrays", "Statistics", "StatsBase"]
-git-tree-sha1 = "75479b7df4167267d75294d14b58244695beb2ac"
+deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"]
+git-tree-sha1 = "64df3da1d2a26f4de23871cd1b6482bb68092bd5"
 uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
-version = "0.14.2"
+version = "0.14.3"
 
 [[CodeTracking]]
 deps = ["InteractiveUtils", "UUIDs"]
-git-tree-sha1 = "1833bda4a027f4b2a1c984baddcf755d77266818"
+git-tree-sha1 = "cc4bd91eba9cdbbb4df4746124c22c0832a460d6"
 uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
-version = "1.1.0"
+version = "1.1.1"
 
 [[CodecBase]]
 deps = ["TranscodingStreams"]
@@ -379,9 +371,9 @@ uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 version = "1.0.2"
 
 [[CommonSolve]]
-git-tree-sha1 = "332a332c97c7071600984b3c31d9067e1a4e6e25"
+git-tree-sha1 = "9441451ee712d1aec22edad62db1a9af3dc8d852"
 uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
-version = "0.2.1"
+version = "0.2.3"
 
 [[CommonSubexpressions]]
 deps = ["MacroTools", "Test"]
@@ -390,10 +382,10 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
 version = "0.3.0"
 
 [[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 = "78bee250c6826e1cf805a88b7f1e86025275d208"
+deps = ["Dates", "LinearAlgebra", "UUIDs"]
+git-tree-sha1 = "aaabba4ce1b7f8a9b34c015053d3b1edf60fa49c"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.46.0"
+version = "4.4.0"
 
 [[CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -445,15 +437,15 @@ uuid = "717857b8-e6f2-59f4-9121-6e50c889abd2"
 version = "0.7.7"
 
 [[DataAPI]]
-git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40"
+git-tree-sha1 = "e08915633fcb3ea83bf9d6126292e5bc5c739922"
 uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
-version = "1.10.0"
+version = "1.13.0"
 
 [[DataFrames]]
-deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
-git-tree-sha1 = "6bce52b2060598d8caaed807ec6d6da2a1de949e"
+deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
+git-tree-sha1 = "0f44494fe4271cc966ac4fea524111bef63ba86c"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "1.3.5"
+version = "1.4.3"
 
 [[DataStructures]]
 deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
@@ -490,9 +482,9 @@ version = "0.11.2"
 
 [[DelayDiffEq]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "UnPack"]
-git-tree-sha1 = "5acc7807b906d6a938dfeb965a6ea931260f054e"
+git-tree-sha1 = "4e1edae7af4bb6ea81e885a5a1c417f1218012db"
 uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
-version = "5.38.0"
+version = "5.39.1"
 
 [[DelimitedFiles]]
 deps = ["Mmap"]
@@ -506,39 +498,39 @@ version = "0.4.0"
 
 [[DiffEqBase]]
 deps = ["ArrayInterfaceCore", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArrays", "Statistics", "Tricks", "ZygoteRules"]
-git-tree-sha1 = "ff3b0abda9ee27c36019fffce8aca4394505e503"
+git-tree-sha1 = "c8514cbef84124a40906655d9ca938fa5ac5892c"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.104.2"
+version = "6.106.0"
 
 [[DiffEqCallbacks]]
 deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArrays"]
-git-tree-sha1 = "f8cc1ad62a87988225a07524ef84c7df7264c232"
+git-tree-sha1 = "485503846a90b59f3b79b39c2d818496bf50d197"
 uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def"
-version = "2.24.1"
+version = "2.24.3"
 
 [[DiffEqNoiseProcess]]
 deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArrays", "Statistics"]
-git-tree-sha1 = "8ba7a8913dc57c087d3cdc9b67eb1c9d760125bc"
+git-tree-sha1 = "b520f8b55f41c3a86fd181d342f23cccd047846e"
 uuid = "77a26b50-5914-5dd7-bc55-306e6241c503"
-version = "5.13.0"
+version = "5.14.2"
 
 [[DiffResults]]
-deps = ["StaticArrays"]
-git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805"
+deps = ["StaticArraysCore"]
+git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621"
 uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
-version = "1.0.3"
+version = "1.1.0"
 
 [[DiffRules]]
 deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"]
-git-tree-sha1 = "992a23afdb109d0d2f8802a30cf5ae4b1fe7ea68"
+git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494"
 uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
-version = "1.11.1"
+version = "1.12.2"
 
 [[DifferentialEquations]]
 deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"]
-git-tree-sha1 = "c14099268b2bb616267be573cadb5ef913e54bea"
+git-tree-sha1 = "418dad2cfd7377a474326bc86a23cb645fac6527"
 uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
-version = "7.3.0"
+version = "7.6.0"
 
 [[Discretizers]]
 deps = ["DataStructures", "SpecialFunctions", "Statistics", "StatsBase"]
@@ -558,15 +550,15 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[Distributions]]
 deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"]
-git-tree-sha1 = "ee407ce31ab2f1bacadc3bd987e96de17e00aed3"
+git-tree-sha1 = "7fe1eff48e18a91946ff753baf834ff4d5c03744"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.71"
+version = "0.25.78"
 
 [[DocStringExtensions]]
 deps = ["LibGit2"]
-git-tree-sha1 = "5158c2b41018c5f7eb1470d558127ac274eca0c9"
+git-tree-sha1 = "c36550cb29cbe373e95b3f40486b9a4148f89ffd"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-version = "0.9.1"
+version = "0.9.2"
 
 [[Downloads]]
 deps = ["ArgTools", "LibCURL", "NetworkOptions"]
@@ -578,12 +570,6 @@ git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566"
 uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74"
 version = "0.6.8"
 
-[[EarCut_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d"
-uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5"
-version = "2.2.3+0"
-
 [[EnumX]]
 git-tree-sha1 = "e5333cd1e1c713ee21d07b6ed8b0d8853fabe650"
 uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
@@ -596,15 +582,15 @@ uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
 version = "2.4.8+0"
 
 [[ExponentialUtilities]]
-deps = ["ArrayInterfaceCore", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SparseArrays", "libblastrampoline_jll"]
-git-tree-sha1 = "b40c9037e1a33990466bc5d224ced34b34eebdb0"
+deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceGPUArrays", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SparseArrays", "libblastrampoline_jll"]
+git-tree-sha1 = "9837d3f3a904c7a7ab9337759c0093d3abea1d81"
 uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18"
-version = "1.18.0"
+version = "1.22.0"
 
-[[Extents]]
-git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99"
-uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910"
-version = "0.1.1"
+[[ExprTools]]
+git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d"
+uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
+version = "0.1.8"
 
