From c59a1576755f109e989545e2510a433487b4ec3a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= <Ciaran.OMara@utas.edu.au>
Date: Tue, 27 Aug 2019 08:52:35 +1000
Subject: [PATCH] Quick fix for BioCore.Ragel.State

This fix is likely to be replaced when migrating to TranscodingStreams.
---
 src/sam/reader.jl |  4 ++--
 src/sam/sam.jl    | 15 +++++++++++++++
 2 files changed, 17 insertions(+), 2 deletions(-)

diff --git a/src/sam/reader.jl b/src/sam/reader.jl
index 5e4f0ea..1dc206b 100644
--- a/src/sam/reader.jl
+++ b/src/sam/reader.jl
@@ -2,11 +2,11 @@
 # =========
 
 mutable struct Reader <: BioGenerics.IO.AbstractReader
-    state::BioGenerics.Ragel.State
+    state::State
     header::Header
 
     function Reader(input::BufferedStreams.BufferedInputStream)
-        reader = new(BioGenerics.Ragel.State(sam_header_machine.start_state, input), Header())
+        reader = new(State(sam_header_machine.start_state, input), Header())
         readheader!(reader)
         reader.state.cs = sam_body_machine.start_state
         return reader
diff --git a/src/sam/sam.jl b/src/sam/sam.jl
index f7b6c92..628b085 100644
--- a/src/sam/sam.jl
+++ b/src/sam/sam.jl
@@ -46,6 +46,21 @@ function unsafe_parse_decimal(::Type{T}, data::Vector{UInt8}, range::UnitRange{I
     return sign * x
 end
 
+#TODO: update BioCore.Ragel.State (will likely change with TrnscodingStreams).
+import BufferedStreams: BufferedStreams, BufferedInputStream
+# A type keeping track of a ragel-based parser's state.
+mutable struct State{T<:BufferedInputStream}
+    stream::T      # input stream
+    cs::Int        # current DFA state of Ragel
+    linenum::Int   # line number: parser is responsible for updating this
+    finished::Bool # true if finished (regardless of where in the stream we are)
+end
+
+function State(initstate::Int, input::BufferedInputStream)
+    return State(input, initstate, 1, false)
+end
+
+
 include("flags.jl")
 include("metainfo.jl")
 include("record.jl")