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BioJulia · Jun 23, 2024 · aad28c8 · aad28c8
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diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md
@@ -0,0 +1,5 @@
+Thank you for making an issue.
+If you are submitting a bug report, it will help us if you include the following information:
+
+- Your version of Julia and all packages in your activated Julia environment
+- A small example that demonstrates the bug. If possible, please make the code copy-pastable into a fresh REPL.
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,7 @@
+Thank you for your contribution! 
+If you have any questions about your PR, or need help completing it, you can ping the maintainers of this repository, who will be happy to help if they can find time.
+
+You can optionally use the following checklist when you work on your PR:
+- [ ] I have updated any relevant documentation and docstrings.
+- [ ] I have added unit tests, and the CodeCov bot shows tests cover my new code.
+- [ ] I have mentioned my changes in the CHANGELOG.md file.
diff --git a/.github/codecov.yml b/.github/codecov.yml
@@ -0,0 +1,28 @@
+coverage:
+  status:
+    project:
+      default:
+        # basic
+        target: auto
+        threshold: 10%
+        base: auto 
+        flags: 
+          - unittest
+        paths: 
+          - "src"
+       # advanced settings
+        if_ci_failed: ignore
+        informational: true
+    patch:
+      default:
+        # basic
+        target: auto
+        threshold: 10%
+        base: auto 
+        flags: 
+          - unittest
+        paths: 
+          - "src"
+       # advanced settings
+        if_ci_failed: ignore
+        informational: true
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -0,0 +1,29 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+      pull-requests: read
+      statuses: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: 'nightly'
+      - uses: julia-actions/cache@v1
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: julia --project=docs/ docs/make.jl
diff --git a/.github/workflows/unittest.yml b/.github/workflows/unittest.yml
@@ -0,0 +1,45 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version:
+          - 'nightly'
+        os: [ ubuntu-latest, windows-latest ]
+        arch: [ x64 ]
+        include:
+          - julia-version: nightly
+            julia-arch: x86
+            os: ubuntu-latest
+            experimental: true
+         # - julia-version: 1
+         #   os: macOS-latest
+         #   experimental: false
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+      - name: Run Tests
+        uses: julia-actions/julia-runtest@latest
+      - name: Create CodeCov
+        uses: julia-actions/julia-processcoverage@v1
+      - name: Upload CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./lcov.info
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/Project.toml b/Project.toml
@@ -12,7 +12,7 @@ XAMAuxData = "e99d641e-1821-45d7-9150-ecb7bf333fe1"
 [compat]
 Aqua = "0.8.7"
 FormatSpecimens = "1.3"
-MemViews = "0.1"
+MemViews = "0.2"
 PrecompileTools = "1.2.1"
 StringViews = "1.3.3"
 Test = "1.11"

diff --git a/README.md b/README.md
@@ -2,12 +2,13 @@
 
 [![Latest Release](https://img.shields.io/github/release/BioJulia/PairwiseMappingFormat.jl.svg)](https://github.com/BioJulia/PairwiseMappingFormat.jl/releases/latest)
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/PairwiseMappingFormat.jl/blob/master/LICENSE)
-[![Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/PairwiseMappingFormat.jl/stable)
+[![Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/PairwiseMappingFormat.jl/dev)
+[![](https://codecov.io/gh/BioJulia/PairwiseMappingFormat.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/PairwiseMappingFormat.jl)
 
 PairwiseMappingFormat.jl provide a parser for Pairwise Mapping Format (PAF) files.
 PAF is a simple, tab-delimited format created by programs such as minimap2.
 
-To learn how to use the package, [read the documentation](https://biojulia.github.io/PairwiseMappingFormat.jl/stable/)
+To learn how to use the package, [read the documentation](https://biojulia.github.io/PairwiseMappingFormat.jl/dev/)
 
 ## Example
 ```julia
@@ -29,4 +30,4 @@ add PairwiseMappingFormat
 ```
 
 ## Contributing
-Get in touch with the BioJulia community over at the [Julia Slack](https://julialang.org/slack/) or Zulip servers.
+Make an issue or PR on this repository, or get in touch with the BioJulia community over at the [Julia Slack](https://julialang.org/slack/) or Zulip servers.
diff --git a/docs/make.jl b/docs/make.jl
@@ -8,22 +8,20 @@ meta = quote
     using PairwiseMappingFormat: try_parse
 end
 
