mirror of
https://github.com/MillironX/XAM.jl.git
synced 2024-12-23 21:28:18 +00:00
Merge branch 'feature/transcodingstreams' into develop
This commit is contained in:
Ciarán O'Mara
commit
2aaab4d9ab
11 changed files with 545 additions and 273 deletions
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@ -7,22 +7,22 @@ version = "0.1.1"
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Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
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BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
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BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
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BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
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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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BGZFStreams = "0.3"
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BioAlignments = "2"
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BioCore = "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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@ -3,7 +3,7 @@
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module BAM
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using BioCore
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using BioGenerics
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using GenomicFeatures
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using XAM.SAM
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@ -11,7 +11,7 @@ import BGZFStreams
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import BioAlignments
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import Indexes
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import BioSequences
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import BioCore: isfilled, header
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import BioGenerics: isfilled, header
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import GenomicFeatures: eachoverlap
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@ -10,7 +10,7 @@ Create a data reader of the BAM file format.
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* `input`: data source
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* `index=nothing`: filepath to a random access index (currently *bai* is supported)
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"""
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mutable struct Reader{T} <: BioCore.IO.AbstractReader
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mutable struct Reader{T} <: BioGenerics.IO.AbstractReader
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stream::BGZFStreams.BGZFStream{T}
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header::SAM.Header
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start_offset::BGZFStreams.VirtualOffset
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@ -23,7 +23,7 @@ function Base.eltype(::Type{Reader{T}}) where T
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return Record
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end
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function BioCore.IO.stream(reader::Reader)
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function BioGenerics.IO.stream(reader::Reader)
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return reader.stream
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end
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@ -566,42 +566,42 @@ function Base.values(record::Record)
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end
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# BioCore Methods
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# BioGenerics Methods
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# -----------
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function BioCore.isfilled(record::Record)
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function BioGenerics.isfilled(record::Record)
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return record.block_size != 0
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end
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function BioCore.seqname(record::Record)
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function BioGenerics.seqname(record::Record)
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return tempname(record)
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end
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function BioCore.hasseqname(record::Record)
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function BioGenerics.hasseqname(record::Record)
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return hastempname(record)
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end
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function BioCore.sequence(record::Record)
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function BioGenerics.sequence(record::Record)
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return sequence(record)
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end
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function BioCore.hassequence(record::Record)
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function BioGenerics.hassequence(record::Record)
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return hassequence(record)
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end
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function BioCore.leftposition(record::Record)
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function BioGenerics.leftposition(record::Record)
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return position(record)
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end
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function BioCore.hasleftposition(record::Record)
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function BioGenerics.hasleftposition(record::Record)
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return hasposition(record)
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end
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function BioCore.rightposition(record::Record)
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function BioGenerics.rightposition(record::Record)
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return rightposition(record)
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end
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function BioCore.hasrightposition(record::Record)
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function BioGenerics.hasrightposition(record::Record)
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return hasrightposition(record)
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end
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@ -10,7 +10,7 @@ Create a data writer of the BAM file format.
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* `output`: data sink
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* `header`: SAM header object
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"""
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mutable struct Writer <: BioCore.IO.AbstractWriter
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mutable struct Writer <: BioGenerics.IO.AbstractWriter
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stream::BGZFStreams.BGZFStream
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end
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@ -25,7 +25,7 @@ function Writer(stream::BGZFStreams.BGZFStream, header::SAM.Header)
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return Writer(stream)
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end