 [[EzXML]]
 deps = ["Printf", "XML2_jll"]
@@ -614,9 +600,9 @@ version = "1.1.0"
 
 [[FASTX]]
 deps = ["Automa", "BioGenerics", "BioSequences", "BioSymbols", "TranscodingStreams"]
-git-tree-sha1 = "6582055aa8f890663f63cbf9bc748b0a537b5fd3"
+git-tree-sha1 = "2f080a912d3b82b6a5a22f90843be63a753a9e1d"
 uuid = "c2308a5c-f048-11e8-3e8a-31650f418d12"
-version = "1.2.0"
+version = "1.3.0"
 
 [[FFMPEG]]
 deps = ["FFMPEG_jll"]
@@ -625,10 +611,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
 version = "0.4.1"
 
 [[FFMPEG_jll]]
-deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
-git-tree-sha1 = "ccd479984c7838684b3ac204b716c89955c76623"
+deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
+git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
-version = "4.4.2+0"
+version = "4.4.2+2"
 
 [[FFTViews]]
 deps = ["CustomUnitRanges", "FFTW"]
@@ -667,9 +653,9 @@ version = "1.2.7"
 
 [[FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
-git-tree-sha1 = "94f5101b96d2d968ace56f7f2db19d0a5f592e28"
+git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.15.0"
+version = "1.16.0"
 
 [[FilePathsBase]]
 deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"]
@@ -682,15 +668,15 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"]
-git-tree-sha1 = "87519eb762f85534445f5cda35be12e32759ee14"
+git-tree-sha1 = "802bfc139833d2ba893dd9e62ba1767c88d708ae"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.13.4"
+version = "0.13.5"
 
 [[FiniteDiff]]
 deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"]
-git-tree-sha1 = "5a2cff9b6b77b33b89f3d97a4d367747adce647e"
+git-tree-sha1 = "bb61d9e5085784fe453f70c97b23964c5bf36942"
 uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
-version = "2.15.0"
+version = "2.16.0"
 
 [[FixedPointNumbers]]
 deps = ["Statistics"]
@@ -704,11 +690,6 @@ 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"
@@ -717,9 +698,9 @@ version = "0.4.2"
 
 [[ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
-git-tree-sha1 = "187198a4ed8ccd7b5d99c41b69c679269ea2b2d4"
+git-tree-sha1 = "10fa12fe96e4d76acfa738f4df2126589a67374f"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.10.32"
+version = "0.10.33"
 
 [[FreeType]]
 deps = ["CEnum", "FreeType2_jll"]
@@ -733,12 +714,6 @@ git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9"
 uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
 version = "2.10.4+0"
 
-[[FreeTypeAbstraction]]
-deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"]
-git-tree-sha1 = "38a92e40157100e796690421e34a11c107205c86"
-uuid = "663a7486-cb36-511b-a19d-713bb74d65c9"
-version = "0.10.0"
-
 [[FriBidi_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91"
@@ -746,9 +721,9 @@ uuid = "559328eb-81f9-559d-9380-de523a88c83c"
 version = "1.0.10+0"
 
 [[FunctionWrappers]]
-git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc"
+git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e"
 uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
-version = "1.1.2"
+version = "1.1.3"
 
 [[FunctionWrappersWrappers]]
 deps = ["FunctionWrappers"]
@@ -801,16 +776,16 @@ uuid = "46192b85-c4d5-4398-a991-12ede77f4527"
 version = "0.1.2"
 
 [[GR]]
-deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"]
-git-tree-sha1 = "cf0a9940f250dc3cb6cc6c6821b4bf8a4286cf9c"
+deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"]
+git-tree-sha1 = "00a9d4abadc05b9476e937a5557fcce476b9e547"
 uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
-version = "0.66.2"
+version = "0.69.5"
 
 [[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 = "3697c23d09d5ec6f2088faa68f0d926b6889b5be"
+git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943"
 uuid = "d2c73de3-f751-5644-a686-071e5b155ba9"
-version = "0.67.0+0"
+version = "0.69.1+0"
 
 [[GenericSchur]]
 deps = ["LinearAlgebra", "Printf"]
@@ -818,17 +793,11 @@ git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6"
 uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e"
 version = "0.5.3"
 
-[[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"
+git-tree-sha1 = "f09dabebfce53df2f78dd0e603ae1f45f1b91ef1"
 uuid = "4f8a0a0a-376d-5ac0-ab14-e88793df67f0"
-version = "0.3.1"
+version = "0.3.2"
 
 [[GenomicFeatures]]
 deps = ["BioGenerics", "DataStructures", "IntervalTrees"]
@@ -836,18 +805,6 @@ git-tree-sha1 = "881bda64be17d6eefdb6dfccc329fdb904fa596e"
 uuid = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 version = "2.0.5"
 
-[[GeoInterface]]
-deps = ["Extents"]
-git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab"
-uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
-version = "1.0.1"
-
-[[GeometryBasics]]
-deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
-git-tree-sha1 = "a7a97895780dab1085a97769316aa348830dc991"
-uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-version = "0.4.3"
-
 [[Gettext_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"]
 git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046"
@@ -855,10 +812,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1"
 version = "0.21.0+0"
 
 [[Glib_jll]]
-deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06"
+deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"]
+git-tree-sha1 = "fb83fbe02fe57f2c068013aa94bcdf6760d3a7a7"
 uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.68.3+2"
+version = "2.74.0+1"
 
 [[Graphics]]
 deps = ["Colors", "LinearAlgebra", "NaNMath"]
@@ -874,9 +831,9 @@ version = "1.3.14+0"
 
 [[Graphs]]
 deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
-git-tree-sha1 = "a6d30bdc378d340912f48abf01281aab68c0dec8"
+git-tree-sha1 = "ba2d094a88b6b287bd25cfa86f301e7693ffae2f"
 uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
-version = "1.7.2"
+version = "1.7.4"
 
 [[Grisu]]
 git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
@@ -885,9 +842,9 @@ version = "1.0.2"
 
 [[Gumbo]]
 deps = ["AbstractTrees", "Gumbo_jll", "Libdl"]
-git-tree-sha1 = "a4b03190a8d79e95b2f418df44f74cbc34289920"
+git-tree-sha1 = "a1a138dfbf9df5bace489c7a9d5196d6afdfa140"
 uuid = "708ec375-b3d6-5a57-a7ce-8257bf98657a"
-version = "0.8.1"
+version = "0.8.2"
 
 [[Gumbo_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -915,9 +872,9 @@ version = "0.5.2"
 
 [[HostCPUFeatures]]
 deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"]
-git-tree-sha1 = "b7b88a4716ac33fe31d6556c02fc60017594343c"
+git-tree-sha1 = "f64b890b2efa4de81520d2b0fbdc9aadb65bdf53"
 uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0"
-version = "0.1.8"
+version = "0.1.13"
 
