Merge branch 'master' into develop

.github/workflows/Documentation.yml

@@ -12,12 +12,13 @@ jobs:
   Documenter:
     permissions:
       contents: write
-    name: Documentation    
+      statuses: write
+    name: Documentation
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/julia-buildpkg@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/julia-buildpkg@v1  # if package requires Pkg.build()
       - uses: julia-actions/julia-docdeploy@v1
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key

.github/workflows/TagBot.yml

@@ -9,7 +9,18 @@ on:
       lookback:
         default: 3
 permissions:
+  actions: read
+  checks: read
   contents: write
+  deployments: read
+  issues: read
+  discussions: read
+  packages: read
+  pages: read
+  pull-requests: read
+  repository-projects: read
+  security-events: read
+  statuses: read
 
 jobs:
   TagBot:

.github/workflows/UnitTests.yml

@@ -29,17 +29,19 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
       - name: Setup Julia
         uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
       - name: Run Tests
         uses: julia-actions/julia-runtest@v1
+        with:
+          annotate: true
       - name: Create CodeCov
         uses: julia-actions/julia-processcoverage@v1
       - name: Upload CodeCov
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v2
         with:
           file: ./lcov.info
           flags: unittests

CHANGELOG.md

@@ -1,44 +1,73 @@
 # Changelog
 
-All notable changes to HapLink.jl will be documented in this file.
+All notable changes to XAM.jl will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
 
+
+## [0.4.0]
+
 ### Added
-- Added BAM.Reader index support for BAI object ([#56](https://github.com/BioJulia/XAM.jl/pull/56/files))
-- Added doi badge
+- Added BAM.Reader index support for BAI object ([#56](https://github.com/BioJulia/XAM.jl/pull/56)).
+- Added doi badge.
+- Added test to ensure EOF_BLOCK gets written.
+- Added `isreversestrand`.
+- Added `isfirstsegment`.
+- Added `islastsegment`.
 
 ### Changed
 
 - Subtype from XAMReader and XAMWriter from common abstract types.
 - Subtype from XAMRecord.
 - Unified flag queries.
+- Improved Slack link.
+- Updated to use [Automa](https://github.com/BioJulia/Automa.jl) v1 ([#65](https://github.com/BioJulia/XAM.jl/pull/65)).
+- Pointed the Unit Tests badge at the develop branch.
+- Pluralised flag.
+- Renamed `ismateunmapped` to `isnextunmapped`.
+- Renamed `isreverse` to `isreversecomplemented`.
+- Renamed `isforward` to `isforwardstrand`.
+- `ispositivestrand` aliases `isforwardstrand`.
+- `isnegativestrand` aliases `isreversestrand`.
+- Renamed `ismatereverse` to `isnextreversecomplemented`.
+- `isread1` aliases `isfirstsegment`.
+- `isread2` aliases `islastsegment`.
+
+### Fixed
+- Updated hts-files.md ([#62](https://github.com/BioJulia/XAM.jl/pull/62)).
+- Corrected the behaviour of `isprimaryalignment` with `isprimary`.
+
+### Removed
+- Moved the functionality of `isprimary` into `isprimaryalignment`.
+
 
 ## [0.3.1]
 
 ### Changed
 
-- Upgraded to BioAlignments v3 ([#55](https://github.com/BioJulia/XAM.jl/pull/55))
+- Upgraded to BioAlignments v3 ([#55](https://github.com/BioJulia/XAM.jl/pull/55)).
+
 
 ## [0.3.0] - 2022-10-10
 
 ## Added
 
-- Crosschecks for SAM and BAM ([#29](https://github.com/BioJulia/XAM.jl/pull/29))
-- Improved documentation for flags ([#43](https://github.com/BioJulia/XAM.jl/pull/43))
+- Crosschecks for SAM and BAM ([#29](https://github.com/BioJulia/XAM.jl/pull/29)).
+- Improved documentation for flags ([#43](https://github.com/BioJulia/XAM.jl/pull/43)).
 
 ### Changed
 
-- `BAM.quality` performance improved ([#21](https://github.com/BioJulia/XAM.jl/issues/21))
-- Updated BioAlignments to v2.2 and BioSequences to v3 ([#48](https://github.com/BioJulia/XAM.jl/pull/48))
+- `BAM.quality` performance improved ([#21](https://github.com/BioJulia/XAM.jl/issues/21)).
+- Updated BioAlignments to v2.2 and BioSequences to v3 ([#48](https://github.com/BioJulia/XAM.jl/pull/48)).
 
 ### Fixed
 
-- `BAM.Record` layout now matches the BAM specs ([#26](https://github.com/BioJulia/XAM.jl/pull/26))
+- `BAM.Record` layout now matches the BAM specs ([#26](https://github.com/BioJulia/XAM.jl/pull/26)).
 
