Merge #1

1: Use TranscodingStreams for FASTA r=BenJWard a=BenJWard

## ☑️ Checklist

- [x] 🎨 The changes implemented is consistent with the [julia style guide](https://docs.julialang.org/en/stable/manual/style-guide/).
- [x] 📘 I have updated and added relevant docstrings, in a manner consistent with the [documentation styleguide](https://docs.julialang.org/en/stable/manual/documentation/).
- [x] 📘 I have added or updated relevant user and developer manuals/documentation in `docs/src/`.
- [x] 🆗 There are unit tests that cover the code changes I have made.
- [x] 🆗 The unit tests cover my code changes AND they pass.
- [x] 📝 I have added an entry to the `[UNRELEASED]` section of the manually curated `CHANGELOG.md` file for this repository.
- [x] 🆗 All changes should be compatible with the latest stable version of Julia.
- [x] 💭 I have commented liberally for any complex pieces of internal code.


Co-authored-by: Ben J. Ward <benjward@protonmail.com>

Project.toml

@@ -1,6 +1,6 @@
 name = "FASTX"
 uuid = "c2308a5c-f048-11e8-3e8a-31650f418d12"
-authors = ["Ben J. Ward <ward9250@gmail.com>"]
+authors = ["Ben J. Ward <benjward@protonmail.com>"]
 version = "0.1.0"
 
 [deps]
@@ -9,16 +9,17 @@ BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
 BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
+TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
+
+[compat]
+Automa = "0.7"
+BioCore = "2.0.3"
+BioSequences = "1.0"
+BioSymbols = "3.1.0"
+julia = "1.0"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
 test = ["Test"]
-
-[compat]
-julia = "1.0"
-Automa = "0.7"
-BioCore = "2.0.3"
-BioSymbols = "3.1.0"
-BioSequences = "1.0"

README.md

@@ -1,11 +1,11 @@
 # <img src="./sticker.svg" width="30%" align="right" /> FASTX
 
-[![Latest Release](https://img.shields.io/github/release/BioJulia/FASTX.jl.svg?style=flat-square)](https://github.com/BioJulia/FASTX.jl/releases/latest)
-[![MIT license](https://img.shields.io/badge/license-MIT-green.svg?style=flat-square)](https://github.com/BioJulia/FASTX.jl/blob/master/LICENSE) 
-[![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg?style=flat-square)](https://biojulia.github.io/FASTX.jl/stable)
-[![Latest documentation](https://img.shields.io/badge/docs-latest-blue.svg?style=flat-square)](https://biojulia.github.io/FASTX.jl/latest/)
-![Lifecycle](https://img.shields.io/badge/lifecycle-maturing-orange.svg?style=flat-square)
-[![Chat on Discord](https://img.shields.io/badge/discord-chat-blue.svg?style=flat-square&logo=discord&colorB=%237289DA)](https://discord.gg/z73YNFz)
+[![Latest Release](https://img.shields.io/github/release/BioJulia/FASTX.jl.svg)](https://github.com/BioJulia/FASTX.jl/releases/latest)
+[![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/FASTX.jl/blob/master/LICENSE) 
+[![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/FASTX.jl/stable)
+[![Latest documentation](https://img.shields.io/badge/docs-latest-blue.svg)](https://biojulia.github.io/FASTX.jl/latest/)
+[![Pkg Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
+[![Chat](https://img.shields.io/gitter/room/BioJulia/FASTX.svg)](https://gitter.im/BioJulia/FASTX.jl)
 
 
 ## Description
@@ -16,9 +16,7 @@ sequence data files.
 
 ## Installation
 
-FASTX is bundled into the [Bio.jl](https://github.com/BioJulia/Bio.jl)
-package, so you may not need to install this package explicitly.
-However, if you do, you can install FASTX from the Julia REPL:
+You can install FASTX from the Julia REPL:
 
 ```julia
 using Pkg
@@ -31,11 +29,13 @@ the master branch to try new features before release.
 
 ## Testing
 
-FASTA is tested against Julia `1.X` on Linux, OS X, and Windows.
+FASTX is tested against Julia `1.X` on Linux, OS X, and Windows.
 
-| **Latest release** | **Latest build status** |
-|:------------------:|:-----------------------:|
-|[![](https://pkg.julialang.org/badges/FASTX_1.0.svg)](https://pkg.julialang.org/?pkg=FASTX) | [![](https://travis-ci.org/BioJulia/FASTX.jl.svg?branch=master)](https://travis-ci.org/BioJulia/FASTX.jl) [![](https://ci.appveyor.com/api/projects/status/jcluuycn0763hnea/branch/master?svg=true)](https://ci.appveyor.com/project/BenJWard/fastx-jl/branch/master)[![](https://codecov.io/gh/BioJulia/FASTX.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/FASTX.jl)|
+**Latest build status:**
+
+[![](https://travis-ci.org/BioJulia/FASTX.jl.svg?branch=master)](https://travis-ci.org/BioJulia/FASTX.jl)
+[![](https://ci.appveyor.com/api/projects/status/jcluuycn0763hnea/branch/master?svg=true)](https://ci.appveyor.com/project/BenJWard/fastx-jl/branch/master)
+[![](https://codecov.io/gh/BioJulia/FASTX.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/BioJulia/FASTX.jl)
 
 
 ## Contributing
@@ -84,5 +84,5 @@ Your logo will show up here with a link to your website.
 ## Questions?
 
 If you have a question about contributing or using BioJulia software, come
-on over and chat to us on [Discord](https://discord.gg/z73YNFz), or you can try the
+on over and chat to us on [Gitter](https://gitter.im/BioJulia/General), or you can try the
 [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

docs/src/index.md

@@ -16,9 +16,7 @@ sequence data files.
 
 ## Installation
 
-FASTX is bundled into the [Bio.jl](https://github.com/BioJulia/Bio.jl)
-package, so you may not need to install this package explicitly.
-However, if you do, you can install FASTX from the Julia REPL:
+You can install FASTX from the Julia REPL:
 
 ```julia
 using Pkg

src/fasta/fasta.jl

@@ -5,16 +5,19 @@ module FASTA
 
 import Automa
 import Automa.RegExp: @re_str
+import Automa.Stream: @mark, @markpos, @relpos, @abspos #
 import BioCore: BioCore, isfilled
 import BioCore.Exceptions: missingerror
 import BioSequences
-import BufferedStreams
+#import BufferedStreams
+import TranscodingStreams: TranscodingStreams, TranscodingStream #
 
 export description,
        identifier
 
 include("record.jl")
 include("index.jl")
+include("readrecord.jl")
 include("reader.jl")
 include("writer.jl")