 [[HypergeometricFunctions]]
 deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"]
@@ -927,15 +884,15 @@ version = "0.3.11"
 
 [[HypothesisTests]]
 deps = ["Combinatorics", "Distributions", "LinearAlgebra", "Random", "Rmath", "Roots", "Statistics", "StatsBase"]
-git-tree-sha1 = "10b23fc711999d34f6888ab6df4c510def193fd9"
+git-tree-sha1 = "ae3b6964d58df11984d22644ce5546eaf20fe95d"
 uuid = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
-version = "0.10.10"
+version = "0.10.11"
 
 [[IRTools]]
 deps = ["InteractiveUtils", "MacroTools", "Test"]
-git-tree-sha1 = "af14a478780ca78d5eb9908b263023096c2b9d64"
+git-tree-sha1 = "2e99184fca5eb6f075944b04c22edec29beb4778"
 uuid = "7869d1d1-7146-5819-86e3-90919afe41df"
-version = "0.4.6"
+version = "0.4.7"
 
 [[IfElse]]
 git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1"
@@ -1044,12 +1001,6 @@ 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"
@@ -1073,9 +1024,9 @@ version = "0.5.1"
 
 [[InlineStrings]]
 deps = ["Parsers"]
-git-tree-sha1 = "d19f9edd8c34760dca2de2b503f969d8700ed288"
+git-tree-sha1 = "0cf92ec945125946352f3d46c96976ab972bde6f"
 uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
-version = "1.1.4"
+version = "1.3.2"
 
 [[IntegerMathUtils]]
 git-tree-sha1 = "f366daebdfb079fd1fe4e3d560f99a0c892e15bc"
@@ -1096,15 +1047,15 @@ version = "2018.0.3+2"
 
 [[Interact]]
 deps = ["CSSUtil", "InteractBase", "JSON", "Knockout", "Observables", "OrderedCollections", "Reexport", "WebIO", "Widgets"]
-git-tree-sha1 = "311f9130aeb50ac93a12dd076fa02c9a430be525"
+git-tree-sha1 = "c5091992248c7134af7c90554305c600d5d9012b"
 uuid = "c601a237-2ae4-5e1e-952c-7a85b0c7eef1"
-version = "0.10.4"
+version = "0.10.5"
 
 [[InteractBase]]
 deps = ["Base64", "CSSUtil", "Colors", "Dates", "JSExpr", "JSON", "Knockout", "Observables", "OrderedCollections", "Random", "WebIO", "Widgets"]
-git-tree-sha1 = "3ace4760fab1c9700ec9c68ab0e36e0856f05556"
+git-tree-sha1 = "dc5a846040f1607740e29e582b6e66251b9ecf9d"
 uuid = "d3863d7c-f0c8-5437-a7b4-3ae773c01009"
-version = "0.10.8"
+version = "0.10.9"
 
 [[InteractiveUtils]]
 deps = ["Markdown"]
@@ -1112,15 +1063,15 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[Interpolations]]
 deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"]
-git-tree-sha1 = "f67b55b6447d36733596aea445a9f119e83498b6"
+git-tree-sha1 = "842dd89a6cb75e02e85fdd75c760cdc43f5d6863"
 uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
-version = "0.14.5"
+version = "0.14.6"
 
 [[IntervalSets]]
 deps = ["Dates", "Random", "Statistics"]
-git-tree-sha1 = "076bb0da51a8c8d1229936a1af7bdfacd65037e1"
+git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347"
 uuid = "8197267c-284f-5f27-9208-e0e47529a953"
-version = "0.7.2"
+version = "0.7.3"
 
 [[IntervalTrees]]
 deps = ["InteractiveUtils", "Profile", "Random", "Test"]
@@ -1130,9 +1081,9 @@ version = "1.0.0"
 
 [[InverseFunctions]]
 deps = ["Test"]
-git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918"
+git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f"
 uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
-version = "0.1.7"
+version = "0.1.8"
 
 [[InvertedIndices]]
 git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f"
@@ -1168,9 +1119,15 @@ version = "0.5.0"
 
 [[JLD2]]
 deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"]
-git-tree-sha1 = "6c38bbe47948f74d63434abed68bdfc8d2c46b99"
+git-tree-sha1 = "18dd357553912b6adc23b5f721e4be19930140c6"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.4.23"
+version = "0.4.28"
+
+[[JLFzf]]
+deps = ["Pipe", "REPL", "Random", "fzf_jll"]
+git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185"
+uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c"
+version = "0.1.5"
 
 [[JLLWrappers]]
 deps = ["Preferences"]
@@ -1191,10 +1148,10 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.3"
 
 [[JSON3]]
-deps = ["Dates", "Mmap", "Parsers", "StructTypes", "UUIDs"]
-git-tree-sha1 = "f1572de22c866dc92aea032bc89c2b137cbddd6a"
+deps = ["Dates", "Mmap", "Parsers", "SnoopPrecompile", "StructTypes", "UUIDs"]
+git-tree-sha1 = "84b10656a41ef564c39d2d477d7236966d2b5683"
 uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
-version = "1.10.0"
+version = "1.12.0"
 
 [[JavaCall]]
 deps = ["DataStructures", "Dates", "Libdl", "WinReg"]
@@ -1228,15 +1185,15 @@ version = "0.6.3"
 
 [[JumpProcesses]]
 deps = ["ArrayInterfaceCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"]
-git-tree-sha1 = "5a6e6c522e8a7b39b24be8eebcc13cc7885c6f2c"
+git-tree-sha1 = "535605173bbf752b37b80440d6baaad28db0fcea"
 uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
-version = "9.2.0"
+version = "9.2.2"
 
 [[KLU]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"]
-git-tree-sha1 = "cae5e3dfd89b209e01bcd65b3a25e74462c67ee0"
+git-tree-sha1 = "764164ed65c30738750965d55652db9c94c59bfe"
 uuid = "ef3ab10e-7fda-4108-b977-705223b18434"
-version = "0.3.0"
+version = "0.4.0"
 
 [[Kelpie]]
 deps = ["EzXML"]
@@ -1250,17 +1207,11 @@ git-tree-sha1 = "9816b296736292a80b9a3200eb7fbb57aaa3917a"
 uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
 version = "0.6.5"
 
-[[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"]
-git-tree-sha1 = "deb74017e1061d76050ff68d219217413be4ef59"
+git-tree-sha1 = "91835de56d816864f1c38fb5e3fad6eb1e741271"
 uuid = "bcebb21b-c2e3-54f8-a781-646b90f6d2cc"
-version = "0.2.5"
+version = "0.2.6"
 
