Ignore .DS_Store files and update docs

Author: Ben J. Ward

.gitignore

@@ -3,3 +3,4 @@
 *.jl.mem
 /docs/build
 /docs/site/
+.DS_Store

.travis.yml

@@ -5,6 +5,7 @@ os:
   - osx
 julia:
   - 0.7
+  - 1.0
   - nightly
 matrix:
   allow_failures:
@@ -13,5 +14,6 @@ notifications:
   email: false
 after_success:
   # push coverage results to Codecov
-  - julia -e 'cd(Pkg.dir("BioAlignments")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
-  - julia -e 'cd(Pkg.dir("BioAlignments")); Pkg.add("Documenter"); include(joinpath("docs", "make.jl"))'
+  - julia -e 'using Pkg; Pkg.add("Documenter"); Pkg.add("Coverage"); Pkg.add("BioAlignments"); Pkg.add("BioSequences")'
+  - julia -e 'using Coverage; import BioAlignments; cd(dirname(dirname(pathof(BioAlignments)))); Codecov.submit(Codecov.process_folder())'
+  - julia --color=yes -e 'import BioAlignments; cd(dirname(dirname(pathof(BioAlignments)))); include(joinpath("docs", "make.jl"))'

README.md

@@ -30,8 +30,7 @@ check out the master branch to try new features before release.
 
 ## Testing
 
-BioAlignments is tested against julia `0.6` and current `0.7-dev` on
-Linux, OS X, and Windows.
+BioAlignments is tested against julia `0.7` and `1.X` on Linux, OS X, and Windows.
 
 | **Latest release** | **Latest build status** |
 |:------------------:|:-----------------------:|

docs/make.jl

@@ -16,7 +16,7 @@ makedocs(
 )
 deploydocs(
     repo = "github.com/BioJulia/BioAlignments.jl.git",
-    julia = "0.6",
+    julia = "1.0",
     osname = "linux",
     target = "build",
     deps = nothing,

docs/src/alignments.md

@@ -81,7 +81,7 @@ julia> Alignment([
            AlignmentAnchor(4,  8, OP_MATCH),
            AlignmentAnchor(4, 12, OP_DELETE)
        ])
-BioAlignments.Alignment:
+Alignment:
   aligned range:
     seq: 0-4
     ref: 4-12

docs/src/hts-files.md

@@ -291,19 +291,19 @@ For example, to create the following simple header:
 
 ```julia
 julia> a = SAM.MetaInfo("HD", ["VN" => 1.6, "SO" => "coordinate"])
-BioAlignments.SAM.MetaInfo:
+SAM.MetaInfo:
     tag: HD
   value: VN=1.6 SO=coordinate
 
 julia> b = SAM.MetaInfo("SQ", ["SN" => "ref", "LN" => 45])
-BioAlignments.SAM.MetaInfo:
+SAM.MetaInfo:
     tag: SQ
   value: SN=ref LN=45
 
 julia> h = SAM.Header([a, b])
-BioAlignments.SAM.Header(BioAlignments.SAM.MetaInfo[BioAlignments.SAM.MetaInfo:
+SAM.Header(SAM.MetaInfo[SAM.MetaInfo:
     tag: HD
-  value: VN=1.6 SO=coordinate, BioAlignments.SAM.MetaInfo:
+  value: VN=1.6 SO=coordinate, SAM.MetaInfo:
     tag: SQ
   value: SN=ref LN=45])
 
@@ -314,18 +314,18 @@ header and an `IO` type:
 
 ```julia
 julia> samw = SAM.Writer(open("my-data.sam", "w"), h)
-BioAlignments.SAM.Writer(IOStream(<file my-data.sam>))
+SAM.Writer(IOStream(<file my-data.sam>))
 
 ```
 
 To make a BAM Writer is slightly different, as you need to use a specific
-stream type from the [BGZFStreams](bgzfstreams) package:
+stream type from the [BGZFStreams][bgzfstreams] package:
 
