Use GenomicInterval type

Author: CiaranOMara

Project.toml

@@ -12,7 +12,7 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 [compat]
 BGZFStreams = "0.3"
 BioGenerics = "0.1"
-GenomicFeatures = "2"
+GenomicFeatures = "3"
 TranscodingStreams = "0.9.5"
 julia = "1"
 

src/Indexes.jl

@@ -12,7 +12,7 @@ using TranscodingStreams
 
 import BGZFStreams
 import BioGenerics
-import GenomicFeatures: Interval
+import GenomicFeatures: GenomicInterval
 
 function Base.bytesavailable(stream::BGZFStreams.BGZFStream{IOStream})
 

src/overlap.jl

@@ -3,7 +3,7 @@
 
 struct TabixOverlapIterator{T}
     reader::T
-    interval::Interval
+    interval::GenomicInterval
 end
 
 function Base.eltype(::Type{TabixOverlapIterator{T}}) where T

src/tabix.jl

@@ -70,13 +70,13 @@ end
 
 
 """
-    overlapchunks(tabix::Tabix, interval::Interval)
+    overlapchunks(tabix::Tabix, interval::GenomicInterval)
 
 Return chunks possibly overlapping with the range specified by `interval`.
 
 Note that records within the returned chunks are not guaranteed to actually overlap the query interval.
 """
-function overlapchunks(tabix::Tabix, interval::Interval)
+function overlapchunks(tabix::Tabix, interval::GenomicInterval)
     seqid = findfirst(isequal(BioGenerics.seqname(interval)), tabix.names)
     if seqid == 0
         throw(ArgumentError("failed to find sequence name '$(BioGenerics.seqname(interval))'"))