millironx/XAM.jl
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Merge branch 'master' into develop

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This commit is contained in:
Ciarán O'Mara 2020-03-21 17:28:02 +11:00
commit 429f69d84b
5 changed files with 60 additions and 23 deletions
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2
Project.toml
View file

@ -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"

4
src/sam/header.jl
View file

@ -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

9
src/sam/metainfo.jl
View file

@ -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)

36
src/sam/readrecord.jl
View file

@ -165,6 +165,19 @@ function appendfrom!(dst, dpos, src, spos, n)
return dst
end
const action_metainfo = quote
let markpos = @markpos()
appendfrom!(metainfo.data, 1, data, markpos, length(markpos:p-1))
metainfo.filled = @relpos(markpos):@relpos(p-1)
found_metainfo = true
end
end
const sam_actions_metainfo = Dict(
:mark => :(@mark),
:pos1 => :(pos1 = @relpos(p)),
@ -173,22 +186,18 @@ const sam_actions_metainfo = Dict(
: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))
metainfo.filled = @relpos(markpos):@relpos(p-1)
found_metainfo = true
end
end
: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

32
test/runtests.jl
View file

@ -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