Merge branch 'release/v0.1.3'

Author: CiaranOMara

Project.toml

@@ -1,19 +1,19 @@
 name = "Indexes"
 uuid = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <benjward@protonmail.com>", "Ciarán O’Mara <CiaranOMara@utas.edu.au>"]
-version = "0.1.2"
+version = "0.1.3"
 
 [deps]
 BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
-BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
-BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
+TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
 [compat]
 BGZFStreams = "0.3"
-BioCore = "2"
-BufferedStreams = "1"
+BioGenerics = "0.1"
 GenomicFeatures = "2"
+TranscodingStreams = "0.9.5"
 julia = "1"
 
 [extras]

src/Indexes.jl

@@ -8,11 +8,24 @@
 
 module Indexes
 
+using TranscodingStreams
+
 import BGZFStreams
-import BioCore
-import BufferedStreams
+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")

src/overlap.jl

@@ -24,16 +24,16 @@ end
 function Base.iterate(iter::TabixOverlapIterator)
     @assert iter.reader.index !== nothing
     # TODO: Use a method that resets the reading position.
-    buffer = BioCore.IO.stream(iter.reader)
-    iter.reader.state = BioCore.Ragel.State(1, BufferedStreams.BufferedInputStream(buffer.source))
+    buffer = BioGenerics.IO.stream(iter.reader)
+    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 = BioCore.IO.stream(iter.reader)
-    source = buffer.source
+    buffer = BioGenerics.IO.stream(iter.reader)
+    source = buffer.stream
     if state.chunkid == 0
         if isempty(state.chunks)
             return true
@@ -76,13 +76,13 @@ function Base.iterate(iter::TabixOverlapIterator, state)
 end
 
 function icmp(record, interval)
-    c = cmp(BioCore.seqname(record), BioCore.seqname(interval))
+    c = cmp(BioGenerics.seqname(record), BioGenerics.seqname(interval))
 
-    if c < 0 || (c == 0 && BioCore.rightposition(record) < BioCore.leftposition(interval))
+    if c < 0 || (c == 0 && BioGenerics.rightposition(record) < BioGenerics.leftposition(interval))
         return -1
     end
 
-    if c > 0 || (c == 0 && BioCore.leftposition(record) > BioCore.rightposition(interval))
+    if c > 0 || (c == 0 && BioGenerics.leftposition(record) > BioGenerics.rightposition(interval))
         return +1
     end
 

src/tabix.jl

@@ -77,11 +77,11 @@ 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)
-    seqid = findfirst(isequal(BioCore.seqname(interval)), tabix.names)
+    seqid = findfirst(isequal(BioGenerics.seqname(interval)), tabix.names)
     if seqid == 0
-        throw(ArgumentError("failed to find sequence name '$(BioCore.seqname(interval))'"))
+        throw(ArgumentError("failed to find sequence name '$(BioGenerics.seqname(interval))'"))
     end
-    return overlapchunks(tabix.index, seqid, BioCore.leftposition(interval):BioCore.rightposition(interval))
+    return overlapchunks(tabix.index, seqid, BioGenerics.leftposition(interval):BioGenerics.rightposition(interval))
 end
 
 # Check if `format` follows the BED rule (half-closed-half-open and 0-based).