millironx/XAM.jl
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Merge branch 'hotfix/issue-31'

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This commit is contained in:
Ciarán O'Mara 2022-08-15 15:32:07 +10:00
commit 4490e7c890
3 changed files with 17 additions and 2 deletions
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5
Project.toml
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@ -1,7 +1,7 @@
name = "XAM" name = "XAM"
uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c" 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>"] authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
version = "0.2.7" version = "0.2.8"
[deps] [deps]
Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
@ -16,10 +16,11 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
[compat] [compat]
Automa = "0.7, 0.8" Automa = "0.7, 0.8"
BGZFStreams = "0.3" BGZFStreams = "0.3.1"
BioAlignments = "2" BioAlignments = "2"
BioGenerics = "0.1" BioGenerics = "0.1"
BioSequences = "2.0.4" BioSequences = "2.0.4"
FormatSpecimens = "1.1"
GenomicFeatures = "2" GenomicFeatures = "2"
Indexes = "0.1" Indexes = "0.1"
TranscodingStreams = "0.6, 0.7, 0.8, 0.9" TranscodingStreams = "0.6, 0.7, 0.8, 0.9"

1
test/runtests.jl
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@ -25,3 +25,4 @@ end
include("test_sam.jl") include("test_sam.jl")
include("test_bam.jl") include("test_bam.jl")
include("test_issues.jl")

13
test/test_issues.jl Normal file
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@ -0,0 +1,13 @@
@testset "Issues" begin
# https://github.com/BioJulia/XAM.jl/issues/31
path_bam = joinpath(path_of_format("BAM"), "SRR7993829_1.100K.forward.bam")
open(BAM.Reader, path_bam, index = path_bam * ".bai") do reader
@test count(overlap -> true, eachoverlap(reader, "JH584304.1", 51000:51200)) == 0
@test count(overlap -> true, eachoverlap(reader, "JH584304.1", 51000:51715)) == 1
end
end