Merge pull request #24 from phaverty/julia_formatter

format files with JuliaFormatter

.JuliaFormatter.toml

@@ -0,0 +1,2 @@
+indent = 4
+margin = 100

Manifest.toml

@@ -35,9 +35,9 @@ version = "0.1.0"
 
 [[BioSequences]]
 deps = ["BioGenerics", "BioSymbols", "Combinatorics", "IndexableBitVectors", "Printf", "Random", "StableRNGs", "Twiddle"]
-git-tree-sha1 = "3b04c643d3308b5c4f7f33bb02a578ab1ff13278"
+git-tree-sha1 = "093ccb9211bdc71924abf8e74a0790af11da35a7"
 uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-version = "2.0.4"
+version = "2.0.5"
 
 [[BioSymbols]]
 deps = ["Automa"]
@@ -51,6 +51,12 @@ git-tree-sha1 = "5d55b9486590fdda5905c275bb21ce1f0754020f"
 uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
 version = "1.0.0"
 
+[[CSTParser]]
+deps = ["Tokenize"]
+git-tree-sha1 = "60e9121d9ea044c30a04397e59b00c5d9eb826ee"
+uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f"
+version = "2.5.0"
+
 [[CategoricalArrays]]
 deps = ["Compat", "DataAPI", "Future", "JSON", "Missings", "Printf", "Reexport", "Statistics", "Unicode"]
 git-tree-sha1 = "23d7324164c89638c18f6d7f90d972fa9c4fa9fb"
@@ -68,11 +74,22 @@ git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860"
 uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 version = "1.0.2"
 
+[[CommonMark]]
+deps = ["Crayons", "JSON", "URIParser"]
+git-tree-sha1 = "df663743a8812677a74c9f3505a29002e017e59b"
+uuid = "a80b9123-70ca-4bc0-993e-6e3bcb318db6"
+version = "0.6.2"
+
 [[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 = "054993b6611376ddb40203e973e954fd9d1d1902"
+git-tree-sha1 = "a6a8197ae253f2c1a22b2ae17c2dfaf5812c03aa"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "3.12.0"
+version = "3.13.0"
+
+[[Crayons]]
+git-tree-sha1 = "c437a9c2114c7ba19322712e58942b383ffbd6c0"
+uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
+version = "4.0.3"
 
 [[DataAPI]]
 git-tree-sha1 = "176e23402d80e7743fc26c19c681bfb11246af32"
@@ -87,9 +104,9 @@ version = "0.20.2"
 
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "be680f1ad03c0a03796aa3fda5a2180df7f83b46"
+git-tree-sha1 = "88d48e133e6d3dd68183309877eac74393daa7eb"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.17.18"
+version = "0.17.20"
 
 [[DataValueInterfaces]]
 git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
@@ -108,6 +125,18 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
+[[DocStringExtensions]]
+deps = ["LibGit2", "Markdown", "Pkg", "Test"]
+git-tree-sha1 = "c5714d9bcdba66389612dc4c47ed827c64112997"
+uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+version = "0.8.2"
+
+[[Documenter]]
+deps = ["Base64", "Dates", "DocStringExtensions", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
+git-tree-sha1 = "fb1ff838470573adc15c71ba79f8d31328f035da"
+uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+version = "0.25.2"
+
 [[Future]]
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
@@ -126,9 +155,9 @@ version = "1.0.0"
 
 [[Indexes]]
 deps = ["BGZFStreams", "BioCore", "BufferedStreams", "GenomicFeatures"]
-git-tree-sha1 = "68352120035ed5a9328ef918d3e867e5e6d5b36e"
+git-tree-sha1 = "c124510dd96e53f9095dbb484f4a8781cbfa0dcc"
 uuid = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
-version = "0.1.0"
+version = "0.1.1"
 
 [[InteractiveUtils]]
 deps = ["Markdown"]
@@ -157,6 +186,12 @@ git-tree-sha1 = "b34d7cef7b337321e97d22242c3c2b91f476748e"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 version = "0.21.0"
 
+[[JuliaFormatter]]
+deps = ["CSTParser", "CommonMark", "DataStructures", "Documenter", "Pkg", "Test", "Tokenize"]
+git-tree-sha1 = "f119630a3439586c1a7d65ed0837cb5ff257945e"
+uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+version = "0.7.2"
+
 [[LibGit2]]
 deps = ["Printf"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -185,15 +220,15 @@ version = "0.4.3"
 uuid = "a63ad114-7e13-5084-954f-fe012c677804"
 
 [[OrderedCollections]]
-git-tree-sha1 = "12ce190210d278e12644bcadf5b21cbdcf225cd3"
+git-tree-sha1 = "293b70ac1780f9584c89268a6e2a560d938a7065"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.2.0"
+version = "1.3.0"
 
 [[Parsers]]
 deps = ["Dates", "Test"]
-git-tree-sha1 = "eb3e09940c0d7ae01b01d9291ebad7b081c844d3"
+git-tree-sha1 = "8077624b3c450b15c087944363606a6ba12f925e"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "1.0.5"
+version = "1.0.10"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -286,14 +321,19 @@ version = "1.0.0"
 
