millironx/XAM.jl
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added method for handling different bam index types

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This commit is contained in:
Jonathan Bieler 2022-10-13 15:06:39 +02:00
parent 946e77a734
commit 93a6b60d26
2 changed files with 21 additions and 6 deletions
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12
src/bam/reader.jl
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@ -28,13 +28,8 @@ function BioGenerics.IO.stream(reader::Reader)
end end
function Reader(input::IO; index=nothing) function Reader(input::IO; index=nothing)
if isa(index, AbstractString)
index = BAI(index)
elseif index != nothing
error("unrecognizable index argument")
end
reader = init_bam_reader(input) reader = init_bam_reader(input)
reader.index = index reader.index = init_bam_index(index)
return reader return reader
end end
@ -125,6 +120,11 @@ function init_bam_reader(input::IO)
return init_bam_reader(BGZFStreams.BGZFStream(input)) return init_bam_reader(BGZFStreams.BGZFStream(input))
end end
init_bam_index(index::AbstractString) = BAI(index)
init_bam_index(index::BAI) = index
init_bam_index(index::Nothing) = nothing
init_bam_index(index) = error("unrecognizable index argument")
function _read!(reader::Reader, record) function _read!(reader::Reader, record)
unsafe_read( unsafe_read(
reader.stream, reader.stream,

15
test/test_bam.jl
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@ -241,6 +241,21 @@
end end
@testset "BAI" begin
filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
index = BAM.BAI(filepath * ".bai")
reader = open(BAM.Reader, filepath, index=index)
@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
close(reader)
@test_throws ErrorException open(BAM.Reader, filepath, index=1234)
end
@testset "Random access" begin @testset "Random access" begin
filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam") filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
reader = open(BAM.Reader, filepath, index=filepath * ".bai") reader = open(BAM.Reader, filepath, index=filepath * ".bai")