 ```julia
 julia> using BGZFStreams
 
 julia> bamw = BAM.Writer(BGZFStream(open("my-data.bam", "w"), "w"))
-BioAlignments.BAM.Writer(BGZFStreams.BGZFStream{IOStream}(<mode=write>))
+BAM.Writer(BGZFStreams.BGZFStream{IOStream}(<mode=write>))
 
 ```
 

docs/src/index.md

@@ -0,0 +1,87 @@
+# BioAlignments
+
+[![Latest release](https://img.shields.io/github/release/BioJulia/BioAlignments.jl.svg?style=flat-square)](https://github.com/BioJulia/BioAlignments.jl/releases/latest)
+[![MIT license](https://img.shields.io/badge/license-MIT-green.svg?style=flat-square)](https://github.com/BioJulia/BioAlignments.jl/blob/master/LICENSE)
+[![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square)](https://biojulia.github.io/BioAlignments.jl/stable)
+[![Latest documentation](https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square)](https://biojulia.github.io/BioAlignments.jl/latest/)
+![Lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg?style=flat-square)
+[![Chat on Discord](https://img.shields.io/badge/discord-chat-blue.svg?style=flat-square&logo=discord&colorB=%237289DA)](https://discord.gg/z73YNFz)
+
+
+## Description
+
+BioAlignments provides alignment algorithms, data structures, and I/O
+tools for SAM and BAM file formats.
+
+
+## Installation
+
+Install BioAlignments from the Julia REPL:
+
+```julia
+using Pkg
+add("BioAlignments")
+#Pkg.add("BioAlignments") for julia prior to v0.7
+```
+
+If you are interested in the cutting edge of the development, please
+check out the master branch to try new features before release.
+
+
+## Testing
+
+BioAlignments is tested against julia `0.7` and `1.x` on Linux, OS X, and Windows.
+
+| **Latest release** | **Latest build status** |
+|:------------------:|:-----------------------:|
+|  [![julia07](https://pkg.julialang.org/badges/BioAlignments_0.7.svg)](https://pkg.julialang.org/?pkg=BioAlignments) | [![travis](https://img.shields.io/travis/BioJulia/BioAlignments.jl/master.svg?label=Linux+/+macOS)](https://travis-ci.org/BioJulia/BioAlignments.jl) [![appveyor](https://ci.appveyor.com/api/projects/status/klkynmkr1tgd30gq/branch/master?svg=true)](https://ci.appveyor.com/project/Ward9250/bioalignments-jl/branch/master) [![coverage](https://codecov.io/github/BioJulia/BioAlignments.jl/coverage.svg?branch=master)](https://codecov.io/github/BioJulia/BioAlignments.jl?branch=master) |
+
+
+## Contributing
+
+We appreciate contributions from users including reporting bugs, fixing
+issues, improving performance and adding new features.
+
+Take a look at the [CONTRIBUTING](https://github.com/BioJulia/BioAlignments.jl/blob/master/CONTRIBUTING.md) file provided with
+every BioJulia package package for detailed contributor and maintainer
+guidelines.
+
+
+### Financial contributions
+
+We also welcome financial contributions in full transparency on our
+[open collective](https://opencollective.com/biojulia).
+Anyone can file an expense. If the expense makes sense for the development
+of the community, it will be "merged" in the ledger of our open collective by
+the core contributors and the person who filed the expense will be reimbursed.
+
+
+## Backers & Sponsors
+
+Thank you to all our backers and sponsors!
+
+Love our work and community? [Become a backer](https://opencollective.com/biojulia#backer).
+
+[![backers](https://opencollective.com/biojulia/backers.svg?width=890)](https://opencollective.com/biojulia#backers)
+
+Does your company use BioJulia? Help keep BioJulia feature rich and healthy by
+[sponsoring the project](https://opencollective.com/biojulia#sponsor)
+Your logo will show up here with a link to your website.
+
+[![](https://opencollective.com/biojulia/sponsor/0/avatar.svg)](https://opencollective.com/biojulia/sponsor/0/website)
+[![](https://opencollective.com/biojulia/sponsor/1/avatar.svg)](https://opencollective.com/biojulia/sponsor/1/website)
+[![](https://opencollective.com/biojulia/sponsor/2/avatar.svg)](https://opencollective.com/biojulia/sponsor/2/website)
+[![](https://opencollective.com/biojulia/sponsor/3/avatar.svg)](https://opencollective.com/biojulia/sponsor/3/website)
+[![](https://opencollective.com/biojulia/sponsor/4/avatar.svg)](https://opencollective.com/biojulia/sponsor/4/website)
+[![](https://opencollective.com/biojulia/sponsor/5/avatar.svg)](https://opencollective.com/biojulia/sponsor/5/website)
+[![](https://opencollective.com/biojulia/sponsor/6/avatar.svg)](https://opencollective.com/biojulia/sponsor/6/website)
+[![](https://opencollective.com/biojulia/sponsor/7/avatar.svg)](https://opencollective.com/biojulia/sponsor/7/website)
+[![](https://opencollective.com/biojulia/sponsor/8/avatar.svg)](https://opencollective.com/biojulia/sponsor/8/website)
+[![](https://opencollective.com/biojulia/sponsor/9/avatar.svg)](https://opencollective.com/biojulia/sponsor/9/website)
+
+
+## Questions?
+
+If you have a question about contributing or using BioJulia software, come
+on over and chat to us on [Discord](https://discord.gg/z73YNFz), or you can try the
+[Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

docs/src/index.md

@@ -55,7 +55,7 @@ cost of substitution, insertion, and deletion:
 julia> costmodel = CostModel(match=0, mismatch=1, insertion=1, deletion=1);
 
 julia> pairalign(EditDistance(), "abcd", "adcde", costmodel)
-BioAlignments.PairwiseAlignmentResult{Int64,String,String}:
+PairwiseAlignmentResult{Int64,String,String}:
   distance: 2
   seq: 1 abcd- 4
          | ||
@@ -74,7 +74,7 @@ julia> s2 = dna"ACCTGGTATGATAGCG";
 julia> scoremodel = AffineGapScoreModel(EDNAFULL, gap_open=-5, gap_extend=-1);
 
 julia> res = pairalign(GlobalAlignment(), s1, s2, scoremodel)  # run pairwise alignment
-BioAlignments.PairwiseAlignmentResult{Int64,BioSequences.BioSequence{BioSequences.DNAAlphabet{4}},BioSequences.BioSequence{BioSequences.DNAAlphabet{4}}}:
+PairwiseAlignmentResult{Int64,BioSequences.BioSequence{BioSequences.DNAAlphabet{4}},BioSequences.BioSequence{BioSequences.DNAAlphabet{4}}}:
   score: 13
   seq:  0 -CCTAGG------AGGG 10
            ||| ||      || |
@@ -85,7 +85,7 @@ julia> score(res)  # get the achieved score of this alignment
 13
 
 julia> aln = alignment(res)
-BioAlignments.PairwiseAlignment{BioSequences.BioSequence{BioSequences.DNAAlphabet{4}},BioSequences.BioSequence{BioSequences.DNAAlphabet{4}}}:
+PairwiseAlignment{BioSequences.BioSequence{BioSequences.DNAAlphabet{4}},BioSequences.BioSequence{BioSequences.DNAAlphabet{4}}}:
   seq:  0 -CCTAGG------AGGG 10
            ||| ||      || |
   ref:  1 ACCT-GGTATGATAGCG 16
@@ -152,7 +152,7 @@ defined:
 
