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560a5cd8df
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946e77a734
17 changed files with 167 additions and 309 deletions
21
CHANGELOG.md
21
CHANGELOG.md
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@ -7,23 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [Unreleased]
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### Added
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- Added BAM.Reader index support for BAI object ([#56](https://github.com/BioJulia/XAM.jl/pull/56/files))
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- Added doi badge
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### Changed
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- Subtype from XAMReader and XAMWriter from common abstract types.
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- Subtype from XAMRecord.
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- Unified flag queries.
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## [0.3.1]
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### Changed
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- Upgraded to BioAlignments v3 ([#55](https://github.com/BioJulia/XAM.jl/pull/55))
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## [0.3.0] - 2022-10-10
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## [0.3.0]
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||||
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## Added
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||||
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||||
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@ -39,6 +23,5 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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||||
- `BAM.Record` layout now matches the BAM specs ([#26](https://github.com/BioJulia/XAM.jl/pull/26))
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[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.1...HEAD
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||||
[0.3.1]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...v0.3.1
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[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...HEAD
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[0.3.0]: https://github.com/BioJulia/XAM.jl/compare/v0.2.8...v0.3.0
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@ -1,7 +1,7 @@
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name = "XAM"
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uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
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authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
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version = "0.3.1"
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version = "0.3.0"
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[deps]
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Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
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@ -17,7 +17,7 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
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[compat]
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Automa = "0.7, 0.8"
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BGZFStreams = "0.3.1"
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BioAlignments = "3"
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BioAlignments = "2.2"
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BioGenerics = "0.1"
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BioSequences = "3"
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FormatSpecimens = "1.1"
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@ -2,7 +2,6 @@
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[](https://www.repostatus.org/#active)
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[](https://github.com/BioJulia/XAM.jl/releases/latest)
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[](https://zenodo.org/badge/latestdoi/201858041)
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[](https://github.com/BioJulia/XAM.jl/blob/master/LICENSE)
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[](https://biojulia.github.io/XAM.jl/stable)
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[](https://biojulia.github.io/XAM.jl/dev/)
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@ -66,4 +65,4 @@ Your logo will show up here with a link to your website.
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|||
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||||
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||||
## Questions?
|
||||
If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.slack.com/channels/biology), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
|
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If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
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@ -64,4 +64,4 @@ Your logo will show up here with a link to your website.
|
|||
|
||||
|
||||
## Questions?
|
||||
If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.slack.com/channels/biology), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
|
||||
If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
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26
src/XAM.jl
26
src/XAM.jl
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@ -1,17 +1,29 @@
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module XAM
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using BioGenerics
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import BioGenerics: isfilled #Note: used by `ismapped`.
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export
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SAM,
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BAM
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abstract type XAMRecord end
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abstract type XAMReader <: BioGenerics.IO.AbstractReader end
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abstract type XAMWriter <: BioGenerics.IO.AbstractWriter end
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"""
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flag(record::Union{SAM.Record, BAM.Record})::UInt16
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include("flags.jl")
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Get the bitwise flags of `record`. The returned value is a `UInt16` of each flag
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being OR'd together. The possible flags are:
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0x0001 template having multiple segments in sequencing
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0x0002 each segment properly aligned according to the aligner
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0x0004 segment unmapped
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0x0008 next segment in the template unmapped
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0x0010 SEQ being reverse complemented
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0x0020 SEQ of the next segment in the template being reverse complemented
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0x0040 the first segment in the template
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0x0080 the last segment in the template
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0x0100 secondary alignment
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0x0200 not passing filters, such as platform/vendor quality controls
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0x0400 PCR or optical duplicate
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0x0800 supplementary alignment
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"""
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function flag end
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include("sam/sam.jl")
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include("bam/bam.jl")
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@ -6,8 +6,7 @@ module BAM
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using BioGenerics
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using GenomicFeatures
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using XAM.SAM
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import ..XAM: flag, XAMRecord, XAMReader, XAMWriter,
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ismapped, isprimary, ispositivestrand, isnextmapped #TODO: Deprecate import of flag queries. These were imported to preseve existing API.
