Version 1.0 updates (#15)

.travis.yml

@@ -4,28 +4,15 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
   - nightly
 matrix:
   allow_failures:
     - julia: nightly
 notifications:
   email: false
-git:
-  depth: 99999999
-
-## uncomment and modify the following lines to manually install system packages
-#addons:
-#  apt: # apt-get for linux
-#    packages:
-#    - gfortran
-#before_script: # homebrew for mac
-#  - if [ $TRAVIS_OS_NAME = osx ]; then brew install gcc; fi
-
-## uncomment the following lines to override the default test script
-#script:
-#  - julia -e 'Pkg.clone(pwd()); Pkg.build("GenomicFeatures"); Pkg.test("GenomicFeatures"; coverage=true)'
 after_success:
-  # push coverage results to Codecov
   - julia -e 'cd(Pkg.dir("GenomicFeatures")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+  - julia -e 'cd(joinpath(Pkg.dir("GenomicFeatures"), "docs/src")); mkdir("assets"); cd("assets"); run(pipeline(`curl https://codeload.github.com/BioJulia/assets/tar.gz/master`, `tar -xz --strip=2 assets-master/doc_assets`))'
   - julia -e 'cd(Pkg.dir("GenomicFeatures")); Pkg.add("Documenter"); include(joinpath("docs", "make.jl"))'

README.md

@@ -1,13 +1,76 @@
-GenomicFeatures.jl
-==================
-
-[![Docs Latest][docs-latest-img]][docs-latest-url]
-[![Build Status][travisci-img]][travisci-url]
-[![codecov.io][codecov-img]][codecov-url]
-
-[travisci-img]: https://travis-ci.org/BioJulia/GenomicFeatures.jl.svg?branch=master
-[travisci-url]: https://travis-ci.org/BioJulia/GenomicFeatures.jl
-[codecov-img]: http://codecov.io/github/BioJulia/GenomicFeatures.jl/coverage.svg?branch=master
-[codecov-url]: http://codecov.io/github/BioJulia/GenomicFeatures.jl?branch=master
-[docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg
-[docs-latest-url]: https://biojulia.github.io/GenomicFeatures.jl/latest/
+# <img src="sticker.svg" width="30%" align="right" /> GenomicFeatures
+
+[![latest release][release-img]][release-url]
+[![MIT license][license-img]][license-url]
+[![stable documentation][docs-stable-img]][docs-stable-url]
+[![latest documentation][docs-latest-img]][docs-latest-url]
+![lifecycle][lifecycle-maturing]
+[![Chat on Discord][discord-img]][discord-url]
+
+## Description
+
+GenomicFeatures provides utilities for working with interval based genomic
+annotations. It builds on [IntervalTrees]() to provide a data-structures,
+algorithms and IO tools for various formats such as BED, GFF3, bigWig and
+bigBed.  
+
+## Installation
+
+Install GenomicFeatures from the Julia REPL:
+
+```julia
+using Pkg
+add("GenomicFeatures")
+#Pkg.add("GenomicFeatures") for julia prior to v 0.7
+```
+
+If you are interested in the cutting edge of the development, please check out
+the master branch to try new features before release.
+
+## Testing
+
+GenomicFeatures is tested against julia `0.6` and current `0.7-dev` on Linux,
+OS X, and Windows.
+
+| **Latest release** | **Latest build status** |
+|:------------------:|:-----------------------:|
+| [![julia06][juliapkg06-img]][juliapkg-url] [![julia07][juliapkg07-img]][juliapkg-url] | [![travis][travis-img]][travis-url] [![appveyor][appveyor-img]][appveyor-url] [![coverage][codecov-img]][codecov-url] |
+
+## Contributing and Questions
+
+We appreciate contributions from users including reporting bugs, fixing issues,
+improving performance and adding new features.
+
+Take a look at the [CONTRIBUTING](CONTRIBUTING.md) file provided with this
+package for detailed contributor and maintainer guidelines.
+
+If you have a question about contributing or using this package, come on over
+and chat to us on [Discord][discord-url], or you can try the
+[Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
+
+[release-img]:            https://img.shields.io/github/release/BioJulia/GenomicFeatures.jl.svg?style=flat-square
+[release-url]:            https://github.com/BioJulia/GenomicFeatures.jl/releases/latest
+[license-img]:            https://img.shields.io/badge/license-MIT-green.svg?style=flat-square
+[license-url]:            https://github.com/BioJulia/GenomicFeatures.jl/blob/master/LICENSE
+[docs-stable-img]:        https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square
+[docs-stable-url]:        https://biojulia.github.io/GenomicFeatures.jl/stable
+[docs-latest-img]:        https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square
+[docs-latest-url]:        https://biojulia.github.io/GenomicFeatures.jl/latest/
+[lifecycle-experimental]: https://img.shields.io/badge/lifecycle-experimental-orange.svg?style=flat-square
+[lifecycle-maturing]:     https://img.shields.io/badge/lifecycle-maturing-blue.svg?style=flat-square
+[lifecycle-stable]:       https://img.shields.io/badge/lifecycle-stable-brightgreen.svg?style=flat-square
+[lifecycle-retired]:      https://img.shields.io/badge/lifecycle-retired-orange.svg?style=flat-square
+[lifecycle-archived]:     https://img.shields.io/badge/lifecycle-archived-red.svg?style=flat-square
+[lifecycle-dormant]:      https://img.shields.io/badge/lifecycle-dormant-blue.svg?style=flat-square
+[lifecycle-questioning]:  https://img.shields.io/badge/lifecycle-questioning-blue.svg?style=flat-square
+[discord-img]:            https://img.shields.io/badge/discord-chat-blue.svg?style=flat-square&logo=discord&colorB=%237289DA
+[discord-url]:            https://discord.gg/z73YNFz
+[juliapkg06-img]:         http://pkg.julialang.org/badges/GenomicFeatures_0.6.svg?style=flat-square
+[juliapkg07-img]:         http://pkg.julialang.org/badges/GenomicFeatures_0.7.svg?style=flat-square
+[juliapkg-url]:           http://pkg.julialang.org/?pkg=GenomicFeatures
+[travis-img]:             https://img.shields.io/travis/BioJulia/GenomicFeatures.jl/master.svg?label=Linux+/+macOS
+[travis-url]:             https://travis-ci.org/BioJulia/GenomicFeatures.jl
+[appveyor-img]:           https://ci.appveyor.com/api/projects/status/dnup6vbbvai92bl8/branch/master?svg=true
+[appveyor-url]:           https://ci.appveyor.com/project/BenJWard/genomicfeatures-jl/branch/master
+[codecov-img]:            http://codecov.io/github/BioJulia/GenomicFeatures.jl/coverage.svg?branch=master
+[codecov-url]:            http://codecov.io/github/BioJulia/GenomicFeatures.jl?branch=master

