From 0d1eec3ed3e9ba65a118e6b86a6a8c80779de153 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 12:48:54 +1100
Subject: [PATCH] Subtype from XAMRecord

---
 CHANGELOG.md      | 2 ++
 src/XAM.jl        | 3 ++-
 src/bam/bam.jl    | 2 +-
 src/bam/record.jl | 2 +-
 src/sam/record.jl | 2 +-
 src/sam/sam.jl    | 2 +-
 6 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cd21a88..938f911 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - Subtype from XAMReader and XAMWriter from common abstract types.
+- Subtype from XAMRecord.
+- Unified flag queries.
 
 ## [0.3.1]
 
diff --git a/src/XAM.jl b/src/XAM.jl
index b3f5e4c..2ae8ac8 100644
--- a/src/XAM.jl
+++ b/src/XAM.jl
@@ -5,7 +5,8 @@ using BioGenerics
 export
     SAM,
     BAM
-
+    
+abstract type XAMRecord end
 abstract type XAMReader <: BioGenerics.IO.AbstractReader end
 abstract type XAMWriter <: BioGenerics.IO.AbstractWriter end
 
diff --git a/src/bam/bam.jl b/src/bam/bam.jl
index 41aea12..03ef9fd 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, XAMReader, XAMWriter
+import ..XAM: flag, XAMRecord, XAMReader, XAMWriter
 
 import BGZFStreams
 import BioAlignments
diff --git a/src/bam/record.jl b/src/bam/record.jl
index bd092e8..db33f88 100644
--- a/src/bam/record.jl
+++ b/src/bam/record.jl
@@ -6,7 +6,7 @@
 
 Create an unfilled BAM record.
 """
-mutable struct Record
+mutable struct Record <: XAMRecord
     # fixed-length fields (see BMA specs for the details)
     block_size::Int32
     refid::Int32
diff --git a/src/sam/record.jl b/src/sam/record.jl
index ef8bb6d..befa967 100644
--- a/src/sam/record.jl
+++ b/src/sam/record.jl
@@ -1,7 +1,7 @@
 # SAM Record
 # ==========
 
-mutable struct Record
+mutable struct Record <: XAMRecord
     # Data and filled range.
     data::Vector{UInt8}
     filled::UnitRange{Int} # Note: Specifies the data in use.
diff --git a/src/sam/sam.jl b/src/sam/sam.jl
index 0e25d39..70cf2de 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, XAMReader, XAMWriter
+import ..XAM: flag, XAMRecord, XAMReader, XAMWriter
 
 using Printf: @sprintf