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import ..XAM: flag
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import BGZFStreams
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import BioAlignments
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@ -8,9 +8,9 @@ Create a data reader of the BAM file format.
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# Arguments
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* `input`: data source
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* `index=nothing`: filepath to a random access index (currently *bai* is supported) or BAI object
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* `index=nothing`: filepath to a random access index (currently *bai* is supported)
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"""
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mutable struct Reader{T} <: XAMReader
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mutable struct Reader{T} <: BioGenerics.IO.AbstractReader
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stream::BGZFStreams.BGZFStream{T}
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header::SAM.Header
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start_offset::BGZFStreams.VirtualOffset
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@ -28,8 +28,13 @@ function BioGenerics.IO.stream(reader::Reader)
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end
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function Reader(input::IO; index=nothing)
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if isa(index, AbstractString)
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index = BAI(index)
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elseif index != nothing
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error("unrecognizable index argument")
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end
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reader = init_bam_reader(input)
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reader.index = init_bam_index(index)
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reader.index = index
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return reader
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end
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@ -120,11 +125,6 @@ function init_bam_reader(input::IO)
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return init_bam_reader(BGZFStreams.BGZFStream(input))
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end
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init_bam_index(index::AbstractString) = BAI(index)
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init_bam_index(index::BAI) = index
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init_bam_index(index::Nothing) = nothing
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init_bam_index(index) = error("unrecognizable index argument")
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function _read!(reader::Reader, record)
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unsafe_read(
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reader.stream,
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|
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@ -6,7 +6,7 @@
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Create an unfilled BAM record.
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"""
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mutable struct Record <: XAMRecord
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mutable struct Record
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# fixed-length fields (see BMA specs for the details)
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block_size::Int32
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refid::Int32
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@ -137,6 +137,37 @@ function hasflag(record::Record)
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return isfilled(record)
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end
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|
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"""
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ismapped(record::Record)::Bool
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Test if `record` is mapped.
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"""
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function ismapped(record::Record)::Bool
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return flag(record) & SAM.FLAG_UNMAP == 0
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end
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"""
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isprimary(record::Record)::Bool
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Test if `record` is a primary line of the read.
|
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This is equivalent to `flag(record) & 0x900 == 0`.
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"""
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function isprimary(record::Record)::Bool
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return flag(record) & 0x900 == 0
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end
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"""
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ispositivestrand(record::Record)::Bool
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Test if `record` is aligned to the positive strand.
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|
||||
This is equivalent to `flag(record) & 0x10 == 0`.
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||||
"""
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function ispositivestrand(record::Record)::Bool
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flag(record) & 0x10 == 0
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end
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||||
"""
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refid(record::Record)::Int
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@ -222,6 +253,15 @@ function hasrightposition(record::Record)
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return isfilled(record) && ismapped(record)
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end
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|
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"""
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isnextmapped(record::Record)::Bool
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Test if the mate/next read of `record` is mapped.
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"""
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function isnextmapped(record::Record)::Bool
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return isfilled(record) && (flag(record) & SAM.FLAG_MUNMAP == 0)
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end
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"""
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nextrefid(record::Record)::Int
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@ -390,12 +430,28 @@ end
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Get the alignment of `record`.
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"""
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function alignment(record::Record)::BioAlignments.Alignment
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if ismapped(record)
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return BioAlignments.Alignment(cigar(record), 1, position(record))
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end
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checkfilled(record)
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if !ismapped(record)
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return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
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end
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seqpos = 0
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refpos = position(record) - 1
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anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, BioAlignments.OP_START)]
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for (op, len) in zip(cigar_rle(record)...)
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if BioAlignments.ismatchop(op)
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seqpos += len
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refpos += len
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elseif BioAlignments.isinsertop(op)
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seqpos += len
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elseif BioAlignments.isdeleteop(op)
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refpos += len
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else
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error("operation $(op) is not supported")
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end
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push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, op))
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end
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return BioAlignments.Alignment(anchors)
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end
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|
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function hasalignment(record::Record)
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return ismapped(record)
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|
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@ -10,7 +10,7 @@ Create a data writer of the BAM file format.