-[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.1...HEAD
+[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.4.0...HEAD
+[0.4.0]: https://github.com/BioJulia/XAM.jl/compare/v0.3.1...0.4.0
 [0.3.1]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...v0.3.1
 [0.3.0]: https://github.com/BioJulia/XAM.jl/compare/v0.2.8...v0.3.0

Project.toml

@@ -1,7 +1,7 @@
 name = "XAM"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 authors = ["Kenta Sato <[email protected]>", "Ben J. Ward <[email protected]>", "Ciarán O'Mara <[email protected]>"]
-version = "0.3.1"
+version = "0.4.0"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"

README.md

@@ -27,7 +27,7 @@ XAM is tested against Julia `1.X` on Linux, OS X, and Windows.
 
 **Latest build status:**
 
-[![Unit tests](https://github.com/BioJulia/XAM.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
+[![Unit Tests](https://github.com/BioJulia/XAM.jl/actions/workflows/UnitTests.yml/badge.svg?branch=develop)](https://github.com/BioJulia/XAM.jl/actions/workflows/UnitTests.yml)
 [![Documentation](https://github.com/BioJulia/XAM.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
 [![codecov](https://codecov.io/gh/BioJulia/XAM.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/XAM.jl)
 

docs/src/index.md

@@ -25,7 +25,7 @@ XAM is tested against Julia `1.X` on Linux, OS X, and Windows.
 
 **Latest build status:**
 
-[![Unit tests](https://github.com/BioJulia/XAM.jl/workflows/Unit%20tests/badge.svg?branch=master)](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3A%22Unit+tests%22+branch%3Amaster)
+[![Unit Tests](https://github.com/BioJulia/XAM.jl/actions/workflows/UnitTests.yml/badge.svg?branch=develop)](https://github.com/BioJulia/XAM.jl/actions/workflows/UnitTests.yml)
 [![Documentation](https://github.com/BioJulia/XAM.jl/workflows/Documentation/badge.svg?branch=master)](https://github.com/BioJulia/XAM.jl/actions?query=workflow%3ADocumentation+branch%3Amaster)
 [![codecov](https://codecov.io/gh/BioJulia/XAM.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/XAM.jl)
 

docs/src/man/hts-files.md

@@ -110,9 +110,9 @@ In the above we can see there were 7 sequences in the reference: 5 chromosomes,
 The `XAM` package supports the following accessors for `SAM.Record` types.
 
 ```@docs
-XAM.SAM.flag
+XAM.SAM.flags
 XAM.SAM.ismapped
-XAM.SAM.isprimary
+XAM.SAM.isprimaryalignment
 XAM.SAM.refname
 XAM.SAM.position
 XAM.SAM.rightposition
@@ -135,9 +135,9 @@ XAM.SAM.auxdata
 The `XAM` package supports the following accessors for `BAM.Record` types.
 
 ```@docs
-XAM.BAM.flag
+XAM.BAM.flags
 XAM.BAM.ismapped
-XAM.BAM.isprimary
+XAM.BAM.isprimaryalignment
 XAM.BAM.refid
 XAM.BAM.refname
 XAM.BAM.reflen

src/bam/bam.jl

@@ -6,8 +6,8 @@ module BAM
 using BioGenerics
 using GenomicFeatures
 using XAM.SAM
-import ..XAM: flag, XAMRecord, XAMReader, XAMWriter,
-	ismapped, isprimary, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.
+import ..XAM: flags, XAMRecord, XAMReader, XAMWriter,
+	ismapped, isprimaryalignment, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.
 
 import BGZFStreams
 import BioAlignments

src/bam/record.jl

@@ -15,7 +15,7 @@ mutable struct Record <: XAMRecord
     mapq::UInt8
     bin::UInt16
     n_cigar_op::UInt16
-    flag::UInt16
+    flags::UInt16
     l_seq::Int32
     next_refid::Int32
     next_pos::Int32
@@ -56,7 +56,7 @@ function Base.:(==)(a::Record, b::Record)
         a.mapq          == b.mapq &&
         a.bin           == b.bin &&
         a.n_cigar_op    == b.n_cigar_op &&
-        a.flag          == b.flag &&
+        a.flags         == b.flags &&
         a.l_seq         == b.l_seq &&
         a.next_refid    == b.next_refid &&
         a.next_pos      == b.next_pos &&
@@ -83,7 +83,7 @@ function Base.empty!(record::Record)
     record.l_read_name = 0
     record.mapq = 0
     record.bin = 0
-    record.flag = 0
+    record.flags = 0
     record.n_cigar_op = 0
     record.l_seq      = 0
     record.next_refid = 0
@@ -100,7 +100,7 @@ function Base.show(io::IO, record::Record)
     if isfilled(record)
         println(io)
         println(io, "      template name: ", tempname(record))
-        println(io, "               flag: ", flag(record))
+        println(io, "              flags: ", flags(record))
         println(io, "       reference ID: ", refid(record))
         println(io, "           position: ", position(record))
         println(io, "    mapping quality: ", mappingquality(record))
@@ -128,12 +128,12 @@ end
 # Accessor Fuctions
 # -----------------
 
-function flag(record::Record)::UInt16
+function flags(record::Record)::UInt16
     checkfilled(record)
-    return record.flag
+    return record.flags
 end
 
-function hasflag(record::Record)
+function hasflags(record::Record)
     return isfilled(record)
 end