diff --git a/Project.toml b/Project.toml index 292961d..19c279d 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "XAM" uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c" authors = ["Kenta Sato ", "Ben J. Ward ", "CiarĂ¡n O'Mara "] -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" diff --git a/test/runtests.jl b/test/runtests.jl index 75bffe5..d0a243e 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -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. diff --git a/test/test_issues.jl b/test/test_issues.jl new file mode 100644 index 0000000..c42bf73 --- /dev/null +++ b/test/test_issues.jl @@ -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