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* `output`: data sink
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* `header`: SAM header object
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"""
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mutable struct Writer <: XAMWriter
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mutable struct Writer <: BioGenerics.IO.AbstractWriter
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stream::BGZFStreams.BGZFStream
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end
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|
|
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226
src/flags.jl
226
src/flags.jl
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@ -1,226 +0,0 @@
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# Flags
|
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# =========
|
||||
#
|
||||
|
||||
"""
|
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flag(record::XAMRecord})::UInt16
|
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|
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Get the bitwise flags of `record`.
|
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The returned value is a `UInt16` of each flag being OR'd together.
|
||||
The possible flags are:
|
||||
|
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0x0001 template having multiple segments in sequencing
|
||||
0x0002 each segment properly aligned according to the aligner
|
||||
0x0004 segment unmapped
|
||||
0x0008 next segment in the template unmapped
|
||||
0x0010 SEQ being reverse complemented
|
||||
0x0020 SEQ of the next segment in the template being reverse complemented
|
||||
0x0040 the first segment in the template
|
||||
0x0080 the last segment in the template
|
||||
0x0100 secondary alignment
|
||||
0x0200 not passing filters, such as platform/vendor quality controls
|
||||
0x0400 PCR or optical duplicate
|
||||
0x0800 supplementary alignment
|
||||
"""
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function flag end
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|
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# Bitwise flags (or FLAG).
|
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for (name, bits, doc) in [
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(:PAIRED, UInt16(0x001), "the read is paired in sequencing, no matter whether it is mapped in a pair"),
|
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(:PROPER_PAIR, UInt16(0x002), "the read is mapped in a proper pair" ),
|
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(:UNMAP, UInt16(0x004), "the read itself is unmapped; conflictive with FLAG_PROPER_PAIR" ),
|
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(:MUNMAP, UInt16(0x008), "the mate is unmapped" ),
|
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(:REVERSE, UInt16(0x010), "the read is mapped to the reverse strand" ),
|
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(:MREVERSE, UInt16(0x020), "the mate is mapped to the reverse strand" ),
|
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(:READ1, UInt16(0x040), "this is read1" ),
|
||||
(:READ2, UInt16(0x080), "this is read2" ),
|
||||
(:SECONDARY, UInt16(0x100), "not primary alignment" ),
|
||||
(:QCFAIL, UInt16(0x200), "QC failure" ),
|
||||
(:DUP, UInt16(0x400), "optical or PCR duplicate" ),
|
||||
(:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment" ),]
|
||||
@assert bits isa UInt16 "The bits must be of type UInt16."
|
||||
sym = Symbol("FLAG_", name)
|
||||
docstring = """ $sym
|
||||
SAM/BAM flag: $doc
|
||||
|
||||
See also: [`flag`](@ref)
|
||||
"""
|
||||
@eval begin
|
||||
@doc $(docstring) const $(sym) = $(bits)
|
||||
end
|
||||
end
|
||||
|
||||
"""
|
||||
ispaired(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record`'s template has multiple segments in sequencing.
|
||||
"""
|
||||
function ispaired(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_PAIRED == FLAG_PAIRED
|
||||
end
|
||||
|
||||
"""
|
||||
isproperpair(record::XAMRecord)::Bool
|
||||
|
||||
Query whether each segment of the `record`'s template properly aligned according to the aligner.
|
||||
"""
|
||||
function isproperpair(record::XAMRecord)::Bool
|
||||
return flag(record) & PROPER_PAIR == PROPER_PAIR
|
||||
end
|
||||
|
||||
"""
|
||||
isunmapped(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is unmapped.
|
||||
"""
|
||||
function isunmapped(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_UNMAP == FLAG_UNMAP
|
||||
end
|
||||
|
||||
"""
|
||||
ismapped(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is mapped.
|
||||
"""
|
||||
function ismapped(record::XAMRecord)::Bool
|
||||
# return flag(record) & FLAG_UNMAP == 0
|
||||
return isfilled(record) && (flag(record) & FLAG_UNMAP == 0)
|
||||
end
|
||||
|
||||
"""
|
||||
ismateunmapped(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record`'s mate is unmapped.
