Merge branch 'release/v2.1.2'

CiaranOMara · Jul 4, 2019 · d7c295a · d7c295a · CiaranOMara · Jul 4, 2019
2 parents 390742a + 3f1ed9d
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diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "BedgraphFiles"
 uuid = "85eb9095-274b-55ce-be28-9e90f41ac741"
 authors = ["Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "2.1.1"
+version = "2.1.2"
 
 [deps]
 Bedgraph = "0bcc2ff6-69eb-520d-bede-0374fc5bd2fd"
@@ -15,19 +15,20 @@ TableTraits = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
 TableTraitsUtils = "382cd787-c1b6-5bf2-a167-d5b971a19bda"
 
 [compat]
-julia = "0.7, ^1"
 Bedgraph = "^1.1"
 FileIO = "^1.0.1"
-IteratorInterfaceExtensions = "^0.1.1, ^1"
 IterableTables = ">=0.9.0"
+IteratorInterfaceExtensions = "^0.1.1, ^1"
 TableShowUtils = "^0.2.0"
 TableTraits = "^0.4, ^1"
 TableTraitsUtils = "^0.3, ^0.4"
+julia = "0.7, ^1"
 
 [extras]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Query = "1a8c2f83-1ff3-5112-b086-8aa67b057ba1"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [targets]
-test = ["DataFrames", "Test", "Query"]
+test = ["DataFrames", "Test", "Query", "Logging"]
diff --git a/README.md b/README.md
@@ -8,13 +8,11 @@
 
 ## Overview
 
-This package provides load and save support for [Bedgraph files](https://github.com/CiaranOMara/Bedgraph.jl)
-under the [FileIO.jl](https://github.com/JuliaIO/FileIO.jl) package.
-
-This package is largely -- if not completely -- inspired by the work of [David Anthoff](https://github.com/davidanthoff).
+This package provides load and save support for [Bedgraph](https://github.com/CiaranOMara/Bedgraph.jl)
+under the [FileIO](https://github.com/JuliaIO/FileIO.jl) package, and also implements the [IterableTables](https://github.com/davidanthoff/IterableTables.jl) interface for easy conversion between tabular data structures.
 
 ## Installation
-Install BedgraphFiles from the Julia REPL:
+You can install BedgraphFiles from the Julia REPL:
 ```julia
 using Pkg
 add("BedgraphFiles")
@@ -23,21 +21,20 @@ add("BedgraphFiles")
 
 ## Usage
 
-### Loading a Bedgraph file
-
-To load a Bedgraph file into a ``Vector{Bedgraph.Record}``, use the following Julia code:
+### Loading bedGraph files
 
+To load a bedGraph file into a ``Vector{Bedgraph.Record}``, use the following Julia code:
 ````julia
 using FileIO, BedgraphFiles, Bedgraph
 
 records = Vector{Bedgraph.Record}(load("data.bedgraph"))
 ````
 
-### Saving a Bedgraph file
+### Saving bedGraph files
 
 > **Note:** saving on top of an existing file will overwrite metadata/header information with a minimal working header.
 
-The following example saves a ``Vector{Bedgraph.Record}`` to a Bedgraph file:
+The following example saves a ``Vector{Bedgraph.Record}`` to a bedGraph file:
 ````julia
 using FileIO, BedgraphFiles, Bedgraph
 
@@ -47,18 +44,16 @@ save("output.bedgraph", records)
 ````
 
 ### IterableTables
-The call to ``load`` returns a ``struct`` that is an [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl), so it can be passed to any function that can handle iterable tables, i.e. all the sinks in [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl).
-
-To load a Bedgraph file into a `DataFrame`, use the following Julia code:
+The execution of ``load`` returns a ``struct`` that adheres to the [IterableTables](https://github.com/davidanthoff/IterableTables.jl) interface, and can be passed to any function that also implements the interface, i.e. all the sinks in [IterableTable.jl](https://github.com/davidanthoff/IterableTables.jl).
 
+The following code shows an example of loading a bedGraph file into a [DataFrame](https://github.com/JuliaData/DataFrames.jl):
 ```julia
 using FileIO, BedgraphFiles, DataFrames
 
 df = DataFrame(load("data.bedgraph"))
 ```
 
-Here are some examples of materialising a Bedgraph file into data structures that are not a `DataFrame`:
-
+Here are some more examples of materialising a bedGraph file into other data structures:
 ```julia
 using FileIO, BedgraphFiles, DataTables, IndexedTables, Gadfly
 
@@ -69,49 +64,45 @@ dt = DataTable(load("data.bedgraph"))
 it = IndexedTable(load("data.bedgraph"))
 
 # Plot directly with Gadfly
-plot(load("data.bedgraph"), x=:a, y=:b, Geom.line)
+plot(load("data.bedgraph"), xmin=:leftposition, xmax=:rightposition, y=:value, Geom.bar)
 ```
 
-The following code saves any iterable table as a Bedgraph file:
+The following code saves any compatible source to a bedGraph file:
 ```julia
 using FileIO, BedgraphFiles
 
 it = getiterator(data)
 
 save("output.bedgraph", it)
 ```
-This will work as long as `it` is any of the types supported as sources in [IterableTables.jl](https://github.com/davidanthoff/IterableTables.jl).
-
 
 ### Using the pipe syntax
 
-Both `load` and `save` also support the pipe syntax. For example, to load a Bedgraph file into a `DataFrame`, one can use the following code:
-
+Both `load` and `save` also support the pipe syntax. For example, to load a bedGraph file into a `DataFrame`, one can use the following code:
 ```julia
 using FileIO, BedgraphFiles, DataFrame
 
 df = load("data.bedgraph") |> DataFrame
 ```
 
 To save an iterable table, one can use the following form:
-
 ```julia
 using FileIO, BedgraphFiles, DataFrame
 
-df = # Aquire a DataFrame somehow
+df = # Aquire a DataFrame somehow.
 
 df |> save("output.bedgraph")
 ```
 
 The `save` method returns the data provided or `Vector{Bedgraph.Record}`. This is useful when periodically saving your work during a sequence of operations.
-
 ```julia
 records = some sequence of operations |> save("output.bedgraph")
 ```
 
-The pipe syntax is especially useful when combining it with [Query.jl](https://github.com/davidanthoff/Query.jl) queries. For example, one can easily load a Bedgraph file, pipe it into a query, then pipe it to the `save` function to store the results in a new file.
-
+The pipe syntax is especially useful when combining it with [Query.jl](https://github.com/davidanthoff/Query.jl) queries. For example, one can easily load a bedGraph file, pipe its data into a query, and then store the query result by piping it to the `save` function.
 ```julia
 using FileIO, BedgraphFiles, Query
 load("data.bedgraph") |> @filter(_.chrom == "chr19") |> save("data-chr19.bedgraph")
 ```
+## Acknowledgements
+This package is largely -- if not completely -- inspired by the work of [David Anthoff](https://github.com/davidanthoff). Other influences are from the [BioJulia](https://github.com/BioJulia) community.