-DocMeta.setdocmeta!(
-    PairwiseMappingFormat,
-    :DocTestSetup,
-    meta,
-    recursive=true
-)
+DocMeta.setdocmeta!(PairwiseMappingFormat, :DocTestSetup, meta; recursive=true)
 
-makedocs(
-    sitename = "PairwiseMappingFormat.jl",
-    modules = [PairwiseMappingFormat],
-    pages = [
-        "Home" => "index.md",
-    ],
-    authors = "Jakob Nybo Nissen",
-    checkdocs = :public,
-    remotes=nothing, # TODO: Remove
+makedocs(;
+    sitename="PairwiseMappingFormat.jl",
+    modules=[PairwiseMappingFormat],
+    pages=["Home" => "index.md"],
+    authors="Jakob Nybo Nissen",
+    checkdocs=:public,
+    remotes=nothing,
 )
 
-# TODO: Call deploydocs
+deploydocs(;
+    repo="github.com/BioJulia/PairwiseMappingFormat.jl.git",
+    push_preview=true,
+    deps=nothing,
+    make=nothing,
+)
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -170,9 +170,7 @@ NaN
 ## Low-level interface
 Iterating `PAFReader`s, and the `parse` function will throw a `PairwiseMappingFormat.ParserException` if the data is invalid:
 ```jldoctest
-parse(PAFRecord, "not a PAF line")
-
-# output
+julia> parse(PAFRecord, "not a PAF line")
 ERROR: Error when parsing PAF record on line 1, near byte number 14 in line: Not enough tab-separated fields. Each line must have at least 12 fields
 [...]
 ```
@@ -186,13 +184,10 @@ It either returns a valid `PAFRecord`, or else returns the [`ParserException`](@
 but does not throw the exception:
 
 ```jldoctest public
-const PAF = PairwiseMappingFormat
+julia> const PAF = PairwiseMappingFormat;
 
-println(PAF.try_parse("not a PAF line"))
-
-# output
+julia> println(PAF.try_parse("not a PAF line"))
 PairwiseMappingFormat.ParserException(PairwiseMappingFormat.Errors.TooFewFields, 14, 1)
-
 ```
 
 Similarly, the next record of a `PAFReader` may be obtained with the unexported [`try_next!`](@ref)
@@ -234,11 +229,10 @@ The [`ParserException`](@ref) type contains the error type as an `Enum`, and the
 the exception occurred. These can be obtained with the `.kind` and `.line` properties.
 
 ```jldoctest public
-println(err.line)
-println(err.kind)
-
-# output
+julia> err.line
 1
+
+julia> err.kind
 TooFewFields
 ```
 

diff --git a/src/PairwiseMappingFormat.jl b/src/PairwiseMappingFormat.jl
@@ -149,9 +149,9 @@ function Base.show(io::IO, ::MIME"text/plain", record::PAFRecord)
     buf = IOBuffer()
     is_mapped(record) || print(buf, "Unmapped ")
     println(buf, "PAFRecord:")
-    println(buf, "  Query:    ", qname(record))
+    println(buf, "  Query:    \"", qname(record), '"')
     if is_mapped(record)
-        println(buf, "  Target:   ", tname(record))
+        println(buf, "  Target:   \"", tname(record), '"')
         println(buf, "  Q cov:    ", round(query_coverage(record); digits=4))
         println(buf, "  T cov:    ", round(target_coverage(record); digits=4))
         println(buf, "  Identity: ", round(aln_identity(record); digits=4))
@@ -165,7 +165,7 @@ function Base.show(io::IO, ::MIME"text/plain", record::PAFRecord)
 end
 
 # Print the AUX fields indented
-function repr_aux(record::PAFRecord)
+function repr_aux(record::PAFRecord)::Vector{UInt8}
     buf = IOBuffer()
     out = IOBuffer()
     show(buf, MIME"text/plain"(), aux_data(record))
@@ -220,10 +220,7 @@ end
 """
     query_coverage(rec::Record) -> Float64
 
-Compute the approximate fraction of the query covered by the alignment.
-This is computed as the alignment length divided by the query length,
-and thus may be inaccurate if there are deletions in the alignment.
-The result is guaranteed to be non-negative.
+Compute the fraction of the query covered by the alignment.
 