|
||||
"""
|
||||
function ismateunmapped(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_MUNMAP == FLAG_MUNMAP
|
||||
end
|
||||
|
||||
"""
|
||||
isnextmapped(record::XAMRecord)::Bool
|
||||
|
||||
Test if the mate/next read of `record` is mapped.
|
||||
"""
|
||||
function isnextmapped(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_MUNMAP == 0
|
||||
end
|
||||
|
||||
"""
|
||||
isreverse(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is mapped to the reverse strand.
|
||||
"""
|
||||
function isreverse(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_REVERSE == FLAG_REVERSE
|
||||
end
|
||||
|
||||
"""
|
||||
isforward(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is mapped to the forward strand.
|
||||
"""
|
||||
function isforward(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_REVERSE == 0
|
||||
end
|
||||
|
||||
"""
|
||||
ispositivestrand(record::XAMRecord)::Bool
|
||||
|
||||
Query whether `record` is aligned to the positive strand.
|
||||
"""
|
||||
function ispositivestrand(record::XAMRecord)::Bool
|
||||
return isforward(record)
|
||||
end
|
||||
|
||||
"""
|
||||
ispositivestrand(record::XAMRecord)::Bool
|
||||
|
||||
Query whether `record` is aligned to the negative strand.
|
||||
"""
|
||||
function isnegativestrand(record::XAMRecord)::Bool
|
||||
return isreverse(record)
|
||||
end
|
||||
|
||||
"""
|
||||
ismatereverse(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record`'s mate is mapped to the reverse strand.
|
||||
"""
|
||||
function ismatereverse(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_MREVERSE == FLAG_MREVERSE
|
||||
end
|
||||
|
||||
"""
|
||||
isread1(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is read1.
|
||||
"""
|
||||
function isread1(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_READ1 == FLAG_READ1
|
||||
end
|
||||
|
||||
"""
|
||||
isread2(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is read2.
|
||||
"""
|
||||
function isread2(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_READ2 == FLAG_READ2
|
||||
end
|
||||
|
||||
"""
|
||||
issecondaryalignment(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is a secondary alignment.
|
||||
"""
|
||||
function issecondaryalignment(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_SECONDARY == FLAG_SECONDARY
|
||||
end
|
||||
|
||||
"""
|
||||
isprimaryalignment(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is the primary alignment.
|
||||
"""
|
||||
function isprimaryalignment(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_SECONDARY == 0
|
||||
end
|
||||
|
||||
"""
|
||||
isqcfail(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` did not pass filters, such as platform/vendor quality controls.
|
||||
"""
|
||||
function isqcfail(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_QCFAIL == FLAG_QCFAIL
|
||||
end
|
||||
|
||||
"""
|
||||
isduplicate(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is a PCR or optical duplicate.
|
||||
"""
|
||||
function isduplicate(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_DUP == FLAG_DUP
|
||||
end
|
||||
|
||||
"""
|
||||
issupplementaryalignment(record::XAMRecord)::Bool
|
||||
|
||||
Query whether the `record` is a supplementary alignment.
|
||||
"""
|
||||
function issupplementaryalignment(record::XAMRecord)::Bool
|
||||
return flag(record) & FLAG_SUPPLEMENTARY == FLAG_SUPPLEMENTARY
|
||||
end
|
||||
|
||||
"""
|
||||
isprimary(record::XAMRecord)::Bool
|
||||
|
||||
Query whether `record` is a primary line of the read.
|
||||
|
||||
This is equivalent to `flag(record) & 0x900 == 0`.