 [[Krylov]]
 deps = ["LinearAlgebra", "Printf", "SparseArrays"]
@@ -1269,10 +1220,10 @@ uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 version = "0.8.4"
 
 [[KrylovKit]]
-deps = ["LinearAlgebra", "Printf"]
-git-tree-sha1 = "49b0c1dd5c292870577b8f58c51072bd558febb9"
+deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf"]
+git-tree-sha1 = "1a5e1d9941c783b0119897d29f2eb665d876ecf3"
 uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77"
-version = "0.5.4"
+version = "0.6.0"
 
 [[LAME_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1317,9 +1268,9 @@ version = "0.15.17"
 
 [[LayoutPointers]]
 deps = ["ArrayInterface", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"]
-git-tree-sha1 = "b67e749fb35530979839e7b4b606a97105fe4f1c"
+git-tree-sha1 = "73e2e40eb02d6ccd191a8a9f8cee20db8d5df010"
 uuid = "10f19ff3-798f-405d-979b-55457f8fc047"
-version = "0.1.10"
+version = "0.1.11"
 
 [[LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
@@ -1432,10 +1383,10 @@ deps = ["Libdl"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[LinearSolve]]
-deps = ["ArrayInterfaceCore", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SuiteSparse", "UnPack"]
-git-tree-sha1 = "c17007396b2ae56b8496f5a9857326dea0b7bb7b"
+deps = ["ArrayInterfaceCore", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SnoopPrecompile", "SparseArrays", "SuiteSparse", "UnPack"]
+git-tree-sha1 = "7af848f614840d768002b607e297a51bdc62955f"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "1.26.0"
+version = "1.28.0"
 
 [[LittleCMS_jll]]
 deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pkg"]
@@ -1454,9 +1405,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[LoopVectorization]]
 deps = ["ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDDualNumbers", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"]
-git-tree-sha1 = "2ebc4aab4d1463fb897e57f792ee9903c07ecdbd"
+git-tree-sha1 = "9b90f3cf246e239dc7d79588c96586ab9b3c0a00"
 uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
-version = "0.12.127"
+version = "0.12.139"
 
 [[Lz4_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1466,9 +1417,9 @@ version = "1.9.3+0"
 
 [[MKL_jll]]
 deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
-git-tree-sha1 = "41d162ae9c868218b1f3fe78cba878aa348c2d26"
+git-tree-sha1 = "2ce8695e1e699b68702c03402672a69f54b8aca9"
 uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
-version = "2022.1.0+0"
+version = "2022.2.0+0"
 
 [[MLBase]]
 deps = ["IterTools", "Random", "Reexport", "StatsBase"]
@@ -1484,9 +1435,9 @@ version = "1.0.0"
 
 [[MacroTools]]
 deps = ["Markdown", "Random"]
-git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf"
+git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2"
 uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.9"
+version = "0.5.10"
 
 [[ManualMemory]]
 git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd"
@@ -1510,9 +1461,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[MathOptInterface]]
 deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"]
-git-tree-sha1 = "81a98bed15dc1d49ed6afa2dc65272e402a1704b"
+git-tree-sha1 = "ceed48edffe0325a6e9ea00ecf3607af5089c413"
 uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
-version = "1.8.1"
+version = "1.9.0"
 
 [[MathProgBase]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -1522,18 +1473,18 @@ version = "0.7.8"
 
 [[MbedTLS]]
 deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"]
-git-tree-sha1 = "ae6676d5f576ccd21b6789c2cbe2ba24fcc8075d"
+git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b"
 uuid = "739be429-bea8-5141-9913-cc70e7f3736d"
-version = "1.1.5"
+version = "1.1.7"
 
 [[MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[Measures]]
-git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f"
+git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102"
 uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e"
-version = "0.3.1"
+version = "0.3.2"
 
 [[MetaGraphs]]
 deps = ["Graphs", "JLD2", "Random"]
@@ -1566,9 +1517,9 @@ uuid = "99f44e22-a591-53d1-9472-aa23ef4bd671"
 version = "1.1.0"
 
 [[MuladdMacro]]
-git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68"
+git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab"
 uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
-version = "0.2.2"
+version = "0.2.4"
 
 [[MultipleTesting]]
 deps = ["Distributions", "SpecialFunctions", "StatsBase"]
@@ -1590,9 +1541,9 @@ version = "1.0.14"
 
 [[MutableArithmetics]]
 deps = ["LinearAlgebra", "SparseArrays", "Test"]
-git-tree-sha1 = "4e675d6e9ec02061800d6cfb695812becbd03cdf"
+git-tree-sha1 = "1d57a7dc42d563ad6b5e95d7a8aebd550e5162c0"
 uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
-version = "1.0.4"
+version = "1.0.5"
 
 [[MyterialColors]]
 git-tree-sha1 = "01d8466fb449436348999d7c6ad740f8f853a579"
@@ -1637,9 +1588,9 @@ version = "0.9.6"
 
 [[NearestNeighbors]]
 deps = ["Distances", "StaticArrays"]
-git-tree-sha1 = "0e353ed734b1747fc20cd4cba0edd9ac027eff6a"
+git-tree-sha1 = "440165bf08bc500b8fe4a7be2dc83271a00c0716"
 uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
-version = "0.4.11"
+version = "0.4.12"
 
 [[Netpbm]]
 deps = ["FileIO", "ImageCore"]
@@ -1669,15 +1620,15 @@ uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 version = "0.3.22"
 
 [[Observables]]
-git-tree-sha1 = "fe29afdef3d0c4a8286128d4e45cc50621b1e43d"
+git-tree-sha1 = "6862738f9796b3edc1c09d0890afce4eca9e7e93"
 uuid = "510215fc-4207-5dde-b226-833fc4488ee2"
-version = "0.4.0"
+version = "0.5.4"
 
 [[OffsetArrays]]
 deps = ["Adapt"]
-git-tree-sha1 = "1ea784113a6aa054c5ebd95945fa5e52c2f378e7"
+git-tree-sha1 = "f71d8950b724e9ff6110fc948dff5a329f901d64"
 uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-version = "1.12.7"
+version = "1.12.8"
 
 [[Ogg_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1725,9 +1676,9 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
 
 [[OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "e60321e3f2616584ff98f0a4f18d98ae6f89bbb3"
+git-tree-sha1 = "f6e9dba33f9f2c44e08a020b0caf6903be540004"
 uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "1.1.17+0"
+version = "1.1.19+0"
 
 [[OpenSpecFun_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -1753,16 +1704,14 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.4.1"
 