 ```jldoctest
 julia> EDNAFULL
-BioAlignments.SubstitutionMatrix{BioSymbols.DNA,Int64}:
+SubstitutionMatrix{BioSymbols.DNA,Int64}:
      A  C  M  G  R  S  V  T  W  Y  H  K  D  B  N
   A  5 -4  1 -4  1 -4 -1 -4  1 -4 -1 -4 -1 -4 -2
   C -4  5  1 -4 -4  1 -1 -4 -4  1 -1 -4 -4 -1 -2
@@ -177,7 +177,7 @@ For amino acids, PAM (Point Accepted Mutation) and BLOSUM (BLOcks SUbstitution M
 
 ```jldoctest
 julia> BLOSUM62
-BioAlignments.SubstitutionMatrix{BioSymbols.AminoAcid,Int64}:
+SubstitutionMatrix{BioSymbols.AminoAcid,Int64}:
      A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  O  U  B  J  Z  X  *
   A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0  0̲  0̲ -2  0̲ -1  0 -4
   R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3  0̲  0̲ -1  0̲  0 -1 -4
@@ -244,7 +244,7 @@ important than flexibility because looking up score is faster than
 
 ```jldoctest
 julia> submat = DichotomousSubstitutionMatrix(1, -1)
-BioAlignments.DichotomousSubstitutionMatrix{Int64}:
+DichotomousSubstitutionMatrix{Int64}:
      match =  1
   mismatch = -1
 

docs/src/pairalign.md

@@ -104,29 +104,30 @@ function Base.show(io::IO, submat::SubstitutionMatrix{T,S}) where {T,S}
     for (i, x) in enumerate(alpha), (j, y) in enumerate(alpha)
         i′ = index(x)
         j′ = index(y)
-        mat[i,j] = string(submat.data[i′,j′])
-        if !submat.defined[i′,j′]
-            mat[i,j] = underline(mat[i,j])
+        mat[i, j] = string(submat.data[i′, j′])
+        if !submat.defined[i′, j′]
+            mat[i, j] = underline(mat[i, j])
         end
     end
 
     # add rows and columns
     rows = map(string, alpha)
-    cols = vcat("", rows)
+    cols = vcat(" ", rows)
     mat = hcat(rows, mat)
     mat = vcat(reshape(cols, 1, length(cols)), mat)
 
     println(io, summary(submat), ':')
     width = maximum(map(x -> length(x), mat))
-    for i in 1:n+1
-        for j in 1:n+1
-            print(io, lpad(mat[i,j], width + 1))
+    for i in 1:n + 1
+        for j in 1:n + 1
+            print(io, lpad(mat[i, j], width + ifelse(last(mat[i, j]) == '\U0332', 2, 1)))
         end
         println(io)
     end
     print(io, "(underlined values are default ones)")
 end
 
+
 underline(s) = join([string(c, '\U0332') for c in s])
 
 # Return a vector of all symbols of `T` except the gap symbol.