|
||||
"""
|
||||
function isprimary(record::XAMRecord)::Bool
|
||||
return flag(record) & 0x900 == 0
|
||||
end
|
||||
29
src/sam/flags.jl
Normal file
29
src/sam/flags.jl
Normal file
|
|
@ -0,0 +1,29 @@
|
|||
# SAM Flags
|
||||
# =========
|
||||
#
|
||||
# Bitwise flags (or FLAG).
|
||||
|
||||
for (name, bits, doc) in [
|
||||
(:PAIRED, UInt16(0x001), "the read is paired in sequencing, no matter whether it is mapped in a pair"),
|
||||
(:PROPER_PAIR, UInt16(0x002), "the read is mapped in a proper pair" ),
|
||||
(:UNMAP, UInt16(0x004), "the read itself is unmapped; conflictive with SAM.FLAG_PROPER_PAIR" ),
|
||||
(:MUNMAP, UInt16(0x008), "the mate is unmapped" ),
|
||||
(:REVERSE, UInt16(0x010), "the read is mapped to the reverse strand" ),
|
||||
(:MREVERSE, UInt16(0x020), "the mate is mapped to the reverse strand" ),
|
||||
(:READ1, UInt16(0x040), "this is read1" ),
|
||||
(:READ2, UInt16(0x080), "this is read2" ),
|
||||
(:SECONDARY, UInt16(0x100), "not primary alignment" ),
|
||||
(:QCFAIL, UInt16(0x200), "QC failure" ),
|
||||
(:DUP, UInt16(0x400), "optical or PCR duplicate" ),
|
||||
(:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment" ),]
|
||||
@assert bits isa UInt16 "The bits must be of type UInt16."
|
||||
sym = Symbol("FLAG_", name)
|
||||
docstring = """ $sym
|
||||
SAM/BAM flag: $doc
|
||||
|
||||
See also: [`flag`](@ref)
|
||||
"""
|
||||
@eval begin
|
||||
@doc $(docstring) const $(sym) = $(bits)
|
||||
end
|
||||
end
|
||||
|
|
@ -1,7 +1,7 @@
|
|||
# SAM Reader
|
||||
# =========
|
||||
|
||||
mutable struct Reader{S <: TranscodingStream} <: XAMReader
|
||||
mutable struct Reader{S <: TranscodingStream} <: BioGenerics.IO.AbstractReader
|
||||
state::State{S}
|
||||
header::Header
|
||||
end
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
# SAM Record
|
||||
# ==========
|
||||
|
||||
mutable struct Record <: XAMRecord
|
||||
mutable struct Record
|
||||
# Data and filled range.
|
||||
data::Vector{UInt8}
|
||||
filled::UnitRange{Int} # Note: Specifies the data in use.
|
||||
|
|
@ -159,6 +159,26 @@ function hasflag(record::Record)
|
|||
return isfilled(record)
|
||||
end
|
||||
|
||||
"""
|
||||
ismapped(record::Record)::Bool
|
||||
|
||||
Test if `record` is mapped.
|
||||
"""
|
||||
function ismapped(record::Record)::Bool
|
||||
return isfilled(record) && (flag(record) & FLAG_UNMAP == 0)
|
||||
end
|
||||
|
||||
"""
|
||||
isprimary(record::Record)::Bool
|
||||
|
||||
Test if `record` is a primary line of the read.
|
||||
|
||||
This is equivalent to `flag(record) & 0x900 == 0`.
|
||||
"""
|
||||
function isprimary(record::Record)::Bool
|
||||
return flag(record) & 0x900 == 0
|
||||
end
|
||||
|
||||
"""
|
||||
refname(record::Record)::String
|
||||
|
||||
|
|
@ -207,6 +227,15 @@ function hasrightposition(record::Record)
|
|||
return hasposition(record) && hasalignment(record)
|
||||
end
|
||||
|
||||
"""
|
||||
isnextmapped(record::Record)::Bool
|
||||
|
||||
Test if the mate/next read of `record` is mapped.