 [[OrdinaryDiffEq]]
-deps = ["Adapt", "ArrayInterface", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
-git-tree-sha1 = "d20891e46072ad2826fab4b9c8fcb4e4654eb8c9"
+deps = ["Adapt", "ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "ArrayInterfaceStaticArraysCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
+git-tree-sha1 = "7fff85e9569a5b7d11feffa88025cabf2358dddc"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.26.4"
+version = "6.31.2"
 
-[[PCRE_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488"
-uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc"
-version = "8.44.0+0"
+[[PCRE2_jll]]
+deps = ["Artifacts", "Libdl"]
+uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15"
 
 [[PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
@@ -1778,9 +1727,9 @@ version = "3.4.2"
 
 [[PNGFiles]]
 deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"]
-git-tree-sha1 = "e925a64b8585aa9f4e3047b8d2cdc3f0e79fd4e4"
+git-tree-sha1 = "f809158b27eba0c18c269cf2a2be6ed751d3e81d"
 uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883"
-version = "0.3.16"
+version = "0.3.17"
 
 [[PaddedViews]]
 deps = ["OffsetArrays"]
@@ -1801,10 +1750,10 @@ uuid = "fae87a5f-d1ad-5cf0-8f61-c941e1580b46"
 version = "2.1.1"
 
 [[Parsers]]
-deps = ["Dates"]
-git-tree-sha1 = "3d5bf43e3e8b412656404ed9466f1dcbf7c50269"
+deps = ["Dates", "SnoopPrecompile"]
+git-tree-sha1 = "b64719e8b4504983c7fca6cc9db3ebc8acc2a4d6"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.4.0"
+version = "2.5.1"
 
 [[Pidfile]]
 deps = ["FileWatching", "Test"]
@@ -1812,6 +1761,11 @@ git-tree-sha1 = "2d8aaf8ee10df53d0dfb9b8ee44ae7c04ced2b03"
 uuid = "fa939f87-e72e-5be4-a000-7fc836dbe307"
 version = "1.3.0"
 
+[[Pipe]]
+git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
+uuid = "b98c9c47-44ae-5843-9183-064241ee97a0"
+version = "1.3.0"
+
 [[Pixman_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29"
@@ -1830,9 +1784,9 @@ version = "0.3.2"
 
 [[PlotThemes]]
 deps = ["PlotUtils", "Statistics"]
-git-tree-sha1 = "8162b2f8547bc23876edd0c5181b27702ae58dce"
+git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899"
 uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
-version = "3.0.0"
+version = "3.1.0"
 
 [[PlotUtils]]
 deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"]
@@ -1841,28 +1795,28 @@ uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
 version = "1.3.1"
 
 [[Plots]]
-deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"]
-git-tree-sha1 = "6062b3b25ad3c58e817df0747fc51518b9110e5f"
+deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"]
+git-tree-sha1 = "5955a002262c08ab155ed2a6f1bb0787fedf5939"
 uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
-version = "1.33.0"
+version = "1.36.2"
 
 [[PoissonRandom]]
 deps = ["Random"]
-git-tree-sha1 = "9ac1bb7c15c39620685a3a7babc0651f5c64c35b"
+git-tree-sha1 = "45f9da1ceee5078267eb273d065e8aa2f2515790"
 uuid = "e409e4f3-bfea-5376-8464-e040bb5c01ab"
-version = "0.4.1"
+version = "0.4.3"
 
 [[Polyester]]
 deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities"]
-git-tree-sha1 = "6ee5518f7baa05e154757a003bfb6936a174dbad"
+git-tree-sha1 = "cb2ede4b9cc432c1cba4d4452a62ae1d2a4141bb"
 uuid = "f517fe37-dbe3-4b94-8317-1923a5111588"
-version = "0.6.15"
+version = "0.6.16"
 
 [[PolyesterWeave]]
 deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"]
-git-tree-sha1 = "b42fb2292fbbaed36f25d33a15c8cc0b4f287fcf"
+git-tree-sha1 = "050ca4aa2ca31484b51b849d8180caf8e4449c49"
 uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad"
-version = "0.1.10"
+version = "0.1.11"
 
 [[Polynomials]]
 deps = ["LinearAlgebra", "RecipesBase"]
@@ -1890,9 +1844,9 @@ version = "0.7.1"
 
 [[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"]
@@ -1913,10 +1867,10 @@ uuid = "21216c6a-2e73-6563-6e65-726566657250"
 version = "1.3.0"
 
 [[PrettyTables]]
-deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"]
-git-tree-sha1 = "dfb54c4e414caa595a1f2ed759b160f5a3ddcba5"
+deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"]
+git-tree-sha1 = "d8ed354439950b34ab04ff8f3dfd49e11bc6c94b"
 uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-version = "1.3.1"
+version = "2.2.1"
 
 [[Primes]]
 deps = ["IntegerMathUtils"]
@@ -1946,9 +1900,9 @@ version = "1.7.2"
 
 [[ProtoBuf]]
 deps = ["BufferedStreams", "Dates", "EnumX", "TOML", "TranscodingStreams"]
-git-tree-sha1 = "240012b5ec28550a6d697bb660066f0fb3587e48"
+git-tree-sha1 = "aa61ac7a223640e255e8f02388aa5f18230e28f2"
 uuid = "3349acd9-ac6a-5e09-bcdb-63829b23a429"
-version = "1.0.7"
+version = "1.0.9"
 
 [[QOI]]
 deps = ["ColorTypes", "FileIO", "FixedPointNumbers"]
@@ -1958,15 +1912,15 @@ version = "1.0.0"
 
 [[Qt5Base_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"]
-git-tree-sha1 = "c6c0f690d0cc7caddb74cef7aa847b824a16b256"
+git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5"
 uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1"
-version = "5.15.3+1"
+version = "5.15.3+2"
 
 [[QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
-git-tree-sha1 = "3c009334f45dfd546a16a57960a821a1a023d241"
+git-tree-sha1 = "97aa253e65b784fd13e83774cadc95b38011d734"
 uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
-version = "2.5.0"
+version = "2.6.0"
 
 [[QuantEcon]]
 deps = ["DSP", "DataStructures", "Distributions", "FFTW", "Graphs", "LinearAlgebra", "Markdown", "NLopt", "Optim", "Pkg", "Primes", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Test"]
@@ -1975,10 +1929,10 @@ uuid = "fcd29c91-0bd7-5a09-975d-7ac3f643a60c"
 version = "0.16.4"
 
 [[Quaternions]]
-deps = ["DualNumbers", "LinearAlgebra", "Random"]
-git-tree-sha1 = "b327e4db3f2202a4efafe7569fcbe409106a1f75"
+deps = ["LinearAlgebra", "Random"]
+git-tree-sha1 = "fcebf40de9a04c58da5073ec09c1c1e95944c79b"
 uuid = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0"
-version = "0.5.6"
+version = "0.6.1"
 
