mirror of
https://github.com/MillironX/XAM.jl.git
synced 2024-12-23 13:28:16 +00:00
Migrate from BufferedStreams to TranscodingStreams
This commit is contained in:
Ciarán O'Mara
parent
12db2c4ea8
commit
de56faf066
4 changed files with 327 additions and 273 deletions
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@ -9,10 +9,10 @@ BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
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BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
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BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
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BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
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BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
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GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
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Indexes = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
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Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
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TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
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[compat]
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Automa = "0.7, 0.8"
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@ -20,9 +20,9 @@ BGZFStreams = "0.3"
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BioAlignments = "2"
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BioGenerics = "0.1"
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BioSequences = "2"
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BufferedStreams = "1"
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GenomicFeatures = "2"
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Indexes = "0.1"
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TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
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julia = "1.1"
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[extras]
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@ -1,16 +1,22 @@
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# SAM Reader
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# =========
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mutable struct Reader <: BioGenerics.IO.AbstractReader
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state::State
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mutable struct Reader{S <: TranscodingStream} <: BioGenerics.IO.AbstractReader
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state::State{S}
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header::Header
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end
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function Reader(input::BufferedStreams.BufferedInputStream)
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reader = new(State(sam_header_machine.start_state, input), Header())
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readheader!(reader)
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reader.state.cs = sam_body_machine.start_state
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return reader
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end
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function Reader(state::State{S}) where {S <: TranscodingStream}
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rdr = Reader(state, Header())
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cs, ln, f = readheader!(rdr.state.stream, rdr.header, (sam_machine_header.start_state, rdr.state.linenum))
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rdr.state.state = sam_machine_body.start_state
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rdr.state.linenum = ln
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rdr.state.filled = false
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return rdr
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end
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"""
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@ -22,7 +28,19 @@ Create a data reader of the SAM file format.
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* `input`: data source
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"""
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function Reader(input::IO)
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return Reader(BufferedStreams.BufferedInputStream(input))
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if input isa TranscodingStream
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return Reader(State(input, 1, 1, false))
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end
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stream = TranscodingStreams.NoopStream(input)
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return Reader(State(stream, 1, 1, false))
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end
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function Base.eltype(::Type{<:Reader})
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return Record
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end
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function BioGenerics.IO.stream(reader::Reader)
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@ -38,6 +56,42 @@ function header(reader::Reader)::Header
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return reader.header
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end
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function Base.eltype(::Type{Reader})
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return Record
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function Base.close(reader::Reader)
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if reader.state.stream isa IO
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close(reader.state.stream)
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end
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return nothing
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end
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function index!(record::MetaInfo)
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stream = TranscodingStreams.NoopStream(IOBuffer(record.data))
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found = index!(stream, record)
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if !found
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throw(ArgumentError("invalid SAM metadata"))
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end
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return record
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end
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function index!(record::Record)
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stream = TranscodingStreams.NoopStream(IOBuffer(record.data))
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found = index!(stream, record)
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if !found
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throw(ArgumentError("invalid SAM record"))
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end
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return record
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end
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function Base.read!(rdr::Reader, rec::Record)
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cs, ln, f = readrecord!(rdr.state.stream, rec, (rdr.state.state, rdr.state.linenum))
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rdr.state.state = cs
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rdr.state.linenum = ln
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rdr.state.filled = f
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if !f
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cs == 0 && throw(EOFError())
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throw(ArgumentError("malformed SAM file"))
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end
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return rec
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end
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@ -1,179 +1,10 @@
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@inline function anchor!(stream::BufferedStreams.BufferedInputStream, p, immobilize = true)
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stream.anchor = p
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stream.immobilized = immobilize
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return stream
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end
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@inline function upanchor!(stream::BufferedStreams.BufferedInputStream)
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@assert stream.anchor != 0 "upanchor! called with no anchor set"
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anchor = stream.anchor
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stream.anchor = 0
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stream.immobilized = false
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return anchor
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end
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function ensure_margin!(stream::BufferedStreams.BufferedInputStream)
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if stream.position * 20 > length(stream.buffer) * 19
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BufferedStreams.shiftdata!(stream)
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end
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return nothing
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end
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@inline function resize_and_copy!(dst::Vector{UInt8}, src::Vector{UInt8}, r::UnitRange{Int})
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return resize_and_copy!(dst, 1, src, r)
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end
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@inline function resize_and_copy!(dst::Vector{UInt8}, dstart::Int, src::Vector{UInt8}, r::UnitRange{Int})
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rlen = length(r)
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if length(dst) != dstart + rlen - 1
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resize!(dst, dstart + rlen - 1)
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end
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copyto!(dst, dstart, src, first(r), rlen)
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return dst
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end
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function generate_index_function(record_type, machine, init_code, actions; kwargs...)
