mirror of
https://github.com/MillironX/XAM.jl.git
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Merge branch 'hotfix/header'
This commit is contained in:
commit
6ae1180cfa
5 changed files with 60 additions and 23 deletions
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@ -1,7 +1,7 @@
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name = "XAM"
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name = "XAM"
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uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
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uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
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authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
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authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
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version = "0.2.0"
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version = "0.2.1"
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[deps]
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[deps]
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Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
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Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
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@ -14,6 +14,10 @@ function Header()
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return Header(MetaInfo[])
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return Header(MetaInfo[])
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end
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end
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function Base.:(==)(a::Header, b::Header)
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return a.metainfo == b.metainfo
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end
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function Base.copy(header::Header)
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function Base.copy(header::Header)
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return Header(header.metainfo)
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return Header(header.metainfo)
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end
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end
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@ -12,6 +12,15 @@ mutable struct MetaInfo
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dictval::Vector{UnitRange{Int}}
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dictval::Vector{UnitRange{Int}}
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end
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end
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function Base.:(==)(a::MetaInfo, b::MetaInfo)
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return a.data == b.data &&
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a.filled == b.filled &&
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a.tag == b.tag &&
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a.val == b.val &&
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a.dictkey == b.dictkey &&
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a.dictval == b.dictval
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end
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function MetaInfo(data::Vector{UInt8}=UInt8[])
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function MetaInfo(data::Vector{UInt8}=UInt8[])
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metainfo = MetaInfo(data, 1:0, 1:0, 1:0, UnitRange{Int}[], UnitRange{Int}[])
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metainfo = MetaInfo(data, 1:0, 1:0, 1:0, UnitRange{Int}[], UnitRange{Int}[])
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if !isempty(data)
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if !isempty(data)
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@ -165,6 +165,19 @@ function appendfrom!(dst, dpos, src, spos, n)
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return dst
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return dst
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end
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end
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const action_metainfo = quote
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let markpos = @markpos()
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appendfrom!(metainfo.data, 1, data, markpos, length(markpos:p-1))
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metainfo.filled = @relpos(markpos):@relpos(p-1)
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found_metainfo = true
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end
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end
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const sam_actions_metainfo = Dict(
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const sam_actions_metainfo = Dict(
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:mark => :(@mark),
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:mark => :(@mark),
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:pos1 => :(pos1 = @relpos(p)),
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:pos1 => :(pos1 = @relpos(p)),
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@ -173,22 +186,18 @@ const sam_actions_metainfo = Dict(
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:metainfo_val => :(metainfo.val = pos1:@relpos(p-1)),
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:metainfo_val => :(metainfo.val = pos1:@relpos(p-1)),
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:metainfo_dict_key => :(push!(metainfo.dictkey, pos2:@relpos(p-1))),
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:metainfo_dict_key => :(push!(metainfo.dictkey, pos2:@relpos(p-1))),
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:metainfo_dict_val => :(push!(metainfo.dictval, pos2:@relpos(p-1))),
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:metainfo_dict_val => :(push!(metainfo.dictval, pos2:@relpos(p-1))),
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:metainfo => quote
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:metainfo => action_metainfo
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let markpos = @markpos()
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appendfrom!(metainfo.data, 1, data, markpos, length(markpos:p-1))
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metainfo.filled = @relpos(markpos):@relpos(p-1)
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found_metainfo = true
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end
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end
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)
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)
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const sam_actions_header = merge(
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const sam_actions_header = merge(
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sam_actions_metainfo,
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sam_actions_metainfo,
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Dict(
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Dict(
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:countline => :(linenum += 1),
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:countline => :(linenum += 1),
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:metainfo => quote
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$(action_metainfo)
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push!(header, metainfo)
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metainfo = MetaInfo()
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end,
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:header => quote
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:header => quote
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finish_header = true
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finish_header = true
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@ -309,13 +318,6 @@ const sam_loopcode_header = quote
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throw(ArgumentError("malformed metainfo at line $(linenum)"))
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throw(ArgumentError("malformed metainfo at line $(linenum)"))
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end
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end
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if found_metainfo
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push!(header, metainfo)
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found_metainfo = false
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end
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metainfo = MetaInfo()
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if finish_header
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if finish_header
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@goto __return__
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@goto __return__
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end
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end
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@ -172,15 +172,27 @@ end
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mktemp() do path, io
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mktemp() do path, io
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# copy
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# copy
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reader = open(SAM.Reader, filepath)
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reader = open(SAM.Reader, filepath)
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writer = SAM.Writer(io, header(reader))
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header_original = header(reader)
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writer = SAM.Writer(io, header_original)
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records = SAM.Record[]
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records = SAM.Record[]
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for record in reader
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for record in reader
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push!(records, record)
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push!(records, record)
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write(writer, record)
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write(writer, record)
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end
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end
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close(reader)
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close(reader)
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close(writer)
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close(writer)
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@test compare_records(open(collect, SAM.Reader, path), records)
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reader = open(SAM.Reader, path)
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@test header(reader) == header_original
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@test compare_records(collect(reader), records)
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close(reader)
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end
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end
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end
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end
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end
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end
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@ -378,8 +390,11 @@ end
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else
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else
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reader = open(BAM.Reader, filepath)
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reader = open(BAM.Reader, filepath)
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end
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end
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writer = BAM.Writer(
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BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
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header_original = header(reader)
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writer = BAM.Writer(BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
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records = BAM.Record[]
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records = BAM.Record[]
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for record in reader
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for record in reader
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push!(records, record)
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push!(records, record)
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@ -387,7 +402,14 @@ end
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end
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end
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close(reader)
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close(reader)
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close(writer)
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close(writer)
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@test compare_records(open(collect, BAM.Reader, path), records)
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reader = open(BAM.Reader, path)
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@test header(reader) == header_original
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@test compare_records(collect(reader), records)
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close(reader)
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end
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end
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end
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end
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end
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end
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