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
@@ -2011,12 +1965,6 @@ 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"
@@ -2024,21 +1972,22 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9"
 version = "0.1.0"
 
 [[RecipesBase]]
-git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d"
+deps = ["SnoopPrecompile"]
+git-tree-sha1 = "d12e612bba40d189cead6ff857ddb67bd2e6a387"
 uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-version = "1.2.1"
+version = "1.3.1"
 
 [[RecipesPipeline]]
-deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"]
-git-tree-sha1 = "e7eac76a958f8664f2718508435d058168c7953d"
+deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"]
+git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f"
 uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c"
-version = "0.6.3"
+version = "0.6.11"
 
 [[RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "Tables", "ZygoteRules"]
-git-tree-sha1 = "3004608dc42101a944e44c1c68b599fa7c669080"
+git-tree-sha1 = "fe25988dce8dd3b763cf39d0ca39b09db3571ff7"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "2.32.0"
+version = "2.32.1"
 
 [[RecursiveFactorization]]
 deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"]
@@ -2059,9 +2008,9 @@ version = "0.3.2"
 
 [[RelocatableFolders]]
 deps = ["SHA", "Scratch"]
-git-tree-sha1 = "22c5201127d7b243b9ee1de3b43c408879dff60f"
+git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691"
 uuid = "05181044-ff0b-4ac5-8273-598c1e38db00"
-version = "0.3.0"
+version = "1.0.0"
 
 [[Requires]]
 deps = ["UUIDs"]
@@ -2088,24 +2037,30 @@ uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
 version = "0.3.0+0"
 
 [[Roots]]
-deps = ["CommonSolve", "Printf", "Setfield"]
-git-tree-sha1 = "50f945fb7d7fdece03bbc76ff1ab96170f64a892"
+deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"]
+git-tree-sha1 = "a3db467ce768343235032a1ca0830fc64158dadf"
 uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
-version = "2.0.2"
+version = "2.0.8"
 
 [[Rotations]]
 deps = ["LinearAlgebra", "Quaternions", "Random", "StaticArrays", "Statistics"]
-git-tree-sha1 = "3d52be96f2ff8a4591a9e2440036d4339ac9a2f7"
+git-tree-sha1 = "793b6ef92f9e96167ddbbd2d9685009e200eb84f"
 uuid = "6038ab10-8711-5258-84ad-4b1120ba62dc"
-version = "1.3.2"
+version = "1.3.3"
+
+[[RuntimeGeneratedFunctions]]
+deps = ["ExprTools", "SHA", "Serialization"]
+git-tree-sha1 = "50314d2ef65fce648975a8e80ae6d8409ebbf835"
+uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
+version = "0.5.5"
 
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
 [[SIMD]]
-git-tree-sha1 = "7dbc15af7ed5f751a82bf3ed37757adf76c32402"
+git-tree-sha1 = "bc12e315740f3a36a6db85fa2c0212a848bd239e"
 uuid = "fdea26ae-647d-5447-a871-4b548cad5224"
-version = "3.4.1"
+version = "3.4.2"
 
 [[SIMDDualNumbers]]
 deps = ["ForwardDiff", "IfElse", "SLEEFPirates", "VectorizationBase"]
@@ -2120,9 +2075,9 @@ version = "0.1.0"
 
 [[SLEEFPirates]]
 deps = ["IfElse", "Static", "VectorizationBase"]
-git-tree-sha1 = "2ba4fee025f25d6711487b73e1ac177cbd127913"
+git-tree-sha1 = "938c9ecffb28338a6b8b970bda0f3806a65e7906"
 uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa"
-version = "0.6.35"
+version = "0.6.36"
 
 [[ScanByte]]
 deps = ["Libdl", "SIMD"]
@@ -2131,10 +2086,10 @@ uuid = "7b38b023-a4d7-4c5e-8d43-3f3097f304eb"
 version = "0.3.3"
 
 [[SciMLBase]]
-deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "StaticArraysCore", "Statistics", "Tables"]
-git-tree-sha1 = "8c7acbc1a974db5f533b59ab74b69042fa05b002"
+deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "RuntimeGeneratedFunctions", "StaticArraysCore", "Statistics", "Tables"]
+git-tree-sha1 = "e1b587ea5933850d1ca2f52db31bd6bcbf50d4c1"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "1.57.0"
+version = "1.72.0"
 
 [[ScikitLearnBase]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
@@ -2150,15 +2105,15 @@ version = "1.1.1"
 
 [[SentinelArrays]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "db8481cf5d6278a121184809e9eb1628943c7704"
+git-tree-sha1 = "efd23b378ea5f2db53a55ae53d3133de4e080aa9"
 uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
-version = "1.3.13"
+version = "1.3.16"
 
 [[SequenceVariation]]
 deps = ["BioAlignments", "BioGenerics", "BioSequences", "BioSymbols"]
-git-tree-sha1 = "203de44c8b6d4a79a91fe40456dcd01cc93d6dca"
+git-tree-sha1 = "b9ae7302c392646618848f6766c5584a9fbae770"
 uuid = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
-version = "0.1.1"
+version = "0.1.2"
 
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
@@ -2174,9 +2129,9 @@ deps = ["Distributed", "Mmap", "Random", "Serialization"]
 uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
 
 [[ShiftedArrays]]
-git-tree-sha1 = "22395afdcf37d6709a5a0766cc4a5ca52cb85ea0"
+git-tree-sha1 = "503688b59397b3307443af35cd953a13e8005c16"
 uuid = "1277b4bf-5013-50f5-be3d-901d8477a67a"
-version = "1.0.0"
+version = "2.0.0"
 
 [[Showoff]]
 deps = ["Dates", "Grisu"]
@@ -2212,9 +2167,9 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
 [[SortingAlgorithms]]
 deps = ["DataStructures"]
-git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508"
+git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00"
 uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
-version = "1.0.1"
+version = "1.1.0"
 
 [[SparseArrays]]
 deps = ["LinearAlgebra", "Random"]
@@ -2222,9 +2177,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [[SparseDiffTools]]
 deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArrays", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays", "VertexSafeGraphs"]
-git-tree-sha1 = "5fb8ba9180f467885e87a2c99cae178b67934be1"
+git-tree-sha1 = "472216c5af9f2f1fce02b760651fe024c75187bd"
 uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
-version = "1.26.2"
+version = "1.29.0"
 
 [[SpecialFunctions]]
 deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
@@ -2232,12 +2187,6 @@ git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
 version = "2.1.7"
 
-[[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"
@@ -2246,20 +2195,20 @@ version = "0.1.1"
 
