From 8151d877e79eda65808f16a968db3e488afa3380 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= <Ciaran.OMara@utas.edu.au>
Date: Mon, 9 Jan 2023 12:30:36 +1100
Subject: [PATCH] Subtype from XAMReader and XAMWriter

---
 CHANGELOG.md      | 4 ++++
 src/XAM.jl        | 5 +++++
 src/bam/bam.jl    | 2 +-
 src/bam/reader.jl | 6 +++---
 src/bam/writer.jl | 2 +-
 src/sam/reader.jl | 2 +-
 src/sam/sam.jl    | 2 +-
 src/sam/writer.jl | 2 +-
 8 files changed, 17 insertions(+), 8 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9ed8c7b..cd21a88 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 - Added BAM.Reader index support for BAI object ([#56](https://github.com/BioJulia/XAM.jl/pull/56/files))
 
+### Changed
+
+- Subtype from XAMReader and XAMWriter from common abstract types.
+
 ## [0.3.1]
 
 ### Changed
diff --git a/src/XAM.jl b/src/XAM.jl
index 2c5bad1..b3f5e4c 100644
--- a/src/XAM.jl
+++ b/src/XAM.jl
@@ -1,9 +1,14 @@
 module XAM
 
+using BioGenerics
+
 export
     SAM,
     BAM
 
+abstract type XAMReader <: BioGenerics.IO.AbstractReader end
+abstract type XAMWriter <: BioGenerics.IO.AbstractWriter end
+
 """
     flag(record::Union{SAM.Record, BAM.Record})::UInt16
 
diff --git a/src/bam/bam.jl b/src/bam/bam.jl
index b3591d7..41aea12 100644
--- a/src/bam/bam.jl
+++ b/src/bam/bam.jl
@@ -6,7 +6,7 @@ module BAM
 using BioGenerics
 using GenomicFeatures
 using XAM.SAM
-import ..XAM: flag
+import ..XAM: flag, XAMReader, XAMWriter
 
 import BGZFStreams
 import BioAlignments
diff --git a/src/bam/reader.jl b/src/bam/reader.jl
index 3dd2f7f..c1686c0 100644
--- a/src/bam/reader.jl
+++ b/src/bam/reader.jl
@@ -8,9 +8,9 @@ Create a data reader of the BAM file format.
 
 # Arguments
 * `input`: data source
-* `index=nothing`: filepath to a random access index (currently *bai* is supported) or BAI object 
+* `index=nothing`: filepath to a random access index (currently *bai* is supported) or BAI object
 """
-mutable struct Reader{T} <: BioGenerics.IO.AbstractReader
+mutable struct Reader{T} <: XAMReader
     stream::BGZFStreams.BGZFStream{T}
     header::SAM.Header
     start_offset::BGZFStreams.VirtualOffset
@@ -124,7 +124,7 @@ init_bam_index(index::AbstractString) = BAI(index)
 init_bam_index(index::BAI) = index
 init_bam_index(index::Nothing) = nothing
 init_bam_index(index) = error("unrecognizable index argument")
-    
+
 function _read!(reader::Reader, record)
     unsafe_read(
         reader.stream,
diff --git a/src/bam/writer.jl b/src/bam/writer.jl
index 81bdf23..8c4268f 100644
--- a/src/bam/writer.jl
+++ b/src/bam/writer.jl
@@ -10,7 +10,7 @@ Create a data writer of the BAM file format.
 * `output`: data sink
 * `header`: SAM header object
 """
-mutable struct Writer <: BioGenerics.IO.AbstractWriter
+mutable struct Writer <: XAMWriter
     stream::BGZFStreams.BGZFStream
 end
 
diff --git a/src/sam/reader.jl b/src/sam/reader.jl
index 46fd286..f38044f 100644
--- a/src/sam/reader.jl
+++ b/src/sam/reader.jl
@@ -1,7 +1,7 @@
 # SAM Reader
 # =========
 
-mutable struct Reader{S <: TranscodingStream} <: BioGenerics.IO.AbstractReader
+mutable struct Reader{S <: TranscodingStream} <: XAMReader
     state::State{S}
     header::Header
 end
diff --git a/src/sam/sam.jl b/src/sam/sam.jl
index fcd0821..0e25d39 100644
--- a/src/sam/sam.jl
+++ b/src/sam/sam.jl
@@ -11,7 +11,7 @@ import BioGenerics.Exceptions: missingerror
 import BioGenerics.Automa: State
 import BioSequences
 import TranscodingStreams: TranscodingStreams, TranscodingStream
-import ..XAM: flag
+import ..XAM: flag, XAMReader, XAMWriter
 
 using Printf: @sprintf
 
diff --git a/src/sam/writer.jl b/src/sam/writer.jl
index 801ed68..c16a346 100644
--- a/src/sam/writer.jl
+++ b/src/sam/writer.jl
@@ -10,7 +10,7 @@ Create a data writer of the SAM file format.
 * `output`: data sink
 * `header=Header()`: SAM header object
 """
-mutable struct Writer <: BioGenerics.IO.AbstractWriter
+mutable struct Writer <: XAMWriter
     stream::IO
 
     function Writer(output::IO, header::Header=Header())