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kwargs = Dict(kwargs)
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context = Automa.CodeGenContext(
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generator = get(kwargs, :generator, :goto),
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checkbounds = get(kwargs, :checkbounds, false),
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loopunroll = get(kwargs, :loopunroll, 0)
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)
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quote
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function index!(record::$(record_type))
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data = record.data
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p = 1
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p_end = p_eof = sizeof(data)
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initialize!(record)
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$(init_code)
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cs = $(machine.start_state)
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$(Automa.generate_exec_code(context, machine, actions))
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if cs != 0
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throw(ArgumentError(string("failed to index ", $(record_type), " ~>", repr(String(data[p:min(p+7,p_end)])))))
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end
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@assert isfilled(record)
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return record
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end
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end
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end
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function generate_readheader_function(reader_type, metainfo_type, machine, init_code, actions, finish_code=:())
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quote
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function readheader!(reader::$(reader_type))
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_readheader!(reader, reader.state)
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end
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function _readheader!(reader::$(reader_type), state::State)
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stream = state.stream
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ensure_margin!(stream)
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cs = state.cs
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linenum = state.linenum
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data = stream.buffer
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p = stream.position
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p_end = stream.available
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p_eof = -1
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finish_header = false
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record = $(metainfo_type)()
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$(init_code)
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while true
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$(Automa.generate_exec_code(Automa.CodeGenContext(generator=:table), machine, actions))
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state.cs = cs
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state.finished = cs == 0
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state.linenum = linenum
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stream.position = p
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if cs < 0
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error("$($(reader_type)) file format error on line ", linenum)
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elseif finish_header
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$(finish_code)
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break
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elseif p > p_eof ≥ 0
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error("incomplete $($(reader_type)) input on line ", linenum)
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else
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hits_eof = BufferedStreams.fillbuffer!(stream) == 0
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p = stream.position
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p_end = stream.available
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if hits_eof
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p_eof = p_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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end
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function generate_read_function(reader_type, machine, init_code, actions; kwargs...)
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kwargs = Dict(kwargs)
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context = Automa.CodeGenContext(
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generator=get(kwargs, :generator, :goto),
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checkbounds=get(kwargs, :checkbounds, false),
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loopunroll=get(kwargs, :loopunroll, 0)
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)
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quote
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function Base.read!(reader::$(reader_type), record::eltype($(reader_type)))::eltype($(reader_type))
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return _read!(reader, reader.state, record)
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end
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function _read!(reader::$(reader_type), state::State, record::eltype($(reader_type)))
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stream = state.stream
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ensure_margin!(stream)
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cs = state.cs
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linenum = state.linenum
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data = stream.buffer
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p = stream.position
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p_end = stream.available
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p_eof = -1
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found_record = false
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initialize!(record)