 [[Tables]]
 deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
-git-tree-sha1 = "c45dcc27331febabc20d86cb3974ef095257dcf3"
+git-tree-sha1 = "b7f762e9820b7fab47544c36f26f54ac59cf8abf"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "1.0.4"
+version = "1.0.5"
 
 [[Test]]
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
+[[Tokenize]]
+git-tree-sha1 = "73c00ad506d88a7e8e4f90f48a70943101728227"
+uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
+version = "0.5.8"
+
 [[TranscodingStreams]]
 deps = ["Random", "Test"]
 git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c"
@@ -305,6 +345,12 @@ git-tree-sha1 = "29509c4862bfb5da9e76eb6937125ab93986270a"
 uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795"
 version = "1.1.2"
 
+[[URIParser]]
+deps = ["Unicode"]
+git-tree-sha1 = "53a9f49546b8d2dd2e688d216421d050c9a31d0d"
+uuid = "30578b45-9adc-5946-b283-645ec420af67"
+version = "0.4.1"
+
 [[UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
@@ -314,9 +360,9 @@ uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[XAM]]
 deps = ["Automa", "BGZFStreams", "BioAlignments", "BioGenerics", "BioSequences", "GenomicFeatures", "Indexes", "Printf", "TranscodingStreams"]
-git-tree-sha1 = "166ad569e0b47e9eb2b575f7c014e56de1f2e948"
+git-tree-sha1 = "fc98c10e8151054353ded66914f38fbac15fc899"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
-version = "0.2.4"
+version = "0.2.6"
 
 [[YAML]]
 deps = ["Base64", "Dates", "Printf"]
@@ -326,6 +372,6 @@ version = "0.4.0"
 
 [[Zlib_jll]]
 deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "a2e0d558f6031002e380a90613b199e37a8565bf"
+git-tree-sha1 = "d5bba6485811931e4b8958e2d7ca3738273ac468"
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.11+10"
+version = "1.2.11+15"

Project.toml

@@ -5,6 +5,7 @@ version = "1.1.0"
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
+JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 RLEVectors = "17b45ede-fd0d-54ef-b825-8cf9fc64da95"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"

src/AbstractGenomicVector_type.jl

@@ -14,11 +14,11 @@ abstract type AbstractGenomicVector{T} <: AbstractVector{T} end
 genostarts(x::AbstractGenomicVector) = copy(_genostarts(x))
 genoends(x::AbstractGenomicVector) = copy(_genoends(x))
 strands(x::AbstractGenomicVector) = copy(_strands(x))
-RLEVectors.starts(x::AbstractGenomicVector) = chrpos(_genostarts(x),chr_info(x))
-RLEVectors.ends(x::AbstractGenomicVector) = chrpos(_genoends(x),chr_info(x))
+RLEVectors.starts(x::AbstractGenomicVector) = chrpos(_genostarts(x), chr_info(x))
+RLEVectors.ends(x::AbstractGenomicVector) = chrpos(_genoends(x), chr_info(x))
 RLEVectors.widths(x::AbstractGenomicVector) = (_genoends(x) - _genostarts(x)) .+ 1
-RLEVectors.eachrange(x::AbstractGenomicVector) = zip(_genostarts(x),_genoends(x))
-chromosomes(x::AbstractGenomicVector) = chromosomes(_genostarts(x),chr_info(x))
+RLEVectors.eachrange(x::AbstractGenomicVector) = zip(_genostarts(x), _genoends(x))
+chromosomes(x::AbstractGenomicVector) = chromosomes(_genostarts(x), chr_info(x))
 
 ## FIXME: add RLEVector creation from AbstractGenomicVector and a Vector of data
 
@@ -74,23 +74,23 @@ in the linear genome.
 starts, ends, widths, chromosomes, genostarts, genoends, strands, each, chrpos, genopos, chrindex
 
 ## Sorting
-Base.sort(x::AbstractGenomicVector; rev::Bool=false) = sort!(copy(x))
-Base.issorted(x::AbstractGenomicVector; rev::Bool=false) = issorted( eachrange(x), rev=rev )
-Base.sortperm(x::AbstractGenomicVector; rev=false) = sortperm( collect(eachrange(x)), rev=rev ) # No method for iterator
+Base.sort(x::AbstractGenomicVector; rev::Bool = false) = sort!(copy(x))
+Base.issorted(x::AbstractGenomicVector; rev::Bool = false) = issorted(eachrange(x), rev = rev)
+Base.sortperm(x::AbstractGenomicVector; rev = false) = sortperm(collect(eachrange(x)), rev = rev) # No method for iterator
 
 ## Modifying
-slide(g::AbstractGenomicVector, x::Integer) = slide!( copy(g), x )
+slide(g::AbstractGenomicVector, x::Integer) = slide!(copy(g), x)
 
