Merge branch 'master' into develop

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 = "0.2.0"
+version = "0.2.1"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"

src/sam/header.jl

@@ -14,6 +14,10 @@ function Header()
     return Header(MetaInfo[])
 end
 
+function Base.:(==)(a::Header, b::Header)
+    return a.metainfo == b.metainfo
+end
+
 function Base.copy(header::Header)
     return Header(header.metainfo)
 end

src/sam/metainfo.jl

@@ -12,6 +12,15 @@ mutable struct MetaInfo
     dictval::Vector{UnitRange{Int}}
 end
 
+function Base.:(==)(a::MetaInfo, b::MetaInfo)
+    return a.data == b.data &&
+        a.filled  == b.filled &&
+        a.tag     == b.tag &&
+        a.val     == b.val &&
+        a.dictkey == b.dictkey &&
+        a.dictval == b.dictval
+end
+
 function MetaInfo(data::Vector{UInt8}=UInt8[])
     metainfo = MetaInfo(data, 1:0, 1:0, 1:0, UnitRange{Int}[], UnitRange{Int}[])
     if !isempty(data)

src/sam/readrecord.jl

@@ -165,15 +165,8 @@ function appendfrom!(dst, dpos, src, spos, n)
     return dst
 end
 
-const sam_actions_metainfo = Dict(
+const action_metainfo = quote
-    :mark => :(@mark),
+
-    :pos1  => :(pos1 = @relpos(p)),
-    :pos2  => :(pos2 = @relpos(p)),
-    :metainfo_tag => :(metainfo.tag = pos1:@relpos(p-1)),
-    :metainfo_val => :(metainfo.val = pos1:@relpos(p-1)),
-    :metainfo_dict_key => :(push!(metainfo.dictkey, pos2:@relpos(p-1))),
-    :metainfo_dict_val => :(push!(metainfo.dictval, pos2:@relpos(p-1))),
-    :metainfo => quote
     let markpos = @markpos()
 
         appendfrom!(metainfo.data, 1, data, markpos, length(markpos:p-1))
@@ -182,13 +175,29 @@ const sam_actions_metainfo = Dict(
 
         found_metainfo = true
     end
+
 end
+
+const sam_actions_metainfo = Dict(
+    :mark => :(@mark),
+    :pos1  => :(pos1 = @relpos(p)),
+    :pos2  => :(pos2 = @relpos(p)),
+    :metainfo_tag => :(metainfo.tag = pos1:@relpos(p-1)),
+    :metainfo_val => :(metainfo.val = pos1:@relpos(p-1)),
+    :metainfo_dict_key => :(push!(metainfo.dictkey, pos2:@relpos(p-1))),
+    :metainfo_dict_val => :(push!(metainfo.dictval, pos2:@relpos(p-1))),
+    :metainfo => action_metainfo
 )
 
 const sam_actions_header = merge(
     sam_actions_metainfo,
     Dict(
         :countline => :(linenum += 1),
+        :metainfo => quote
+            $(action_metainfo)
+            push!(header, metainfo)
+            metainfo = MetaInfo()
+        end,
         :header => quote
 
             finish_header = true
@@ -309,13 +318,6 @@ const sam_loopcode_header = quote
         throw(ArgumentError("malformed metainfo at line $(linenum)"))
     end
 
-    if found_metainfo
-        push!(header, metainfo)
-        found_metainfo = false
-    end
-
-    metainfo = MetaInfo()
-
     if finish_header
         @goto __return__
     end

test/runtests.jl

@@ -172,15 +172,27 @@ end
             mktemp() do path, io
                 # copy
                 reader = open(SAM.Reader, filepath)
-                writer = SAM.Writer(io, header(reader))
+
+                header_original = header(reader)
+
+                writer = SAM.Writer(io, header_original)
+
                 records = SAM.Record[]
                 for record in reader
                     push!(records, record)
                     write(writer, record)
                 end
+
                 close(reader)
                 close(writer)
-                @test compare_records(open(collect, SAM.Reader, path), records)
+
+                reader = open(SAM.Reader, path)
+
+                @test header(reader) == header_original
+                @test compare_records(collect(reader), records)
+
+                close(reader)
+
             end
         end
     end
@@ -378,8 +390,11 @@ end
                 else
                     reader = open(BAM.Reader, filepath)
                 end
-                writer = BAM.Writer(
+
-                    BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
+                header_original = header(reader)
+
+                writer = BAM.Writer(BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
+
                 records = BAM.Record[]
                 for record in reader
                     push!(records, record)
@@ -387,7 +402,14 @@ end
                 end
                 close(reader)
                 close(writer)
-                @test compare_records(open(collect, BAM.Reader, path), records)
+
+                reader = open(BAM.Reader, path)
+
+                @test header(reader) == header_original
+                @test compare_records(collect(reader), records)
+
+                close(reader)
+
             end
         end
     end