Merge branch 'release/v0.2.0'

Author: CiaranOMara

Project.toml

@@ -1,28 +1,28 @@
 name = "GFF3"
 uuid = "af1dc308-cb6b-11e8-32f0-31192efa90f6"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Daniel C. Jones <dcjones@cs.washington.edu>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O’Mara <Ciaran.OMara@utas.edu.au>"]
-version = "0.1.1"
+version = "0.2.0"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
 BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
-BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
 FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 Indexes = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
+TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 URIParser = "30578b45-9adc-5946-b283-645ec420af67"
 
 [compat]
 Automa = "0.7, 0.8"
 BGZFStreams = "0.3"
-BioCore = "2"
+BioGenerics = "0.1"
 BioSequences = "2"
-BufferedStreams = "1"
 FASTX = "1"
 GenomicFeatures = "2"
 Indexes = "0.1"
+TranscodingStreams = "0.9.5"
 URIParser = "0.4"
 julia = "1"
 

docs/src/man/gff3.md

@@ -34,6 +34,30 @@ end
 close(reader)
 ```
 
+The iterator interface demonstrated above allocates an object for each record and that may be a bottleneck of reading data from a file.
+In-place reading reuses a pre-allocated object for every record and less memory allocation happens in reading:
+
+```julia
+# Import the GFF3 module.
+using GFF3
+
+# Open a GFF3 file.
+reader = open(GFF3.Reader, "data.gff3")
+
+# Pre-allocate record.
+record = GFF3.Record()
+
+# Iterate over records.
+while !eof(reader)
+    empty!(record)
+    read!(reader, record)
+    # do something
+end
+
+# Finally, close the reader.
+close(reader)
+```
+
 If you are interested in directives (which starts with '#') in addition to genomic features, you need to pass `skip_directives=false` when initializing a GFF3 constructor:
 ```julia
 # Set skip_directives to true (this is set to false by default).

src/GFF3.jl

@@ -3,16 +3,18 @@
 
 module GFF3
 
-using BioCore
+using BioGenerics
 using Indexes
 using FASTX.FASTA #TODO: move responsibility to FASTX.jl.
+using TranscodingStreams
 
 import Automa
 import Automa.RegExp: @re_str
+import Automa.Stream: @mark, @markpos, @relpos, @abspos
+
 import BGZFStreams
-import BioCore.Exceptions: missingerror
+import BioGenerics.Exceptions: missingerror
 import BioSequences
-import BufferedStreams
 import GenomicFeatures: GenomicFeatures, Interval, IntervalCollection
 import URIParser