From 7609f6e24dedfcdb573bfab462ec7ffeed381bf3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 15 Aug 2022 09:29:13 +1000 Subject: [PATCH 1/3] Increment version --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 0c21bf9..b41a6f0 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 ", "Ciarán O'Mara "] -version = "0.2.7" +version = "0.2.8" [deps] Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b" From 99aa013c2b6687ab466a92a694a5e13cd1ff7dd9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Mon, 15 Aug 2022 12:30:27 +1000 Subject: [PATCH 2/3] Add tests for issue #31 Test for expected results as described in https://github.com/BioJulia/XAM.jl/issues/31. --- Project.toml | 1 + test/runtests.jl | 1 + test/test_issues.jl | 13 +++++++++++++ 3 files changed, 15 insertions(+) create mode 100644 test/test_issues.jl diff --git a/Project.toml b/Project.toml index b41a6f0..2e12e98 100644 --- a/Project.toml +++ b/Project.toml @@ -20,6 +20,7 @@ BGZFStreams = "0.3" BioAlignments = "2" BioGenerics = "0.1" BioSequences = "2.0.4" +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 970c3a1..16f4725 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -25,3 +25,4 @@ end include("test_sam.jl") include("test_bam.jl") +include("test_issues.jl") 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 From 0cc0405ca02a7087c7b157665570152eda6562fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= Date: Sat, 2 Jul 2022 16:31:06 +1000 Subject: [PATCH 3/3] Increment BGZFStreams compatibility --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 2e12e98..9b23f8f 100644 --- a/Project.toml +++ b/Project.toml @@ -16,7 +16,7 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" [compat] Automa = "0.7, 0.8" -BGZFStreams = "0.3" +BGZFStreams = "0.3.1" BioAlignments = "2" BioGenerics = "0.1" BioSequences = "2.0.4"