mirror of
https://github.com/MillironX/XAM.jl.git
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Quick fix for BioGenerics.ReaderHelper functions
This fix is likely to be replaced when migrating to TranscodingStreams.
This commit is contained in:
Ciarán O'Mara
parent
c59a157675
commit
365f7922fa
1 changed files with 180 additions and 11 deletions
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@ -1,6 +1,175 @@
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# SAM Reader
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# =========
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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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mutable struct Reader <: BioGenerics.IO.AbstractReader
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state::State
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header::Header
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@ -184,36 +353,36 @@ const sam_metainfo_actions = Dict(
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:metainfo_dict_key => :(push!(record.dictkey, (mark2:p-1) .- offset)),
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:metainfo_dict_val => :(push!(record.dictval, (mark2:p-1) .- offset)),
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:metainfo => quote
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BioGenerics.ReaderHelper.resize_and_copy!(record.data, data, offset+1:p-1)
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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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:anchor => :(),
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:mark1 => :(mark1 = p),
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:mark2 => :(mark2 = p))
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eval(
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BioGenerics.ReaderHelper.generate_index_function(
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generate_index_function(
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MetaInfo,
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sam_metainfo_machine,
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:(mark1 = mark2 = offset = 0),
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sam_metainfo_actions))
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eval(
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BioGenerics.ReaderHelper.generate_readheader_function(
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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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:(mark1 = mark2 = offset = 0),
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merge(sam_metainfo_actions, Dict(
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:metainfo => quote
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BioGenerics.ReaderHelper.resize_and_copy!(record.data, data, BioGenerics.ReaderHelper.upanchor!(stream):p-1)
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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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BioGenerics.ReaderHelper.ensure_margin!(stream)
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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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:anchor => :(BioGenerics.ReaderHelper.anchor!(stream, p); offset = p - 1))),
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:anchor => :(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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@ -234,28 +403,28 @@ const sam_record_actions = Dict(
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:record_qual => :(record.qual = (mark:p-1) .- offset),
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:record_field => :(push!(record.fields, (mark:p-1) .- offset)),
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:record => quote
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BioGenerics.ReaderHelper.resize_and_copy!(record.data, data, 1:p-1)
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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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:anchor => :(),
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:mark => :(mark = p))
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eval(
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BioGenerics.ReaderHelper.generate_index_function(
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generate_index_function(
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Record,
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sam_record_machine,
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:(mark = offset = 0),
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sam_record_actions))
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eval(
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BioGenerics.ReaderHelper.generate_read_function(
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generate_read_function(
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Reader,
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sam_body_machine,
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:(mark = offset = 0),
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merge(sam_record_actions, Dict(
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:record => quote
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BioGenerics.ReaderHelper.resize_and_copy!(record.data, data, BioGenerics.ReaderHelper.upanchor!(stream):p-1)
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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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found_record = true
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@escape
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end,
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:countline => :(linenum += 1),
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:anchor => :(BioGenerics.ReaderHelper.anchor!(stream, p); offset = p - 1)))))
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:anchor => :(anchor!(stream, p); offset = p - 1)))))
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