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5 changed files with 23 additions and 32 deletions
11
CHANGELOG.md
11
CHANGELOG.md
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@ -7,7 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [Unreleased]
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## [0.3.0]
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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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## Added
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@ -23,5 +29,6 @@ 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/v0.3.0...HEAD
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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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[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 = "0.3.0"
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version = "0.3.1"
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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 = "2.2"
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BioAlignments = "3"
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BioGenerics = "0.1"
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BioSequences = "3"
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FormatSpecimens = "1.1"
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@ -430,27 +430,11 @@ 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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checkfilled(record)
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if !ismapped(record)
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return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
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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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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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return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
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end
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function hasalignment(record::Record)
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@ -79,10 +79,10 @@
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@test BAM.flag(record) === UInt16(16)
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@test BAM.cigar(record) == "27M1D73M"
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@test BAM.alignment(record) == Alignment([
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AlignmentAnchor( 0, 1, OP_START),
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AlignmentAnchor( 27, 28, OP_MATCH),
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AlignmentAnchor( 27, 29, OP_DELETE),
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AlignmentAnchor(100, 102, OP_MATCH)])
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AlignmentAnchor( 0, 1, 0, OP_START),
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AlignmentAnchor( 27, 28, 27, OP_MATCH),
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AlignmentAnchor( 27, 29, 28, OP_DELETE),
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AlignmentAnchor(100, 102, 101, OP_MATCH)])
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@test record["XG"] == 1
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@test record["XM"] == 5
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@test record["XN"] == 0
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@ -104,10 +104,10 @@
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@test SAM.flag(record) == 16
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@test SAM.cigar(record) == "27M1D73M"
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@test SAM.alignment(record) == Alignment([
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AlignmentAnchor( 0, 1, OP_START),
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AlignmentAnchor( 27, 28, OP_MATCH),
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AlignmentAnchor( 27, 29, OP_DELETE),
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AlignmentAnchor(100, 102, OP_MATCH)])
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AlignmentAnchor( 0, 1, 0, OP_START),
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AlignmentAnchor( 27, 28, 27, OP_MATCH),
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AlignmentAnchor( 27, 29, 28, OP_DELETE),
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AlignmentAnchor(100, 102, 101, OP_MATCH)])
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@test record["XG"] == 1
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@test record["XM"] == 5
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@test record["XN"] == 0
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