GenomicInterval type

Project.toml

@@ -20,8 +20,8 @@ BGZFStreams = "0.3"
 BioAlignments = "2"
 BioGenerics = "0.1"
 BioSequences = "2.0.4"
-GenomicFeatures = "2"
-Indexes = "0.1"
+GenomicFeatures = "3"
+Indexes = "0.3"
 TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
 julia = "1"
 

docs/src/man/hts-files.md

@@ -220,7 +220,7 @@ close(reader)
 
 ## Getting records overlapping genomic features
 
-The `eachoverlap` method also accepts the `Interval` type defined in [GenomicFeatures.jl](https://github.com/BioJulia/GenomicFeatures.jl).
+The `eachoverlap` method also accepts the `GenomicInterval` type defined in [GenomicFeatures.jl](https://github.com/BioJulia/GenomicFeatures.jl).
 
 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.
 

src/bam/overlap.jl

@@ -15,12 +15,12 @@ function Base.eltype(::Type{OverlapIterator{T}}) where T
     return Record
 end
 
-function GenomicFeatures.eachoverlap(reader::Reader, interval::Interval)
+function GenomicFeatures.eachoverlap(reader::Reader, interval::GenomicInterval)
     return GenomicFeatures.eachoverlap(reader, GenomicFeatures.seqname(interval), GenomicFeatures.leftposition(interval):GenomicFeatures.rightposition(interval))
 end
 
 function GenomicFeatures.eachoverlap(reader::Reader, interval)
-    return GenomicFeatures.eachoverlap(reader, convert(Interval, interval))
+    return GenomicFeatures.eachoverlap(reader, convert(GenomicInterval, interval))
 end
 
 function GenomicFeatures.eachoverlap(reader::Reader, refname::AbstractString, interval::UnitRange)

test/test_bam.jl

@@ -246,7 +246,7 @@
         reader = open(BAM.Reader, filepath, index=filepath * ".bai")
 
         @test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
-        @test isa(eachoverlap(reader, GenomicFeatures.Interval("chr1", 1, 100)), BAM.OverlapIterator)
+        @test isa(eachoverlap(reader, GenomicFeatures.GenomicInterval("chr1", 1, 100)), BAM.OverlapIterator)
 
         # expected values are counted using samtools
         for (refname, interval, expected) in [