From aaf3710fbed304f7c8bb843ca6151bcdf8d12b84 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciara=CC=81n=20O=E2=80=99Mara?= <Ciaran.OMara@utas.edu.au>
Date: Sat, 27 Mar 2021 00:28:44 +1100
Subject: [PATCH 1/3] Increment version

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index beb4170..0c21bf9 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "XAM"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "0.2.6"
+version = "0.2.7"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"

From 64f371e1e479b07d7d14621b0bd23ad040087842 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciara=CC=81n=20O=E2=80=99Mara?= <Ciaran.OMara@utas.edu.au>
Date: Thu, 1 Apr 2021 12:31:44 +1100
Subject: [PATCH 2/3] Adjust for Automa 0.8.1

Defines an unambiguous state machine.
https://github.com/BioJulia/Automa.jl/pull/49.
---
 src/sam/readrecord.jl | 15 +++------------
 1 file changed, 3 insertions(+), 12 deletions(-)

diff --git a/src/sam/readrecord.jl b/src/sam/readrecord.jl
index 4bc0761..e2d6669 100644
--- a/src/sam/readrecord.jl
+++ b/src/sam/readrecord.jl
@@ -134,11 +134,10 @@ const sam_machine_metainfo, sam_machine_record, sam_machine_header, sam_machine_
         cat(re"\r?", lf)
     end
 
-    header′ = rep(cat(metainfo, newline))
-    header′.actions[:exit] = [:header]
-    header = cat(header′, opt(any() \ cat('@')))  # look ahead
+    header = rep(cat(metainfo, newline))
+    header.actions[:exit] = [:header]
 
-    body = rep(cat(record, newline))
+    body = record * rep(newline * record) * opt(newline)
     body.actions[:exit]  = [:body]
 
     sam = cat(header, body)
@@ -200,10 +199,6 @@ const sam_actions_header = merge(
 
             finish_header = true
 
-            if !eof(stream)
-                p -= 1 # cancel look-ahead
-            end
-
             @escape
         end
     )
@@ -308,10 +303,6 @@ Automa.Stream.generate_reader(
 
 const sam_loopcode_header = quote
 
-    if cs < 0
-        throw(ArgumentError("malformed metainfo at line $(linenum)"))
-    end
-
     if finish_header
         @goto __return__
     end

From c423694f296075e11317f961561744bb60ec664a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciara=CC=81n=20O=E2=80=99Mara?= <Ciaran.OMara@utas.edu.au>
Date: Thu, 1 Apr 2021 11:48:02 +1100
Subject: [PATCH 3/3] Cater for blank sam files

---
 src/sam/reader.jl | 18 +++++++++++-------
 test/test_sam.jl  |  6 ++++++
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/src/sam/reader.jl b/src/sam/reader.jl
index a20fd4c..aa5546e 100644
--- a/src/sam/reader.jl
+++ b/src/sam/reader.jl
@@ -94,17 +94,21 @@ end
 Read a `Record` into `rec`; overwriting or adding to existing field values.
 It is assumed that `rec` is already initialized or empty.
 """
-function Base.read!(rdr::Reader, rec::Record)
+function Base.read!(rdr::Reader, record::Record)
 
-    cs, ln, f = readrecord!(rdr.state.stream, rec, (rdr.state.state, rdr.state.linenum))
+    cs, ln, found = readrecord!(rdr.state.stream, record, (rdr.state.state, rdr.state.linenum))
 
     rdr.state.state = cs
     rdr.state.linenum = ln
-    rdr.state.filled = f
+    rdr.state.filled = found
 
-    if !f
-        cs == 0 && throw(EOFError())
-        throw(ArgumentError("malformed SAM file"))
+    if found
+        return record
     end
-    return rec
+
+    if cs == 0 || eof(rdr.state.stream)
+        throw(EOFError())
+    end
+
+    throw(ArgumentError("malformed SAM file"))
 end
diff --git a/test/test_sam.jl b/test/test_sam.jl
index e669757..c6fadc1 100644
--- a/test/test_sam.jl
+++ b/test/test_sam.jl
@@ -194,5 +194,11 @@
 
         close(reader)
 
+        # Test blank file.
+        file_sam = joinpath(samdir, "xx#blank.sam")
+
+        records = open(collect, SAM.Reader, file_sam)
+        @test records == []
+        
     end
 end