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function BioCore.IO.stream(writer::Writer)
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function BioGenerics.IO.stream(writer::Writer)
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return writer.stream
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end
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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 <: BioCore.IO.AbstractReader
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state::BioCore.Ragel.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(BioCore.Ragel.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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@ -22,10 +28,22 @@ 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 BioCore.IO.stream(reader::Reader)
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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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return reader.state.stream
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end
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@ -38,224 +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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# file = header . body
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# header = metainfo*
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# body = record*
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isinteractive() && info("compiling SAM")
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const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_machine = (function ()
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cat = Automa.RegExp.cat
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rep = Automa.RegExp.rep
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alt = Automa.RegExp.alt
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opt = Automa.RegExp.opt
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any = Automa.RegExp.any
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metainfo = let
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tag = re"[A-Z][A-Z]" \ cat("CO")
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tag.actions[:enter] = [:mark1]
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tag.actions[:exit] = [:metainfo_tag]
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dict = let
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key = re"[A-Za-z][A-Za-z0-9]"
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key.actions[:enter] = [:mark2]
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key.actions[:exit] = [:metainfo_dict_key]
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val = re"[ -~]+"
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val.actions[:enter] = [:mark2]
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val.actions[:exit] = [:metainfo_dict_val]
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keyval = cat(key, ':', val)
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cat(keyval, rep(cat('\t', keyval)))
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end
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dict.actions[:enter] = [:mark1]
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dict.actions[:exit] = [:metainfo_val]
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co = cat("CO")
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co.actions[:enter] = [:mark1]
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co.actions[:exit] = [:metainfo_tag]
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comment = re"[^\r\n]*"
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comment.actions[:enter] = [:mark1]
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comment.actions[:exit] = [:metainfo_val]
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cat('@', alt(cat(tag, '\t', dict), cat(co, '\t', comment)))
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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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metainfo.actions[:enter] = [:anchor]
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metainfo.actions[:exit] = [:metainfo]
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return record
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end
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record = let
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qname = re"[!-?A-~]+"
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qname.actions[:enter] = [:mark]
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qname.actions[:exit] = [:record_qname]
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flag = re"[0-9]+"
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flag.actions[:enter] = [:mark]
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flag.actions[:exit] = [:record_flag]
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rname = re"\*|[!-()+-<>-~][!-~]*"
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rname.actions[:enter] = [:mark]
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rname.actions[:exit] = [:record_rname]
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pos = re"[0-9]+"
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pos.actions[:enter] = [:mark]
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pos.actions[:exit] = [:record_pos]
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mapq = re"[0-9]+"
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mapq.actions[:enter] = [:mark]
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mapq.actions[:exit] = [:record_mapq]
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cigar = re"\*|([0-9]+[MIDNSHPX=])+"
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cigar.actions[:enter] = [:mark]
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cigar.actions[:exit] = [:record_cigar]
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rnext = re"\*|=|[!-()+-<>-~][!-~]*"
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rnext.actions[:enter] = [:mark]
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rnext.actions[:exit] = [:record_rnext]
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pnext = re"[0-9]+"
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pnext.actions[:enter] = [:mark]
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pnext.actions[:exit] = [:record_pnext]
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tlen = re"[-+]?[0-9]+"
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tlen.actions[:enter] = [:mark]
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tlen.actions[:exit] = [:record_tlen]
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seq = re"\*|[A-Za-z=.]+"
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seq.actions[:enter] = [:mark]
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seq.actions[:exit] = [:record_seq]
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qual = re"[!-~]+"
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qual.actions[:enter] = [:mark]
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qual.actions[:exit] = [:record_qual]
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field = let
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tag = re"[A-Za-z][A-Za-z0-9]"
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val = alt(
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re"A:[!-~]",
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re"i:[-+]?[0-9]+",
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re"f:[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?",
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re"Z:[ !-~]*",
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re"H:([0-9A-F][0-9A-F])*",
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re"B:[cCsSiIf](,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)+")
