Merge branch 'master' into develop

# Conflicts:
#	Project.toml
#	test/runtests.jl

Project.toml

@@ -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"

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.

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