REQUIRE

@@ -1,12 +1,12 @@
-julia 0.6
-Automa 0.2
-BioCore 1.0
-BioSequences 0.6
-BufferedStreams 0.3
-BGZFStreams 0.1
-ColorTypes 0.5
-DataStructures 0.5
-FixedPointNumbers 0.3
-IntervalTrees 0.3
-Libz 0.2
-URIParser 0.1
+julia 0.7
+Automa 0.7
+BioCore 2.0.2
+BioSequences 1.0
+BufferedStreams 1.0.0
+BGZFStreams 0.3
+ColorTypes 0.7.4
+DataStructures 0.11.0
+FixedPointNumbers 0.5.2
+IntervalTrees 1.0
+Libz 1.0
+URIParser 0.4

appveyor.yml

@@ -1,13 +1,18 @@
 environment:
   matrix:
-  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+  - julia_version: 0.7
+  - julia_version: 1
+  - julia_version: nightly
 
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-matrix:
-  allow_failures:
-  - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
+
+# # Uncomment the following lines to allow failures on nightly julia
+# # (tests will run but not make your overall status red)
+# matrix:
+#   allow_failures:
+#   - julia_version: nightly
 
 branches:
   only:
@@ -21,24 +26,18 @@ notifications:
     on_build_status_changed: false
 
 install:
-  - ps: "[System.Net.ServicePointManager]::SecurityProtocol = [System.Net.SecurityProtocolType]::Tls12"
-# If there's a newer build queued for the same PR, cancel this one
-  - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
-        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
-        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
-        throw "There are newer queued builds for this pull request, failing early." }
-# Download most recent Julia Windows binary
-  - ps: (new-object net.webclient).DownloadFile(
-        $env:JULIA_URL,
-        "C:\projects\julia-binary.exe")
-# Run installer silently, output to C:\projects\julia
-  - C:\projects\julia-binary.exe /S /D=C:\projects\julia
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
 
 build_script:
-# Need to convert from shallow to complete for Pkg.clone to work
-  - IF EXIST .git\shallow (git fetch --unshallow)
-  - C:\projects\julia\bin\julia -e "versioninfo();
-      Pkg.clone(pwd(), \"GenomicFeatures\"); Pkg.build(\"GenomicFeatures\")"
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
 
 test_script:
-  - C:\projects\julia\bin\julia -e "Pkg.test(\"GenomicFeatures\")"
+  - echo "%JL_TEST_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"
+
+# # Uncomment to support code coverage upload. Should only be enabled for packages
+# # which would have coverage gaps without running on Windows
+# on_success:
+#   - echo "%JL_CODECOV_SCRIPT%"
+#   - C:\julia\bin\julia -e "%JL_CODECOV_SCRIPT%"