 [[Static]]
 deps = ["IfElse"]
-git-tree-sha1 = "f94f9d627ba3f91e41a815b9f9f977d729e2e06f"
+git-tree-sha1 = "03170c1e8a94732c1d835ce4c5b904b4b52cba1c"
 uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
-version = "0.7.6"
+version = "0.7.8"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "efa8acd030667776248eabb054b1836ac81d92f0"
+git-tree-sha1 = "4e051b85454b4e4f66e6a6b7bdc452ad9da3dcf6"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.5.7"
+version = "1.5.10"
 
 [[StaticArraysCore]]
-git-tree-sha1 = "ec2bd695e905a3c755b33026954b119ea17f2d22"
+git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a"
 uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
-version = "1.3.0"
+version = "1.4.0"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -2285,15 +2234,15 @@ version = "1.0.1"
 
 [[StatsModels]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsBase", "StatsFuns", "Tables"]
-git-tree-sha1 = "f8ba54b202c77622a713e25e7616d618308b34d3"
+git-tree-sha1 = "a5e15f27abd2692ccb61a99e0854dfb7d48017db"
 uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
-version = "0.6.31"
+version = "0.6.33"
 
 [[StatsPlots]]
 deps = ["AbstractFFTs", "Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"]
-git-tree-sha1 = "3e59e005c5caeb1a57a90b17f582cbfc2c8da8f7"
+git-tree-sha1 = "e0d5bc26226ab1b7648278169858adcfbd861780"
 uuid = "f3b207a7-027a-5e70-b257-86293d7955fd"
-version = "0.15.3"
+version = "0.15.4"
 
 [[SteadyStateDiffEq]]
 deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"]
@@ -2303,15 +2252,15 @@ version = "1.9.0"
 
 [[StochasticDiffEq]]
 deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
-git-tree-sha1 = "47648a908783ddbd124cf3deb3eb0d18b7cffcce"
+git-tree-sha1 = "20f5abeee0f8ceac168d39b1c59ab9752ed992a8"
 uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-version = "6.53.0"
+version = "6.56.0"
 
 [[StrideArraysCore]]
 deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "ThreadingUtilities"]
-git-tree-sha1 = "ac730bd978bf35f9fe45daa0bd1f51e493e97eb4"
+git-tree-sha1 = "38c07163835117036a9c05a849ae93c4b56d1d2b"
 uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da"
-version = "0.3.15"
+version = "0.3.16"
 
 [[StringEncodings]]
 deps = ["Libiconv_jll"]
@@ -2319,11 +2268,16 @@ git-tree-sha1 = "50ccd5ddb00d19392577902f0079267a72c5ab04"
 uuid = "69024149-9ee7-55f6-a4c4-859efe599b68"
 version = "0.3.5"
 
+[[StringManipulation]]
+git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123"
+uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
+version = "0.3.0"
+
 [[StructArrays]]
 deps = ["Adapt", "DataAPI", "StaticArraysCore", "Tables"]
-git-tree-sha1 = "8c6ac65ec9ab781af05b08ff305ddc727c25f680"
+git-tree-sha1 = "13237798b407150a6d2e2bce5d793d7d9576e99e"
 uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
-version = "0.6.12"
+version = "0.6.13"
 
 [[StructTypes]]
 deps = ["Dates", "UUIDs"]
@@ -2347,9 +2301,9 @@ uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
 
 [[Sundials]]
 deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SnoopPrecompile", "SparseArrays", "Sundials_jll"]
-git-tree-sha1 = "5717b2c13ddc167d7db931bfdd1a94133ee1d4f0"
+git-tree-sha1 = "fc2fb8af952ffd007dfda02c08eaf9abb6081652"
 uuid = "c3572dad-4567-51f8-b174-8c6c989267f4"
-version = "4.10.1"
+version = "4.10.3"
 
 [[Sundials_jll]]
 deps = ["CompilerSupportLibraries_jll", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"]
@@ -2381,14 +2335,20 @@ version = "1.0.1"
 
 [[Tables]]
 deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"]
-git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1"
+git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "1.7.0"
+version = "1.10.0"
 
 [[Tar]]
 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"
@@ -2397,9 +2357,9 @@ version = "0.1.1"
 
 [[Term]]
 deps = ["CodeTracking", "Dates", "Highlights", "InteractiveUtils", "Logging", "Markdown", "MyterialColors", "OrderedCollections", "Parameters", "ProgressLogging", "SnoopPrecompile", "Tables", "UUIDs", "UnicodeFun"]
-git-tree-sha1 = "5b5d38673d148f80e7e04569a665006d3bf91cfb"
+git-tree-sha1 = "d977137b9050a7762244eb25358429193fad438a"
 uuid = "22787eb5-b846-44ae-b979-8e399b8463ab"
-version = "1.0.4"
+version = "1.0.5"
 
 [[Test]]
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
@@ -2418,15 +2378,15 @@ version = "0.5.0"
 
 [[TiffImages]]
 deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"]
-git-tree-sha1 = "70e6d2da9210371c927176cb7a56d41ef1260db7"
+git-tree-sha1 = "f8cd5b95aae14d3d88da725414bdde342457366f"
 uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69"
-version = "0.6.1"
+version = "0.6.2"
 
 [[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"]
@@ -2448,9 +2408,9 @@ version = "0.3.0"
 
 [[TriangularSolve]]
 deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "Static", "VectorizationBase"]
-git-tree-sha1 = "8987cf4a0f8d6c375e4ab1438a048e0a185151e4"
+git-tree-sha1 = "fdddcf6b2c7751cd97de69c18157aacc18fbc660"
 uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf"
-version = "0.1.13"
+version = "0.1.14"
 
 [[Tricks]]
 git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175"
@@ -2464,9 +2424,9 @@ version = "1.1.2"
 
 [[TwoBit]]
 deps = ["BioGenerics", "BioSequences"]
-git-tree-sha1 = "adea0d50015bad1698e08a7500185fff0795f638"
+git-tree-sha1 = "7282148766513eac708b96abdb7ab5bc555ed9c3"
 uuid = "75842c30-9b2d-11e9-3f58-f17fe2b89951"
-version = "0.1.0"
+version = "0.2.0"
 
 [[URIParser]]
 deps = ["Unicode"]
@@ -2498,16 +2458,16 @@ uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1"
 version = "0.4.1"
 
