Subtype from XAMRecord

Author: CiaranOMara

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]
 

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
 

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

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

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.

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