Migrate from BufferedStreams to TranscodingStreams

Author: CiaranOMara

Project.toml

@@ -6,14 +6,14 @@ version = "0.1.2"
 [deps]
 BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
-BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
 GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
+TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
 [compat]
 BGZFStreams = "0.3"
 BioGenerics = "0.1"
-BufferedStreams = "1"
 GenomicFeatures = "2"
+TranscodingStreams = "0.9.5"
 julia = "1"
 
 [extras]

src/Indexes.jl

@@ -8,9 +8,10 @@
 
 module Indexes
 
+using TranscodingStreams
+
 import BGZFStreams
 import BioGenerics
-import BufferedStreams
 import GenomicFeatures: Interval
 
 include("chunk.jl")

src/overlap.jl

@@ -25,15 +25,15 @@ function Base.iterate(iter::TabixOverlapIterator)
     @assert iter.reader.index !== nothing
     # TODO: Use a method that resets the reading position.
     buffer = BioGenerics.IO.stream(iter.reader)
-    iter.reader.state = BioGenerics.Ragel.State(1, BufferedStreams.BufferedInputStream(buffer.source))
+    iter.reader.state = BioGenerics.Automa.State(TranscodingStreams.NoopStream(buffer.stream), 1, 1, false)
     state = TabixOverlapIteratorState(Indexes.overlapchunks(iter.reader.index, iter.interval), 0, false, eltype(iter)())
 
     return iterate(iter, state)
 end
 
 function done(iter::TabixOverlapIterator, state)
     buffer = BioGenerics.IO.stream(iter.reader)
-    source = buffer.source
+    source = buffer.stream
     if state.chunkid == 0
         if isempty(state.chunks)
             return true