docs/make.jl

@@ -1,9 +1,25 @@
 using Documenter, GenomicFeatures
 
-makedocs()
+makedocs(
+    format = :html,
+    sitename = "GenomicFeatures.jl",
+    pages = [
+        "Home" => "index.md",
+        "Intervals" => "intervals.md",
+        "I/O" => [
+            "BED" => "io/bed.md",
+            "GFF3" => "io/gff3.md",
+            "BigWig" => "io/bigwig.md",
+            "BigBed" => "io/bigbed.md"
+        ]
+    ],
+    authors = "Kenta Sato, D. C. Jones, Ben J. Ward, The BioJulia Organisation and other contributors."
+)
 deploydocs(
-    deps = Deps.pip("mkdocs", "pygments", "mkdocs-material"),
     repo = "github.com/BioJulia/GenomicFeatures.jl.git",
-    julia = "0.5",
+    julia = "0.6",
     osname = "linux",
+    target = "build",
+    deps = nothing,
+    make = nothing
 )

src/GenomicFeatures.jl

@@ -34,6 +34,7 @@ import BGZFStreams
 import BioCore: BioCore, seqname, leftposition, rightposition, isoverlapping, isfilled, hasseqname, hasleftposition, hasrightposition, metadata
 import DataStructures
 import IntervalTrees
+import Base.@propagate_inbounds
 
 include("strand.jl")
 include("interval.jl")

src/bbi/btree.jl

@@ -61,7 +61,7 @@ end
 function chromlist(tree::BTree)
     list = Tuple{String,UInt32,UInt32}[]
     # traverse tree
-    key = Vector{UInt8}(tree.header.key_size)
+    key = Vector{UInt8}(undef, tree.header.key_size)
     stack = UInt64[tree.offset + sizeof(BTreeHeader)]
     while !isempty(stack)
         offset = pop!(stack)
@@ -70,8 +70,8 @@ function chromlist(tree::BTree)
         for i in 1:node.count
             if isleaf(node)
                 read!(tree.stream, key)
-                i = findfirst(key, 0x00)
-                chromname = i == 0 ? String(copy(key)) : String(key[1:i-1])
+                i = findfirst(isequal(0x00), key)
+                chromname = i === nothing ? String(copy(key)) : String(key[1:i-1])
                 chromid = read(tree.stream, UInt32)
                 chromsize = read(tree.stream, UInt32)
                 push!(list, (chromname, chromid, chromsize))
@@ -100,7 +100,7 @@ function write_btree(stream::IO, chromlist::Vector{Tuple{String,UInt32,UInt32}})
     n += write(stream, BTreeNode(0x01, 0x00, length(chromlist)))
 
     # write the root node
-    key = Vector{UInt8}(keysize)
+    key = Vector{UInt8}(undef, keysize)
     for (name, id, len) in sort(chromlist, by=x->x[1])  # sort by name
         fill!(key, 0x00)
         @assert sizeof(name) ≤ keysize

src/bbi/compress.jl

@@ -6,7 +6,7 @@ function compress!(dst::Vector{UInt8}, src::Vector{UInt8})::UInt64
     code = ccall(
         (:compress, Libz.zlib),
         Cint,
-        (Ptr{Void}, Ref{Culong}, Ptr{Void}, Culong),
+        (Ptr{Cvoid}, Ref{Culong}, Ptr{Cvoid}, Culong),
         dst, sz, src, sizeof(src))
     if code != Libz.Z_OK
         Libz.zerror(code)
@@ -19,7 +19,7 @@ function uncompress!(dst::Vector{UInt8}, src::Vector{UInt8})::UInt64
     code = ccall(
         (:uncompress, Libz.zlib),
         Cint,
-        (Ptr{Void}, Ref{Culong}, Ptr{Void}, Culong),
+        (Ptr{Cvoid}, Ref{Culong}, Ptr{Cvoid}, Culong),
         dst, sz, src, sizeof(src))
     if code != Libz.Z_OK
         Libz.zerror(code)

src/bbi/rtree.jl

@@ -245,7 +245,7 @@ function write_rtree(stream::IO, blocks::Vector{Block})
         seek(stream, offset)
         @assert position(stream) == offset
         write(stream, RTreeNodeFormat(isleaf(node) ? 0x01 : 0x00, 0x00, length(node.children)))
-        for i in 1:endof(node.children)
+        for i in 1:lastindex(node.children)
             child = node.children[i]
             if isleaf(node)
                 write(stream, RTreeLeafNode(child.lo, child.up, offsets[i], datasizes[i]))
@@ -285,13 +285,13 @@ function build_inmemory_rtree(blocks::Vector{Block}, blocksize::Int)
             d = cld(length(blocks), blocksize)
             children = InMemoryRTree[]
             for i in 1:blocksize
-                idx = (i-1)*d+1:min(i*d,endof(blocks))
+                idx = (i-1)*d+1:min(i*d,lastindex(blocks))
                 push!(children, rec(view(blocks, idx)))
             end
             return InMemoryRTree(children)
         end
     end
-    return rec(view(blocks, 1:endof(blocks)))
+    return rec(view(blocks, 1:lastindex(blocks)))
 end
 
 function readbound(stream::IO)