Merge branch 'release/1.1.0'

.gitignore

@@ -1,3 +1,200 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
+### Linux template
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+### Windows template
+# Windows thumbnail cache files
+Thumbs.db
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+### JetBrains template
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+/.idea
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# CMake
+cmake-build-debug/
+cmake-build-release/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
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+.idea_modules/
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+atlassian-ide-plugin.xml
+
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+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
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+.idea/httpRequests
+### Eclipse template
+
+.metadata
+bin/
+tmp/
+*.tmp
+*.bak
+*.swp
+*~.nib
+local.properties
+.settings/
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+.recommenders
+
+# External tool builders
+.externalToolBuilders/
+
+# Locally stored "Eclipse launch configurations"
+*.launch
+
+# PyDev specific (Python IDE for Eclipse)
+*.pydevproject
+
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+.cache-main
+.scala_dependencies
+.worksheet
+### Vim template
+# Swap
+[._]*.s[a-v][a-z]
+[._]*.sw[a-p]
+[._]s[a-v][a-z]
+[._]sw[a-p]
+
+# Session
+Session.vim
+
+# Temporary
+.netrwhist
+*~
+# Auto-generated tag files
+tags
+### macOS template
+# General
+.DS_Store
+.AppleDouble
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+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+### Vim template
+# Swap
+
+# Session
+
+# Temporary
+# Auto-generated tag files
+

README.md

@@ -47,6 +47,8 @@ plot(load("data.bedgraph"), x=:a, y=:b, Geom.line)
 
 ### Save a Bedgraph file
 
+> **Note:** saving on top of an existing file will overwrite metadata/header information with a minimal working header.
+
 The following code saves any iterable table as a Bedgraph file:
 ````julia
 using FileIO, BedgraphFiles

REQUIRE

@@ -1,5 +1,6 @@
 julia 0.6
 TableTraits 0.0.1
 IterableTables 0.5.0
-FileIO 0.5.1
+FileIO 0.6.0
 DataFrames 0.9.0
+Bedgraph 0.3.0

src/BedgraphFiles.jl

@@ -1,56 +1,69 @@
+__precompile__()
+
 module BedgraphFiles
 
-# using Bedgraph
-using TableTraits, DataValues, DataFrames
+using Bedgraph, TableTraits, IterableTables, DataValues, DataFrames
 using FileIO
-import IterableTables
 
-try add_format(format"Bedgraph", (), [".bedgraph"], [:BedgraphFiles]) end # TODO: Remove once BedgraphFiles is registered with FileIO.
+# try add_format(format"bedGraph", (), [".bedgraph"], [:BedgraphFiles]) end # TODO: Remove once BedgraphFiles is registered with FileIO.
 
-struct BedgraphFile
-    filename::String
-end
+BedgraphFile = File{format"bedGraph"}
 
-function load(f::FileIO.File{FileIO.format"Bedgraph"})
-    return BedgraphFile(f.filename)
+function load(file::BedgraphFile)
+    return BedgraphFile(file.filename)
 end
 
 TableTraits.isiterable(x::BedgraphFile) = true
 TableTraits.isiterabletable(x::BedgraphFile) = true
 
 function TableTraits.getiterator(file::BedgraphFile)
 
-    # TODO: read using bedgraph package.
-    # df = Bedgraph.read(file.filename, DataFrame)
+    # Read file using bedgraph package.
+    tracks = open(file, "r") do stream
+        Bedgraph.readTracks(stream.io)
+    end
 
-    data = readdlm(file.filename)
+    # Pack tracks into DataFrame.
+    df = DataFrame( chrom = Vector{String}() , chromStart = Vector{Int}(), chromEnd = Vector{Int}(), dataValue = Vector{Float64}())
 
-    # Track data format: chrom chromStart chromEnd dataValue
-    df = DataFrame(chrom=data[:,1], chromStart=data[:,2], chromEnd=data[:,3], dataValue=data[:,4])
+    for track in tracks # Note: Track data format is chrom chrom_start chrom_end data_value.
+        append!(df, DataFrame(chrom = track.chrom, chromStart = track.chrom_start, chromEnd = track.chrom_end, dataValue = track.data_value))
+    end
 
     it = getiterator(df)
 
     return it
 end
 
-function save(f::FileIO.File{FileIO.format"Bedgraph"}, data)
-    isiterabletable(data) || error("Can't write this data to a Bedgraph file.")
+function save(file::BedgraphFile, data; bump_forward = true)
+    isiterabletable(data) || error("Can't write this data to bedGraph file.")
 
     it = getiterator(data)
 
-    # TODO: save using bedgraph package.
-    # ds = IterableTables.get_datastreams_source(it)
-    #
-    # try
-    #     Bedgraph.write(f.filename, ds)
-    # finally
-    #     Data.close!(ds)
-    # end
+    df = DataFrame(it)
+
+    # Pack DataFrame in to a vector of type track.
+    tracks = Vector{Track}()
+
+    for row in eachrow(df)
+        push!(tracks, Track(row[1], row[2], row[3], row[4])) # Note: using index to allow flexible column names.
+    end
+
+    return save(file, tracks, bump_forward = bump_forward)
+end
+
+function save(file::BedgraphFile, tracks::Vector{Bedgraph.Track}; bump_forward = true)
+
+    header = Bedgraph.BedgraphHeader( Bedgraph.generateBasicHeader(tracks, bump_forward = bump_forward) )
+
+    return save(file, header, tracks)
+end
 
-    try
-        output = [convert(Array,it.df[:chrom]) convert(Array,it.df[:chromStart]) convert(Array,it.df[:chromEnd]) convert(Array,it.df[:dataValue]) ]
+function save(file::BedgraphFile, header::Bedgraph.BedgraphHeader, tracks::Vector{Bedgraph.Track})
 
-        writedlm(f.filename, output)
+    open(file, "w") do stream
+        write(stream.io, header)
+        write(stream.io, tracks)
     end
 
 end

test/data-headerless.bedgraph

@@ -0,0 +1,9 @@
+chr19 49302000 49302300 -1.0
+chr19 49302300 49302600 -0.75
+chr19 49302600 49302900 -0.50
+chr19 49302900 49303200 -0.25
+chr19 49303200 49303500 0.0
+chr19 49303500 49303800 0.25
+chr19 49303800 49304100 0.50
+chr19 49304100 49304400 0.75
+chr19 49304400 49304700 1.00

test/data.bedgraph

@@ -1,3 +1,12 @@
+browser position chr19:49302001-49304701
+browser hide all
+browser pack refGene encodeRegions
+browser full altGraph
+#	300 base wide bar graph, autoScale is on by default == graphing
+#	limits will dynamically change to always show full range of data
+#	in viewing window, priority = 20 positions this as the second graph
+#	Note, zero-relative, half-open coordinate system in use for bedGraph format
+track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
 chr19 49302000 49302300 -1.0
 chr19 49302300 49302600 -0.75
 chr19 49302600 49302900 -0.50