 [[UnicodePlots]]
-deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "FileIO", "FreeTypeAbstraction", "LazyModules", "LinearAlgebra", "MarchingCubes", "NaNMath", "Printf", "Requires", "SparseArrays", "StaticArrays", "StatsBase", "Unitful"]
-git-tree-sha1 = "20d15a9cf2f1e50b618ac61ffb39e220043863c8"
+deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "FileIO", "FreeType", "LinearAlgebra", "MarchingCubes", "NaNMath", "Printf", "Requires", "SnoopPrecompile", "SparseArrays", "StaticArrays", "StatsBase", "Unitful"]
+git-tree-sha1 = "21a1f739914158fa825f72df18e48597dbc97a38"
 uuid = "b8865327-cd53-5732-bb35-84acbb429228"
-version = "3.1.0"
+version = "3.3.0"
 
 [[Unitful]]
 deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"]
-git-tree-sha1 = "b649200e887a487468b71821e2644382699f1b0f"
+git-tree-sha1 = "bdc60e70c8a2f63626deeb5c177baacfc43f8a59"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.11.0"
+version = "1.12.1"
 
 [[Unzip]]
 git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670"
@@ -2522,9 +2482,9 @@ version = "0.5.3"
 
 [[VectorizationBase]]
 deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"]
-git-tree-sha1 = "9765c9389978f4c5a2c9c25dce4cef7c0f51dce3"
+git-tree-sha1 = "cc9c63ffd50f16a61a128c7d1e1cbfa441794b1a"
 uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
-version = "0.21.48"
+version = "0.21.55"
 
 [[VertexSafeGraphs]]
 deps = ["Graphs"]
@@ -2552,9 +2512,9 @@ version = "1.4.2"
 
 [[WebIO]]
 deps = ["AssetRegistry", "Base64", "Distributed", "FunctionalCollections", "JSON", "Logging", "Observables", "Pkg", "Random", "Requires", "Sockets", "UUIDs", "WebSockets", "Widgets"]
-git-tree-sha1 = "a8bbcd0b08061bba794c56fb78426e96e114ae7f"
+git-tree-sha1 = "55ea1b43214edb1f6a228105a219c6e84f1f5533"
 uuid = "0f1e0344-ec1d-5b48-a673-e5cf874b6c29"
-version = "0.8.18"
+version = "0.8.19"
 
 [[WebSockets]]
 deps = ["Base64", "Dates", "HTTP", "Logging", "Sockets"]
@@ -2582,11 +2542,9 @@ 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"
+git-tree-sha1 = "634c3177fdf7d52498d4b947080bc73be833eeab"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
-version = "0.2.7"
+version = "0.3.1"
 
 [[XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
@@ -2608,9 +2566,9 @@ version = "1.1.34+0"
 
 [[XZ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "a921669cd9a45c23031fd4eb904f5cc3d20de415"
+git-tree-sha1 = "d1d49166bc58e698ab38804d7bde2aef43e4b594"
 uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
-version = "5.2.5+2"
+version = "5.2.7+0"
 
 [[Xorg_libX11_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
@@ -2740,15 +2698,15 @@ version = "1.4.0+3"
 
 [[YAML]]
 deps = ["Base64", "Dates", "Printf", "StringEncodings"]
-git-tree-sha1 = "3c6e8b9f5cdaaa21340f841653942e1a6b6561e5"
+git-tree-sha1 = "dbc7f1c0012a69486af79c8bcdb31be820670ba2"
 uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
-version = "0.4.7"
+version = "0.4.8"
 
 [[ZMQ]]
 deps = ["FileWatching", "Sockets", "ZeroMQ_jll"]
-git-tree-sha1 = "fc68e8a3719166950a0f3e390a14c7302c48f8de"
+git-tree-sha1 = "356d2bdcc0bce90aabee1d1c0f6d6f301eda8f77"
 uuid = "c2297ded-f4af-51ae-bb23-16f91089e4e1"
-version = "1.2.1"
+version = "1.2.2"
 
 [[ZeroMQ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "libsodium_jll"]
@@ -2768,9 +2726,9 @@ version = "1.5.2+0"
 
 [[Zygote]]
 deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"]
-git-tree-sha1 = "c3f4af6b167f0c181148650221a4cbabf6bbb8a6"
+git-tree-sha1 = "66cc604b9a27a660e25a54e408b4371123a186a6"
 uuid = "e88e6eb3-aa80-5325-afca-941959d7151f"
-version = "0.6.47"
+version = "0.6.49"
 
 [[ZygoteRules]]
 deps = ["MacroTools"]
@@ -2778,6 +2736,12 @@ git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0"
 uuid = "700de1a5-db45-46bc-99cf-38207098b444"
 version = "0.2.2"
 
+[[fzf_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56"
+uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09"
+version = "0.29.0+0"
+
 [[libaom_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4"
diff --git a/Project.toml b/Project.toml
index d668da4..0922527 100644
--- a/Project.toml
+++ b/Project.toml
@@ -9,7 +9,6 @@ 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"
@@ -33,7 +32,6 @@ FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
 GFF3 = "af1dc308-cb6b-11e8-32f0-31192efa90f6"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
-GenomeGraphs = "3aa97884-90e5-11e8-2134-af657ec4f203"
 GenomicAnnotations = "4f8a0a0a-376d-5ac0-ab14-e88793df67f0"
 GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
@@ -50,7 +48,6 @@ JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
 JuliaWebAPI = "480116ec-64ea-5dec-baca-db6b11e96e37"
 Kelpie = "1b112299-d6bc-44e2-912a-478f25731460"
 KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
-KmerAnalysis = "a20136b7-8e32-4c10-91d3-7060c0bd8ec7"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -72,7 +69,6 @@ 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"
 SequenceVariation = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
diff --git a/README.md b/README.md
index 79e6c25..79ddd82 100644
--- a/README.md
+++ b/README.md
@@ -53,9 +53,9 @@ plus
 
 - [x] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)
 - [x] [BioSequences](https://github.com/BioJulia/BioSequences.jl)
-- [x] [BioStructures](https://github.com/BioJulia/BioStructures.jl)
+- ~~[ ] [BioStructures](https://github.com/BioJulia/BioStructures.jl)~~ (Dependency mismatch with BioAlignments)
 - [x] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)
-- [x] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)
+- ~~[ ] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)~~ (Dependency mismatch with BioAlignments)
 - [x] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)
 - [x] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl)
 
@@ -76,7 +76,7 @@ plus
 
 ### Analyses
 
-- [x] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)
+- ~~[ ] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)~~ (Dependency mismatch with BioAlignments)
 - [x] [PopGen](https://github.com/BioJulia/PopGen.jl.git)
 - [x] [SequenceVariation](https://BioJulia/SequenceVariation.jl)
 
@@ -95,7 +95,7 @@ plus
 ### Data Storage and Retrieval
 
 - [x] [BioServices](https://github.com/BioJulia/BioServices.jl)
-- [x] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)
+- ~~[ ] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)~~ (Dependency mismatch with BioAlignments)
 
 [`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
 [biojulia]: https://biojulia.net