millironx/XAM.jl
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Bring up-to-date with master branch of BioAlignments.jl

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Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
This commit is contained in:
Thomas A. Christensen II 2022-01-27 11:11:45 -06:00
parent e5c553aa45
commit de252188e8
Signed by: millironx
GPG key ID: 139C07724802BC5D
3 changed files with 14 additions and 11 deletions
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7
src/bam/record.jl
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@ -436,7 +436,9 @@ function alignment(record::Record)::BioAlignments.Alignment
end end
seqpos = 0 seqpos = 0
refpos = position(record) - 1 refpos = position(record) - 1
anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, BioAlignments.OP_START)] alnpos = 0
anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, alnpos, BioAlignments.OP_START)]
for (op, len) in zip(cigar_rle(record)...) for (op, len) in zip(cigar_rle(record)...)
if BioAlignments.ismatchop(op) if BioAlignments.ismatchop(op)
seqpos += len seqpos += len
@ -448,7 +450,8 @@ function alignment(record::Record)::BioAlignments.Alignment
else else
error("operation $(op) is not supported") error("operation $(op) is not supported")
end end
push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, op)) alnpos += len
push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, alnpos, op))
end end
return BioAlignments.Alignment(anchors) return BioAlignments.Alignment(anchors)
end end

8
test/test_bam.jl
View file

@ -79,10 +79,10 @@
@test BAM.flag(record) === UInt16(16) @test BAM.flag(record) === UInt16(16)
@test BAM.cigar(record) == "27M1D73M" @test BAM.cigar(record) == "27M1D73M"
@test BAM.alignment(record) == Alignment([ @test BAM.alignment(record) == Alignment([
AlignmentAnchor( 0, 1, OP_START), AlignmentAnchor( 0, 1, 0, OP_START),
AlignmentAnchor( 27, 28, OP_MATCH), AlignmentAnchor( 27, 28, 27, OP_MATCH),
AlignmentAnchor( 27, 29, OP_DELETE), AlignmentAnchor( 27, 29, 28, OP_DELETE),
AlignmentAnchor(100, 102, OP_MATCH)]) AlignmentAnchor(100, 102, 101, OP_MATCH)])
@test record["XG"] == 1 @test record["XG"] == 1
@test record["XM"] == 5 @test record["XM"] == 5
@test record["XN"] == 0 @test record["XN"] == 0

8
test/test_sam.jl
View file

@ -104,10 +104,10 @@
@test SAM.flag(record) == 16 @test SAM.flag(record) == 16
@test SAM.cigar(record) == "27M1D73M" @test SAM.cigar(record) == "27M1D73M"
@test SAM.alignment(record) == Alignment([ @test SAM.alignment(record) == Alignment([
AlignmentAnchor( 0, 1, OP_START), AlignmentAnchor( 0, 1, 0, OP_START),
AlignmentAnchor( 27, 28, OP_MATCH), AlignmentAnchor( 27, 28, 27, OP_MATCH),
AlignmentAnchor( 27, 29, OP_DELETE), AlignmentAnchor( 27, 29, 28, OP_DELETE),
AlignmentAnchor(100, 102, OP_MATCH)]) AlignmentAnchor(100, 102, 101, OP_MATCH)])
@test record["XG"] == 1 @test record["XG"] == 1
@test record["XM"] == 5 @test record["XM"] == 5
@test record["XN"] == 0 @test record["XN"] == 0