|
||||
"""
|
||||
function isnextmapped(record::Record)::Bool
|
||||
return isfilled(record) && (flag(record) & FLAG_MUNMAP == 0)
|
||||
end
|
||||
|
||||
"""
|
||||
nextrefname(record::Record)::String
|
||||
|
||||
|
|
|
|||
|
|
@ -11,8 +11,7 @@ import BioGenerics.Exceptions: missingerror
|
|||
import BioGenerics.Automa: State
|
||||
import BioSequences
|
||||
import TranscodingStreams: TranscodingStreams, TranscodingStream
|
||||
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: flag
|
||||
|
||||
using Printf: @sprintf
|
||||
|
||||
|
|
@ -49,6 +48,7 @@ function unsafe_parse_decimal(::Type{T}, data::Vector{UInt8}, range::UnitRange{I
|
|||
end
|
||||
|
||||
|
||||
include("flags.jl")
|
||||
include("metainfo.jl")
|
||||
include("record.jl")
|
||||
include("header.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 <: XAMWriter
|
||||
mutable struct Writer <: BioGenerics.IO.AbstractWriter
|
||||
stream::IO
|
||||
|
||||
function Writer(output::IO, header::Header=Header())
|
||||
|
|
|
|||
|
|
@ -79,10 +79,10 @@
|
|||
@test BAM.flag(record) === UInt16(16)
|
||||
@test BAM.cigar(record) == "27M1D73M"
|
||||
@test BAM.alignment(record) == Alignment([
|
||||
AlignmentAnchor( 0, 1, 0, OP_START),
|
||||
AlignmentAnchor( 27, 28, 27, OP_MATCH),
|
||||
AlignmentAnchor( 27, 29, 28, OP_DELETE),
|
||||
AlignmentAnchor(100, 102, 101, OP_MATCH)])
|
||||
AlignmentAnchor( 0, 1, OP_START),
|
||||
AlignmentAnchor( 27, 28, OP_MATCH),
|
||||
AlignmentAnchor( 27, 29, OP_DELETE),
|
||||
AlignmentAnchor(100, 102, OP_MATCH)])
|
||||
@test record["XG"] == 1
|
||||
@test record["XM"] == 5
|
||||
@test record["XN"] == 0
|
||||
|
|
@ -209,14 +209,6 @@
|
|||
close(reader)
|
||||
close(writer)
|
||||
|
||||
|
||||
# Check that EOF_BLOCK gets written.
|
||||
nbytes = filesize(path)
|
||||
@test BAM.BGZFStreams.EOF_BLOCK == open(path) do io
|
||||
seek(io, nbytes - length(BAM.BGZFStreams.EOF_BLOCK))
|
||||
read(io)
|
||||
end
|
||||
|
||||
reader = open(BAM.Reader, path)
|
||||
|
||||
@test header(reader) == header_original
|
||||
|
|
@ -249,21 +241,6 @@
|
|||
|
||||
end
|
||||
|
||||
@testset "BAI" begin
|
||||
|
||||
filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
|
||||
|
||||
index = BAM.BAI(filepath * ".bai")
|
||||
reader = open(BAM.Reader, filepath, index=index)
|
||||
|
||||
@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
|
||||
|
||||
close(reader)
|
||||
|
||||
@test_throws ErrorException open(BAM.Reader, filepath, index=1234)
|
||||
|
||||
end
|
||||
|
||||
@testset "Random access" begin
|
||||
filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
|
||||
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
||||
|
|
|
|||
|
|
@ -104,10 +104,10 @@
|
|||
@test SAM.flag(record) == 16
|
||||
@test SAM.cigar(record) == "27M1D73M"
|
||||
@test SAM.alignment(record) == Alignment([
|
||||
AlignmentAnchor( 0, 1, 0, OP_START),
|
||||
AlignmentAnchor( 27, 28, 27, OP_MATCH),
|
||||
AlignmentAnchor( 27, 29, 28, OP_DELETE),
|
||||
AlignmentAnchor(100, 102, 101, OP_MATCH)])
|
||||
AlignmentAnchor( 0, 1, OP_START),
|
||||
AlignmentAnchor( 27, 28, OP_MATCH),
|
||||
AlignmentAnchor( 27, 29, OP_DELETE),
|
||||
AlignmentAnchor(100, 102, OP_MATCH)])
|
||||
@test record["XG"] == 1
|
||||
@test record["XM"] == 5
|
||||
@test record["XN"] == 0
|
||||
|
|
|
|||
Loading…
Reference in a new issue