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$(init_code)
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if state.finished
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throw(EOFError())
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end
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while true
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$(Automa.generate_exec_code(context, machine, actions))
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state.cs = cs
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state.finished |= cs == 0
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state.linenum = linenum
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stream.position = p
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if cs < 0
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error($(reader_type), " file format error on line ", linenum, " ~>", repr(String(data[p:min(p+7,p_end)])))
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elseif found_record
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break
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elseif cs == 0
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throw(EOFError())
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elseif p > p_eof ≥ 0
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error("incomplete $($(reader_type)) input on line ", linenum)
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elseif BufferedStreams.available_bytes(stream) < 64
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hits_eof = BufferedStreams.fillbuffer!(stream) == 0
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p = stream.position
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p_end = stream.available
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if hits_eof
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p_eof = p_end
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end
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end
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end
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@assert isfilled(record)
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return record
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end
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end
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end
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# Automa.jl generated readrecord! and readmetainfo! functions
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# ========================================
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# file = header . body
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# header = metainfo*
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# body = record*
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const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_machine = (function ()
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const sam_machine_metainfo, sam_machine_record, sam_machine_header, sam_machine_body, sam_machine = (function ()
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isinteractive() && info("compiling SAM")
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@ -304,95 +135,261 @@ const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_mac
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header = cat(header′, opt(any() \ cat('@'))) # look ahead
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body = rep(cat(record, newline))
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body.actions[:exit] = [:body]
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return map(Automa.compile, (metainfo, record, header, body))
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sam = cat(header, body)
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return map(Automa.compile, (metainfo, record, header, body, sam))
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end)()
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const sam_metainfo_actions = Dict(
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:metainfo_tag => :(record.tag = (pos1:p-1) .- offset),
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:metainfo_val => :(record.val = (pos1:p-1) .- offset),
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:metainfo_dict_key => :(push!(record.dictkey, (pos2:p-1) .- offset)),
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:metainfo_dict_val => :(push!(record.dictval, (pos2:p-1) .- offset)),
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# write("sam_machine_metainfo.dot", Automa.machine2dot(sam_machine_metainfo))
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# run(`dot -Tsvg -o sam_machine_metainfo.svg sam_machine_metainfo.dot`)
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#
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# write("sam_machine_record.dot", Automa.machine2dot(sam_machine_record))
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# run(`dot -Tsvg -o sam_machine_record.svg sam_machine_record.dot`)
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#
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# write("sam_machine_header.dot", Automa.machine2dot(sam_machine_header))
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# run(`dot -Tsvg -o sam_machine_header.svg sam_machine_header.dot`)
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#
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# write("sam_machine_body.dot", Automa.machine2dot(sam_machine_body))
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# run(`dot -Tsvg -o sam_machine_body.svg sam_machine_body.dot`)
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#
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# write("sam_machine.dot", Automa.machine2dot(sam_machine))
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# run(`dot -Tsvg -o sam_machine.svg sam_machine.dot`)
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function appendfrom!(dst, dpos, src, spos, n)
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if length(dst) < dpos + n - 1
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resize!(dst, dpos + n - 1)
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end
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copyto!(dst, dpos, src, spos, n)
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return dst
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end
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const sam_actions_metainfo = Dict(
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:mark => :(@mark),
