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added method for handling different bam index types
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2 changed files with 21 additions and 6 deletions
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@ -28,13 +28,8 @@ function BioGenerics.IO.stream(reader::Reader)
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end
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function Reader(input::IO; index=nothing)
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if isa(index, AbstractString)
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index = BAI(index)
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elseif index != nothing
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error("unrecognizable index argument")
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end
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reader = init_bam_reader(input)
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reader.index = index
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reader.index = init_bam_index(index)
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return reader
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end
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@ -125,6 +120,11 @@ function init_bam_reader(input::IO)
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return init_bam_reader(BGZFStreams.BGZFStream(input))
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end
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init_bam_index(index::AbstractString) = BAI(index)
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init_bam_index(index::BAI) = index
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init_bam_index(index::Nothing) = nothing
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init_bam_index(index) = error("unrecognizable index argument")
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function _read!(reader::Reader, record)
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unsafe_read(
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reader.stream,
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@ -241,6 +241,21 @@
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end
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@testset "BAI" begin
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filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
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index = BAM.BAI(filepath * ".bai")
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reader = open(BAM.Reader, filepath, index=index)
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@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
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close(reader)
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@test_throws ErrorException open(BAM.Reader, filepath, index=1234)
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end
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@testset "Random access" begin
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filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
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reader = open(BAM.Reader, filepath, index=filepath * ".bai")
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