Amendments

Base.bytesavailable is provided by CodecBGZF.
Add compat entry for CodecBGZF.
Keep using TranscodingStreams.

Author: CiaranOMara

Project.toml

@@ -4,13 +4,14 @@ authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <benjward@protonma
 version = "0.1.3"
 
 [deps]
-BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 CodecBGZF = "d9d91ef6-315d-495b-8131-db2ca24339d6"
 GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
 [compat]
-BioCore = "2"
+BioGenerics = "0.1"
+CodecBGZF = "0.1"
 GenomicFeatures = "2"
 TranscodingStreams = "0.9.5"
 julia = "1.3"

src/Indexes.jl

@@ -8,22 +8,12 @@
 
 module Indexes
 
+using TranscodingStreams
+
 import CodecBGZF
-import BioCore
+import BioGenerics
 import GenomicFeatures: Interval
 
-function Base.bytesavailable(stream::BGZFStreams.BGZFStream{IOStream})
-
-    block_index = BGZFStreams.ensure_buffered_data(stream)
-    if block_index == 0
-        return 0
-    end
-    block = stream.blocks[block_index]
-
-    return length(block.position:block.size)
-
-end
-
 include("chunk.jl")
 include("bgzfindex.jl")
 include("tabix.jl")