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:pos1 => :(pos1 = @relpos(p)),
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:pos2 => :(pos2 = @relpos(p)),
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:metainfo_tag => :(metainfo.tag = 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_val => :(push!(metainfo.dictval, pos2:@relpos(p-1))),
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:metainfo => quote
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resize_and_copy!(record.data, data, offset+1:p-1)
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record.filled = (offset+1:p-1) .- offset
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end,
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:mark => :(),
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:pos1 => :(pos1 = p),
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:pos2 => :(pos2 = p)
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)
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let markpos = @markpos()
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generate_index_function(
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MetaInfo,
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sam_metainfo_machine,
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:(pos1 = pos2 = offset = 0),
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sam_metainfo_actions
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) |> eval
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appendfrom!(metainfo.data, 1, data, markpos, length(markpos:p-1))
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generate_readheader_function(
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Reader,
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MetaInfo,
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sam_header_machine,
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:(pos1 = pos2 = offset = 0),
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merge(sam_metainfo_actions, Dict(
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:metainfo => quote
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resize_and_copy!(record.data, data, upanchor!(stream):p-1)
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record.filled = (offset+1:p-1) .- offset
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@assert isfilled(record)
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push!(reader.header.metainfo, record)
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ensure_margin!(stream)
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record = MetaInfo()
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end,
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:header => :(finish_header = true; @escape),
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:countline => :(linenum += 1),
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:mark => :(anchor!(stream, p); offset = p - 1))),
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quote
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if !eof(stream)
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stream.position -= 1 # cancel look-ahead
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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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) |> eval
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const sam_record_actions = Dict(
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:record_qname => :(record.qname = (pos:p-1) .- offset),
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:record_flag => :(record.flag = (pos:p-1) .- offset),
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:record_rname => :(record.rname = (pos:p-1) .- offset),
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:record_pos => :(record.pos = (pos:p-1) .- offset),
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:record_mapq => :(record.mapq = (pos:p-1) .- offset),
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:record_cigar => :(record.cigar = (pos:p-1) .- offset),
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:record_rnext => :(record.rnext = (pos:p-1) .- offset),
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:record_pnext => :(record.pnext = (pos:p-1) .- offset),
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:record_tlen => :(record.tlen = (pos:p-1) .- offset),
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:record_seq => :(record.seq = (pos:p-1) .- offset),
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:record_qual => :(record.qual = (pos:p-1) .- offset),
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:record_field => :(push!(record.fields, (pos:p-1) .- offset)),
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:record => quote
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resize_and_copy!(record.data, data, 1:p-1)
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record.filled = (offset+1:p-1) .- offset
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end,
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:mark => :(),
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:pos => :(pos = p)
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)
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generate_index_function(
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Record,
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sam_record_machine,
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:(pos = offset = 0),
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sam_record_actions
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) |> eval
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const sam_actions_header = merge(
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sam_actions_metainfo,
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Dict(
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:countline => :(linenum += 1),
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:header => quote
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finish_header = true
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if !eof(stream)
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p -= 1 # cancel look-ahead
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end
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@escape
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end
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)
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)
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const sam_actions_record = Dict(
