millironx/XAM.jl
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Subtype from XAMRecord

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Ciarán O'Mara 2023-01-09 12:48:54 +11:00
parent 8151d877e7
commit 0d1eec3ed3
6 changed files with 8 additions and 5 deletions
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2
CHANGELOG.md
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@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Changed ### Changed
- Subtype from XAMReader and XAMWriter from common abstract types. - Subtype from XAMReader and XAMWriter from common abstract types.
- Subtype from XAMRecord.
- Unified flag queries.
## [0.3.1] ## [0.3.1]

3
src/XAM.jl
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@ -5,7 +5,8 @@ using BioGenerics
export export
SAM, SAM,
BAM BAM
abstract type XAMRecord end
abstract type XAMReader <: BioGenerics.IO.AbstractReader end abstract type XAMReader <: BioGenerics.IO.AbstractReader end
abstract type XAMWriter <: BioGenerics.IO.AbstractWriter end abstract type XAMWriter <: BioGenerics.IO.AbstractWriter end

2
src/bam/bam.jl
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@ -6,7 +6,7 @@ module BAM
using BioGenerics using BioGenerics
using GenomicFeatures using GenomicFeatures
using XAM.SAM using XAM.SAM
import ..XAM: flag, XAMReader, XAMWriter import ..XAM: flag, XAMRecord, XAMReader, XAMWriter
import BGZFStreams import BGZFStreams
import BioAlignments import BioAlignments

2
src/bam/record.jl
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@ -6,7 +6,7 @@
Create an unfilled BAM record. Create an unfilled BAM record.
""" """
mutable struct Record mutable struct Record <: XAMRecord
# fixed-length fields (see BMA specs for the details) # fixed-length fields (see BMA specs for the details)
block_size::Int32 block_size::Int32
refid::Int32 refid::Int32

2
src/sam/record.jl
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@ -1,7 +1,7 @@
# SAM Record # SAM Record
# ========== # ==========
mutable struct Record mutable struct Record <: XAMRecord
# Data and filled range. # Data and filled range.
data::Vector{UInt8} data::Vector{UInt8}
filled::UnitRange{Int} # Note: Specifies the data in use. filled::UnitRange{Int} # Note: Specifies the data in use.

2
src/sam/sam.jl
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@ -11,7 +11,7 @@ import BioGenerics.Exceptions: missingerror
import BioGenerics.Automa: State import BioGenerics.Automa: State
import BioSequences import BioSequences
import TranscodingStreams: TranscodingStreams, TranscodingStream import TranscodingStreams: TranscodingStreams, TranscodingStream
import ..XAM: flag, XAMReader, XAMWriter import ..XAM: flag, XAMRecord, XAMReader, XAMWriter
using Printf: @sprintf using Printf: @sprintf