Merge pull request #57 from BioJulia/release/0.3.1

Release v0.3.1

Author: CiaranOMara

CHANGELOG.md

@@ -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
 
@@ -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

Project.toml

@@ -1,7 +1,7 @@
 name = "XAM"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "0.3.0"
+version = "0.3.1"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
@@ -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"

src/bam/record.jl

@@ -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)

test/test_bam.jl

@@ -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

test/test_sam.jl

@@ -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