 ## Show
 function Base.show(io::IO, x::AbstractGenomicVector)
     if length(x) > 8
-        out = convert(Vector{String},x[1:8])
+        out = convert(Vector{String}, x[1:8])
         Base.show_vector(io, out[1:4], "[", "")
         print(io, " … ")
         Base.show_vector(io, out[5:8], "", "]")
     else
-        out = convert(Vector{String},x)
-        println(io,convert(Vector{String},out))
+        out = convert(Vector{String}, x)
+        println(io, convert(Vector{String}, out))
     end
 end
 
@@ -106,45 +106,49 @@ end
 
 ## Indexing
 Base.IndexStyle(::Type{<:AbstractGenomicVector}) = IndexLinear()
-Base.getindex(x::AbstractGenomicVector,i::AbstractGenomicVector) = getindex(x, findall(in(x), y))
+Base.getindex(x::AbstractGenomicVector, i::AbstractGenomicVector) = getindex(x, findall(in(x), y))
 
 ## Searching
-_exact_overlap(el_a::Interval, el_b::Interval) = first(el_a) == first(el_b) && last(el_a) == last(el_b)
+_exact_overlap(el_a::Interval, el_b::Interval) =
+    first(el_a) == first(el_b) && last(el_a) == last(el_b)
 
-function findoverlaps(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool=false)
+function findoverlaps(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool = false)
     same_genome(x, y) || throw(ArgumentError("Both inputs must be from the same genome."))
-    xit = convert(IntervalCollection,x)
-    yit = convert(IntervalCollection,y)
+    xit = convert(IntervalCollection, x)
+    yit = convert(IntervalCollection, y)
     if exact
-        ol = eachoverlap(xit, yit, filter=_exact_overlap)
+        ol = eachoverlap(xit, yit, filter = _exact_overlap)
     else
-        ol = eachoverlap(xit,yit)
+        ol = eachoverlap(xit, yit)
     end
     ol
 end
 
-function Base.indexin(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool=true)
-    ol = findoverlaps(x,y,exact)
-    inds = Array{Union{Nothing, Int64}}(nothing, length(x))
-    for (el_a,el_b) in ol
+function Base.indexin(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool = true)
+    ol = findoverlaps(x, y, exact)
+    inds = Array{Union{Nothing,Int64}}(nothing, length(x))
+    for (el_a, el_b) in ol
         m_a = metadata(el_a)
         m_b = metadata(el_b)
         if inds[m_a] === nothing || inds[m_a] > m_b
-            inds[ m_a ] = m_b
+            inds[m_a] = m_b
         end
     end
     inds
 end
 
-function overlap_table(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool=true)
-    ol = findoverlaps(x,y,exact)
-    olap_pairs = [ [metadata(el_a), metadata(el_b)]' for (el_a,el_b) in ol ]
+function overlap_table(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool = true)
+    ol = findoverlaps(x, y, exact)
+    olap_pairs = [[metadata(el_a), metadata(el_b)]' for (el_a, el_b) in ol]
     vcat(olap_pairs...)
 end
 
-Base.in(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool=true) = indexin(x,y,exact) .!= nothing
-Base.intersect(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool=true) = x[ in(x,y,exact) ]
-Base.setdiff(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool=true) = x[in(x,y,exact) .== false]
+Base.in(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool = true) =
+    indexin(x, y, exact) .!= nothing
+Base.intersect(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool = true) =
+    x[in(x, y, exact)]
+Base.setdiff(x::AbstractGenomicVector, y::AbstractGenomicVector, exact::Bool = true) =
+    x[in(x, y, exact).==false]
 
 #nearest(x::AbstractGenomicVector, query::Interval)
 #
@@ -198,10 +202,10 @@ set of ranges in `gr`.
 """
 function coverage(gr::AbstractGenomicVector)
     out = RLEVector(0, last(chr_ends(gr)))
-    @inbounds for (s,e) in eachrange(gr)
+    @inbounds for (s, e) in eachrange(gr)
         r = s:e
         x = out[r]
-        for i in 1:length(x.runvalues)
+        for i = 1:length(x.runvalues)
             @inbounds x.runvalues[i] = x.runvalues[i] + 1
         end
         out[r] = x
@@ -230,7 +234,7 @@ AbstractGenomicVector. The vector must span the full length of the genome
 specified by the chr_info of the AbstractGenomicVector. This is useful for summarizing
 an RLEVector of data (say DNA copy number) by genome regions (e.g. genes).
 """
-function Base.getindex(v::T1, g::T2) where T2 <: AbstractGenomicVector where T1 <: RLEVector
+function Base.getindex(v::T1, g::T2) where {T2<:AbstractGenomicVector} where {T1<:RLEVector}
     if length(v) != chr_ends(g)[end]
         error("When subsetting an Vector with a GenomicVector, the Vector must span the entire genome.")
     end
@@ -240,9 +244,9 @@ end
 function Base.iterate(x::GenomicVectorIterator, state = 1)
     state > length(x) && return nothing
     newstate = state + 1
-   ( x.v[ x.genostarts[state]:x.genoends[state] ], newstate )
+    (x.v[x.genostarts[state]:x.genoends[state]], newstate)
 end
 
 function Base.length(x::GenomicVectorIterator)
-    size(x.genostarts,1)
+    size(x.genostarts, 1)
 end