 # Examples
 ```jldoctest
@@ -240,10 +237,7 @@ end
 """
     target_coverage(rec::Record) -> Float64
 
-Compute the approximate fraction of the target covered by the alignment.
-This is computed as the alignment length divided by the target length,
-and thus may be inaccurate if there are deletions in the alignment.
-The result is guaranteed to be non-negative.
+Compute the fraction of the target covered by the alignment.
 
 # Examples
 ```jldoctest
@@ -450,9 +444,9 @@ function parse_line!(
     strand = if b == UInt8('*')
         return finish_unmapped!(record, mem, qname, qlen, i + 2)
     elseif b == UInt8('-')
-        0x01
-    elseif b == UInt8('+')
         0x02
+    elseif b == UInt8('+')
+        0x01
     else
         return ParserException(i % Int32, Errors.InvalidStrand)
     end
@@ -484,11 +478,11 @@ function parse_line!(
     length(data) == filled || resize!(data, filled)
     doff = 1
     dataview = MemView(data)
-    unsafe_copyto!(dataview, doff, mem, first(qname), length(qname))
+    unsafe_copyto!(dataview, mem[qname])
     doff += length(qname)
-    unsafe_copyto!(dataview, doff, mem, first(tname), length(tname))
+    unsafe_copyto!(dataview[doff:end], mem[tname])
     doff += length(tname)
-    iszero(auxlen) || unsafe_copyto!(dataview, doff, mem, i, auxlen)
+    iszero(auxlen) || unsafe_copyto!(dataview[doff:end], mem[i:end])
 
 
     # Fill in fields of the struct
@@ -529,7 +523,7 @@ function finish_unmapped!(
             i + 1
         end
     end
-    i = findnext(==(0x00), mem, i)
+    i = findnext(==(UInt8('\t')), mem, i)
     aux_end = lastindex(mem)
     aux_start = isnothing(i) ? aux_end + 1 : i + 1
     aux = aux_start:aux_end
@@ -539,8 +533,8 @@ function finish_unmapped!(
     data = getfield(record, :data)
     dataview = MemView(data)
     length(data) == filled || resize!(data, filled)
-    unsafe_copyto!(dataview, 1, mem, first(qname), length(qname))
-    unsafe_copyto!(dataview, length(qname) + 1, mem, aux_start, length(aux))
+    unsafe_copyto!(dataview, mem[qname])
+    unsafe_copyto!(dataview[length(qname)+1:end], mem[aux])
 
     # Fill in fields
     record.qname_len = length(qname) % Int32
@@ -594,13 +588,15 @@ function parse_int(
         n < 0 && return ParserException(i % Int32, Errors.IntegerOverflow)
         n = Int32(10) * n + (b - Int32(48))
     end
+    # Note: It is not possible to get an InvalidZero error here, because
+    # the last field (mapq) does allow zero, and for any other fields,
+    # if they do not end with a \t and thus reach this line, a TooFewFields
+    # error will be returned.
     # at_end is if this is the mapq field, which does not need to end with a tab
     if !at_end
         ParserException(lastindex(v) % Int32, Errors.TooFewFields)
     elseif from > lastindex(v)
         ParserException(i % Int32, Errors.EmptyInteger)
-    elseif !allow_zero & iszero(n)
-        ParserException(i % Int32, Errors.InvalidZero)
     else
         (n, i + 1)
     end
@@ -660,9 +656,8 @@ mutable struct PAFReader{I <: IO}
     copy::Bool
 end
 
-function PAFReader(io::IO; copy::Bool=true)
-    # 2^16 and 512 are reasonable buffer sizes, they are arbitrary
-    mem = Memory{UInt8}(undef, 2^16)
+function PAFReader(io::IO; buf_size::Int=2^16, copy::Bool=true)
+    mem = Memory{UInt8}(undef, max(buf_size, 16))
     rec = PAFRecord(512)
     PAFReader{typeof(io)}(io, rec, mem, 1, 0, 1, copy)
 end
@@ -671,8 +666,8 @@ Base.IteratorSize(::Type{<:PAFReader}) = Base.SizeUnknown()
 Base.eltype(::Type{<:PAFReader}) = PAFRecord
 Base.close(reader::PAFReader) = close(reader.io) # TODO: Docstring
 
-function PAFReader(f::Function, io::IO; copy::Bool=true)
-    reader = PAFReader(io; copy)
+function PAFReader(f::Function, io::IO; kwargs...)
+    reader = PAFReader(io; kwargs...)
     try
         f(reader)
     finally