millironx/XAM.jl
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Merge branch 'master' into develop

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# Conflicts:
#	Project.toml
#	test/runtests.jl
This commit is contained in:
Ciarán O'Mara 2022-08-15 15:34:24 +10:00
commit 8424757cc2
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"
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 = "0.2.7"
version = "0.2.8"
[deps]
Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
@ -16,10 +16,11 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
[compat]
Automa = "0.7, 0.8"
BGZFStreams = "0.3"
BGZFStreams = "0.3.1"
BioAlignments = "2.2"
BioGenerics = "0.1"
BioSequences = "3"
FormatSpecimens = "1.1"
GenomicFeatures = "2"
Indexes = "0.1"
TranscodingStreams = "0.6, 0.7, 0.8, 0.9"

1
test/runtests.jl
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@ -27,6 +27,7 @@ end
@testset "XAM" begin
include("test_sam.jl")
include("test_bam.jl")
include("test_issues.jl")
include("test_crosscheck.jl")
# Include doctests.

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