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:mark => :(@mark),
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:pos => :(pos = @relpos(p)),
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:record_qname => :(record.qname = pos:@relpos(p-1)),
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:record_flag => :(record.flag = pos:@relpos(p-1)),
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:record_rname => :(record.rname = pos:@relpos(p-1)),
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:record_pos => :(record.pos = pos:@relpos(p-1)),
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:record_mapq => :(record.mapq = pos:@relpos(p-1)),
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:record_cigar => :(record.cigar = pos:@relpos(p-1)),
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:record_rnext => :(record.rnext = pos:@relpos(p-1)),
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:record_pnext => :(record.pnext = pos:@relpos(p-1)),
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:record_tlen => :(record.tlen = pos:@relpos(p-1)),
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:record_seq => :(record.seq = pos:@relpos(p-1)),
|
||||
:record_qual => :(record.qual = pos:@relpos(p-1)),
|
||||
:record_field => :(push!(record.fields, pos:@relpos(p-1))),
|
||||
:record => quote
|
||||
let markpos = @markpos()
|
||||
|
||||
appendfrom!(record.data, 1, data, markpos, length(markpos:p-1))
|
||||
|
||||
record.filled = @relpos(markpos):@relpos(p-1)
|
||||
|
||||
generate_read_function(
|
||||
Reader,
|
||||
sam_body_machine,
|
||||
:(pos = offset = 0),
|
||||
merge(sam_record_actions, Dict(
|
||||
:record => quote
|
||||
resize_and_copy!(record.data, data, upanchor!(stream):p-1)
|
||||
record.filled = (offset+1:p-1) .- offset
|
||||
found_record = true
|
||||
@escape
|
||||
end,
|
||||
end
|
||||
end
|
||||
)
|
||||
|
||||
const sam_actions_body = merge(
|
||||
sam_actions_record,
|
||||
Dict(
|
||||
:countline => :(linenum += 1),
|
||||
:mark => :(anchor!(stream, p); offset = p - 1))
|
||||
:body => quote
|
||||
finish_body = true
|
||||
@escape
|
||||
end
|
||||
)
|
||||
)
|
||||
|
||||
# const sam_actions = merge(
|
||||
# sam_actions_header,
|
||||
# sam_actions_body
|
||||
# )
|
||||
|
||||
const sam_context = Automa.CodeGenContext(
|
||||
generator = :goto,
|
||||
checkbounds = false,
|
||||
loopunroll = 0
|
||||
)
|
||||
|
||||
const sam_initcode_metainfo = quote
|
||||
pos1 = 0
|
||||
pos2 = 0
|
||||
found_metainfo = false
|
||||
end
|
||||
|
||||
const sam_initcode_record = quote
|
||||
pos = 0
|
||||
found_record = false
|
||||
end
|
||||
|
||||
const sam_initcode_header = quote
|
||||
$(sam_initcode_metainfo)
|
||||
metainfo = MetaInfo()
|
||||
finish_header = false
|
||||
cs, linenum = state
|
||||
end
|
||||
|
||||
const sam_initcode_body = quote
|
||||
$(sam_initcode_record)
|
||||
finish_body = false
|
||||
cs, linenum = state
|
||||
end
|
||||
|
||||
const sam_loopcode_metainfo = quote
|
||||
|
||||
if cs < 0
|
||||
throw(ArgumentError("malformed metainfo at pos $(p)"))
|
||||
end
|
||||
|
||||
if found_metainfo
|
||||
@goto __return__
|
||||
end
|
||||
end
|
||||
|
||||
const sam_returncode_metainfo = quote
|
||||
return found_metainfo
|
||||
end
|
||||
|
||||
|
||||
Automa.Stream.generate_reader(
|
||||
:index!,
|
||||
sam_machine_metainfo,
|
||||
arguments = (:(metainfo::MetaInfo),),
|
||||
actions = sam_actions_metainfo,
|
||||
context = sam_context,
|
||||
initcode = sam_initcode_metainfo,
|
||||
loopcode = sam_loopcode_metainfo,
|
||||
returncode = sam_returncode_metainfo
|
||||
) |> eval
|
||||
|
||||
const sam_loopcode_header = quote
|
||||
|
||||
if cs < 0
|
||||
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
|
||||
end
|
||||
|
||||
const sam_returncode_header = quote
|
||||
return cs, linenum, finish_header
|
||||
end
|
||||
|
||||
Automa.Stream.generate_reader(
|
||||
:readheader!,
|
||||
sam_machine_header,
|
||||
arguments = (:(header::SAM.Header), :(state::Tuple{Int,Int})),
|
||||
actions = sam_actions_header,
|
||||
context = sam_context,
|
||||
initcode = sam_initcode_header,
|
||||
loopcode = sam_loopcode_header,
|
||||
returncode = sam_returncode_header
|
||||
) |> eval
|
||||
|
||||
|
||||
const sam_loopcode_record = quote
|
||||
|
||||
if cs < 0
|
||||
throw(ArgumentError("malformed SAM record at position $(p), line $(linenum)"))
|
||||
end
|
||||
|
||||
# # if cs != 0
|
||||
# # throw(ArgumentError(string("failed to index ", $(record_type), " ~>", repr(String(data[p:min(p+7,p_end)])))))
|
||||
# # end
|
||||
|
||||
if found_record
|
||||
@goto __return__
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
const sam_loopcode_body = quote
|
||||
|
||||
$(sam_loopcode_record)
|
||||
|
||||
if finish_body
|
||||
@goto __return__
|
||||
end
|
||||
end
|
||||
|
||||
const sam_returncode_record = quote
|
||||
return found_record
|
||||
end
|
||||
|
||||
Automa.Stream.generate_reader(
|
||||
:index!,
|
||||
sam_machine_record,
|
||||
arguments = (:(record::Record),),
|
||||
actions = sam_actions_record,
|
||||
context = sam_context,
|
||||
initcode = sam_initcode_record,
|
||||
loopcode = sam_loopcode_record,
|
||||
returncode = sam_returncode_record
|
||||
) |> eval
|
||||
|
||||
|
||||
|
||||
const sam_returncode_body = quote
|
||||
return cs, linenum, found_record
|
||||
end
|
||||
|
||||
Automa.Stream.generate_reader(
|
||||
:readrecord!,
|
||||
sam_machine_body,
|
||||
arguments = (:(record::Record), :(state::Tuple{Int,Int})),
|
||||
actions = sam_actions_body,
|
||||
context = sam_context,
|
||||
initcode = sam_initcode_body,
|
||||
loopcode = sam_loopcode_body,
|
||||
returncode = sam_returncode_body
|
||||
) |> eval
|
||||
|
|
|
|||
|
|
@ -7,11 +7,14 @@ using BioGenerics
|
|||
|
||||
import Automa
|
||||
import Automa.RegExp: @re_str
|
||||
import Automa.Stream: @mark, @markpos, @relpos, @abspos
|
||||
import BioAlignments
|
||||
import BioGenerics: BioGenerics, isfilled, header
|
||||
import BioGenerics.Exceptions: missingerror
|
||||
import BioGenerics: isfilled, header
|
||||
import BioGenerics.Automa: State
|
||||
import BioSequences
|
||||
import BufferedStreams
|
||||
import TranscodingStreams: TranscodingStreams, TranscodingStream
|
||||
|
||||
using Printf: @sprintf
|
||||
|
||||
|
||||
|
|
@ -46,19 +49,19 @@ 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
|
||||
# #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
|
||||
# function State(initstate::Int, input::BufferedInputStream)
|
||||
# return State(input, initstate, 1, false)
|
||||
# end
|
||||
|
||||
|
||||
include("flags.jl")
|
||||
|
|
|
|||
Loading…
Reference in a new issue