Merge branch 'release/v1.1.0'

Project.toml

@@ -1,7 +1,7 @@
 name = "Bedgraph"
 uuid = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
 authors = ["Ciarán O'Mara <[email protected]>"]
-version = "1.0.5"
+version = "1.1.0"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -76,6 +76,9 @@ const lasts = [49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304
 const values = [-1.0, -0.75, -0.50, -0.25, 0.0, 0.25, 0.50, 0.75, 1.00]
 
 records = convert(Vector{Bedgraph.Record}, chroms, firsts, lasts, values)
+
+sort!(records)
+
 header = Bedgraph.generateBasicHeader(records)
 
 write("data.bedgraph", header, records)
@@ -93,7 +96,7 @@ open(output_file, "w") do io
 end
 
 ```
-### Expansion and compression of data
+### Compression and decompression of data
 
 #### Compress data values
 Compress data to chromosome coordinates of the zero-based, half-open format.
@@ -103,30 +106,31 @@ using Bedgraph
 
 chrom "chr1"
 n = 49302000:49304700
-expanded_values = [-1.0, -1.0, -1.0, ..., 1.00, 1.00, 1.00]
+decompressed_values = [-1.0, -1.0, -1.0, ..., 1.00, 1.00, 1.00]
 
-compressed_records = Bedgraph.compress(chrom, n, expanded_values)
+compressed_records = Bedgraph.compress(chrom, n, decompressed_values)
 ```
 
 ```julia
 using Bedgraph
 
 const records = [Record("chr19", 49302000, 49302300, -1.0), Record("chr19", 49302300, 49302600, -1.75)]
 
-compressed_records = Bedgraph.compress("chr19", n, expanded_value)
+compressed_records = Bedgraph.compress("chr19", n, decompressed_value)
 ```
 
-#### Expand record data
-Expand chromosome coordinates from the zero-based, half-open format.
+#### Decompress record data
+Decompress chromosome coordinates from the zero-based, half-open format.
 > **Note:**  please be aware of the order of returned items.
+
 ```julia
 using Bedgraph
 
 const firsts = [49302000, 49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304100, 49304400]
 const lasts = [49302300, 49302600, 49302900, 49303200, 49303500, 49303800, 49304100, 49304400, 49304700]
 const values = [-1.0, -0.75, -0.50, -0.25, 0.0, 0.25, 0.50, 0.75, 1.00]
 
-(n, expanded_values, expanded_chroms) = Bedgraph.expand(chroms, firsts, lasts, values)
+(n, decompressed_values, decompressed_chroms) = Bedgraph.expand(chroms, firsts, lasts, values)
 ```
 
 ```julia
@@ -135,5 +139,5 @@ using Bedgraph
 
 const records = [Record("chr19", 49302000, 49302300, -1.0), Record("chr19", 49302300, 49302600, -1.75)]
 
-n, expanded_values, expanded_chroms = Bedgraph.expand(records)
+n, decompressed_values, decompressed_chroms = Bedgraph.expand(records)
 ```

src/header.jl

@@ -12,7 +12,7 @@ function Base.convert(::Type{String}, header::BedgraphHeader{Vector{String}}) ::
     return str
 end
 
-function generateBasicHeader(records::Vector{Record}; bump_forward=true) :: BedgraphHeader{Vector{String}}
+function generateBasicHeader(records::Vector{Record}; bump_forward=true) :: BedgraphHeader{Vector{String}} #Note: we assume that records are sorted by chrom and left position.
 
     chrom = records[1].chrom
 

src/record.jl

@@ -14,6 +14,20 @@ function Base.:(==)(a::Record, b::Record)
            a.value == b.value
 end
 
+function Base.isless(a::Record, b::Record, chrom_isless::Function=isless) :: Bool
+    if a.chrom != b.chrom
+        return chrom_isless(a.chrom, b.chrom) :: Bool
+    elseif a.first != b.first
+        return a.first < b.first
+    elseif a.last != b.last
+        return a.last < b.last
+    elseif a.value != b.value
+        return a.value < b.value
+    else
+        return false
+    end
+end
+
 function Record(data::Vector{String})
     return convert(Record, data)
 end

test/runtests.jl

@@ -201,6 +201,23 @@ end #testset Matching
 end #testset Parsing
 
 
+@testset "Sorting" begin
+
+# Testing isless function.
+@test isless(Record(Bag.line1), Record(Bag.line2)) == true
+@test isless(Record(Bag.line2), Record(Bag.line1)) == false
+
+unordered = Bag.records[[9,4,5,6,8,7,1,3,2]]
+
+@test Bag.records != unordered
+@test Bag.records == sort(unordered)
+
+# Testing sort by concept.
+@test Bag.records == sort(unordered, by=x->[x.chrom, x.first, x.last])
+
+end #testset Sorting
+
+
 @testset "Conversion" begin
 
 @test_throws ErrorException Bedgraph._convertCells([Bag.cells1; "extra_cell"]) == Bag.cells1