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Release 0.3.1 #57

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merged 7 commits into from
Oct 14, 2022
Merged

Release 0.3.1 #57

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e6f542a
Change alignment getter for BAM.Record to use existing cigar constructor
MillironX Oct 10, 2022
9720fd0
Bump BioAlignments version compat to 3
MillironX Oct 10, 2022
f7b9d9f
Update tests to use new AlignmentAnchor structure
MillironX Oct 10, 2022
32e3213
Update CHANGELOG
MillironX Oct 10, 2022
e2b22be
Merge pull request #55 from MillironX/feature/bioalignments-3
MillironX Oct 13, 2022
1c57e9b
Bump version number in Project.toml to 0.3.1
MillironX Oct 13, 2022
fe83a74
Update CHANGELOG for v0.3.1
MillironX Oct 13, 2022
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11 changes: 9 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -7,7 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [Unreleased]

## [0.3.0]
## [0.3.1]

### Changed

- Upgraded to BioAlignments v3 ([#55](https://github.com/BioJulia/XAM.jl/pull/55))

## [0.3.0] - 2022-10-10

## Added

Expand All @@ -23,5 +29,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- `BAM.Record` layout now matches the BAM specs ([#26](https://github.com/BioJulia/XAM.jl/pull/26))

[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...HEAD
[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.1...HEAD
[0.3.1]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...v0.3.1
[0.3.0]: https://github.com/BioJulia/XAM.jl/compare/v0.2.8...v0.3.0
4 changes: 2 additions & 2 deletions Project.toml
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@@ -1,7 +1,7 @@
name = "XAM"
uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
authors = ["Kenta Sato <[email protected]>", "Ben J. Ward <[email protected]>", "Ciarán O'Mara <[email protected]>"]
version = "0.3.0"
version = "0.3.1"

[deps]
Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
Expand All @@ -17,7 +17,7 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
[compat]
Automa = "0.7, 0.8"
BGZFStreams = "0.3.1"
BioAlignments = "2.2"
BioAlignments = "3"
BioGenerics = "0.1"
BioSequences = "3"
FormatSpecimens = "1.1"
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24 changes: 4 additions & 20 deletions src/bam/record.jl
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Expand Up @@ -430,27 +430,11 @@ end
Get the alignment of `record`.
"""
function alignment(record::Record)::BioAlignments.Alignment
checkfilled(record)
if !ismapped(record)
return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
end
seqpos = 0
refpos = position(record) - 1
anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, BioAlignments.OP_START)]
for (op, len) in zip(cigar_rle(record)...)
if BioAlignments.ismatchop(op)
seqpos += len
refpos += len
elseif BioAlignments.isinsertop(op)
seqpos += len
elseif BioAlignments.isdeleteop(op)
refpos += len
else
error("operation $(op) is not supported")
end
push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, op))
if ismapped(record)
return BioAlignments.Alignment(cigar(record), 1, position(record))
end
return BioAlignments.Alignment(anchors)

return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
end

function hasalignment(record::Record)
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8 changes: 4 additions & 4 deletions test/test_bam.jl
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Expand Up @@ -79,10 +79,10 @@
@test BAM.flag(record) === UInt16(16)
@test BAM.cigar(record) == "27M1D73M"
@test BAM.alignment(record) == Alignment([
AlignmentAnchor( 0, 1, OP_START),
AlignmentAnchor( 27, 28, OP_MATCH),
AlignmentAnchor( 27, 29, OP_DELETE),
AlignmentAnchor(100, 102, OP_MATCH)])
AlignmentAnchor( 0, 1, 0, OP_START),
AlignmentAnchor( 27, 28, 27, OP_MATCH),
AlignmentAnchor( 27, 29, 28, OP_DELETE),
AlignmentAnchor(100, 102, 101, OP_MATCH)])
@test record["XG"] == 1
@test record["XM"] == 5
@test record["XN"] == 0
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8 changes: 4 additions & 4 deletions test/test_sam.jl
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Expand Up @@ -104,10 +104,10 @@
@test SAM.flag(record) == 16
@test SAM.cigar(record) == "27M1D73M"
@test SAM.alignment(record) == Alignment([
AlignmentAnchor( 0, 1, OP_START),
AlignmentAnchor( 27, 28, OP_MATCH),
AlignmentAnchor( 27, 29, OP_DELETE),
AlignmentAnchor(100, 102, OP_MATCH)])
AlignmentAnchor( 0, 1, 0, OP_START),
AlignmentAnchor( 27, 28, 27, OP_MATCH),
AlignmentAnchor( 27, 29, 28, OP_DELETE),
AlignmentAnchor(100, 102, 101, OP_MATCH)])
@test record["XG"] == 1
@test record["XM"] == 5
@test record["XN"] == 0
Expand Down