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GenomicInterval type
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4 changed files with 6 additions and 6 deletions
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@ -20,8 +20,8 @@ BGZFStreams = "0.3"
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BioAlignments = "2"
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BioGenerics = "0.1"
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BioSequences = "2.0.4"
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GenomicFeatures = "2"
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Indexes = "0.1"
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GenomicFeatures = "3"
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Indexes = "0.3"
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TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
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julia = "1"
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@ -220,7 +220,7 @@ close(reader)
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## Getting records overlapping genomic features
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The `eachoverlap` method also accepts the `Interval` type defined in [GenomicFeatures.jl](https://github.com/BioJulia/GenomicFeatures.jl).
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The `eachoverlap` method also accepts the `GenomicInterval` type defined in [GenomicFeatures.jl](https://github.com/BioJulia/GenomicFeatures.jl).
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This allows you to do things like first read in the genomic features from a GFF3 file, and then for each feature, iterate over all the BAM records that overlap with that feature.
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@ -15,12 +15,12 @@ function Base.eltype(::Type{OverlapIterator{T}}) where T
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return Record
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end
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function GenomicFeatures.eachoverlap(reader::Reader, interval::Interval)
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function GenomicFeatures.eachoverlap(reader::Reader, interval::GenomicInterval)
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return GenomicFeatures.eachoverlap(reader, GenomicFeatures.seqname(interval), GenomicFeatures.leftposition(interval):GenomicFeatures.rightposition(interval))
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end
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function GenomicFeatures.eachoverlap(reader::Reader, interval)
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return GenomicFeatures.eachoverlap(reader, convert(Interval, interval))
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return GenomicFeatures.eachoverlap(reader, convert(GenomicInterval, interval))
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end
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function GenomicFeatures.eachoverlap(reader::Reader, refname::AbstractString, interval::UnitRange)
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@ -246,7 +246,7 @@
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reader = open(BAM.Reader, filepath, index=filepath * ".bai")
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@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
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@test isa(eachoverlap(reader, GenomicFeatures.Interval("chr1", 1, 100)), BAM.OverlapIterator)
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@test isa(eachoverlap(reader, GenomicFeatures.GenomicInterval("chr1", 1, 100)), BAM.OverlapIterator)
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# expected values are counted using samtools
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for (refname, interval, expected) in [
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