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cat(tag, ':', val)
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end
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field.actions[:enter] = [:mark]
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field.actions[:exit] = [:record_field]
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cat(
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qname, '\t',
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flag, '\t',
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rname, '\t',
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pos, '\t',
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mapq, '\t',
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cigar, '\t',
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rnext, '\t',
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pnext, '\t',
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tlen, '\t',
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seq, '\t',
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qual,
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rep(cat('\t', field)))
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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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record.actions[:enter] = [:anchor]
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record.actions[:exit] = [:record]
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return record
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end
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newline = let
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lf = re"\n"
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lf.actions[:enter] = [:countline]
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function Base.read!(rdr::Reader, rec::Record)
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cat(re"\r?", lf)
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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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header′ = rep(cat(metainfo, newline))
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header′.actions[:exit] = [:header]
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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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return map(Automa.compile, (metainfo, record, header, body))
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end)()
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const sam_metainfo_actions = Dict(
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:metainfo_tag => :(record.tag = (mark1:p-1) .- offset),
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:metainfo_val => :(record.val = (mark1:p-1) .- offset),
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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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BioCore.ReaderHelper.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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BioCore.ReaderHelper.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))
|
||||
eval(
|
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BioCore.ReaderHelper.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),
|
||||
merge(sam_metainfo_actions, Dict(
|
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:metainfo => quote
|
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BioCore.ReaderHelper.resize_and_copy!(record.data, data, BioCore.ReaderHelper.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)
|
||||
BioCore.ReaderHelper.ensure_margin!(stream)
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record = MetaInfo()
|
||||
end,
|
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:header => :(finish_header = true; @escape),
|
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:countline => :(linenum += 1),
|
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:anchor => :(BioCore.ReaderHelper.anchor!(stream, p); offset = p - 1))),
|
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quote
|
||||
if !eof(stream)
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stream.position -= 1 # cancel look-ahead
|
||||
end
|
||||
end))
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||||
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const sam_record_actions = Dict(
|
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:record_qname => :(record.qname = (mark:p-1) .- offset),
|
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:record_flag => :(record.flag = (mark:p-1) .- offset),
|
||||
:record_rname => :(record.rname = (mark:p-1) .- offset),
|
||||
:record_pos => :(record.pos = (mark:p-1) .- offset),
|
||||
:record_mapq => :(record.mapq = (mark:p-1) .- offset),
|
||||
:record_cigar => :(record.cigar = (mark:p-1) .- offset),
|
||||
:record_rnext => :(record.rnext = (mark:p-1) .- offset),
|
||||
:record_pnext => :(record.pnext = (mark:p-1) .- offset),
|
||||
:record_tlen => :(record.tlen = (mark:p-1) .- offset),
|
||||
:record_seq => :(record.seq = (mark:p-1) .- offset),
|
||||
:record_qual => :(record.qual = (mark:p-1) .- offset),
|
||||
:record_field => :(push!(record.fields, (mark:p-1) .- offset)),
|
||||
:record => quote
|
||||
BioCore.ReaderHelper.resize_and_copy!(record.data, data, 1:p-1)
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record.filled = (offset+1:p-1) .- offset
|
||||
end,
|
||||
:anchor => :(),
|
||||
:mark => :(mark = p))
|
||||
eval(
|
||||
BioCore.ReaderHelper.generate_index_function(
|
||||
Record,
|
||||
sam_record_machine,
|
||||
:(mark = offset = 0),
|
||||
sam_record_actions))
|
||||
eval(
|
||||
BioCore.ReaderHelper.generate_read_function(
|
||||
Reader,
|
||||
sam_body_machine,
|
||||
:(mark = offset = 0),
|
||||
merge(sam_record_actions, Dict(
|
||||
:record => quote
|
||||
BioCore.ReaderHelper.resize_and_copy!(record.data, data, BioCore.ReaderHelper.upanchor!(stream):p-1)
|
||||
record.filled = (offset+1:p-1) .- offset
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||||
found_record = true
|
||||
@escape
|
||||
end,
|
||||
:countline => :(linenum += 1),
|
||||
:anchor => :(BioCore.ReaderHelper.anchor!(stream, p); offset = p - 1)))))
|
||||
return rec
|
||||
end
|
||||
|
|
|
|||
395
src/sam/readrecord.jl
Normal file
395
src/sam/readrecord.jl
Normal file
|
|
@ -0,0 +1,395 @@
|
|||
# Automa.jl generated readrecord! and readmetainfo! functions
|
||||
# ========================================
|
||||
|
||||
# file = header . body
|
||||
# header = metainfo*
|
||||
# body = record*
|
||||
const sam_machine_metainfo, sam_machine_record, sam_machine_header, sam_machine_body, sam_machine = (function ()
|
||||
|
||||
isinteractive() && info("compiling SAM")
|
||||
|
||||
cat = Automa.RegExp.cat
|
||||
rep = Automa.RegExp.rep
|
||||
alt = Automa.RegExp.alt
|
||||
opt = Automa.RegExp.opt
|
||||
any = Automa.RegExp.any
|
||||
|
||||
metainfo = let
|
||||
tag = re"[A-Z][A-Z]" \ cat("CO")
|
||||
tag.actions[:enter] = [:pos1]
|
||||
tag.actions[:exit] = [:metainfo_tag]
|
||||
|
||||
dict = let
|
||||
key = re"[A-Za-z][A-Za-z0-9]"
|
||||
key.actions[:enter] = [:pos2]
|
||||
key.actions[:exit] = [:metainfo_dict_key]
|
||||
val = re"[ -~]+"
|
||||
val.actions[:enter] = [:pos2]
|
||||
val.actions[:exit] = [:metainfo_dict_val]
|
||||
keyval = cat(key, ':', val)
|
||||
|
||||
cat(keyval, rep(cat('\t', keyval)))
|
||||
end
|
||||
dict.actions[:enter] = [:pos1]
|
||||
dict.actions[:exit] = [:metainfo_val]
|
||||
|
||||
co = cat("CO")
|
||||
co.actions[:enter] = [:pos1]
|
||||
co.actions[:exit] = [:metainfo_tag]
|
||||
|
||||
comment = re"[^\r\n]*"
|
||||
comment.actions[:enter] = [:pos1]
|
||||
comment.actions[:exit] = [:metainfo_val]
|
||||
|
||||
cat('@', alt(cat(tag, '\t', dict), cat(co, '\t', comment)))
|
||||
end
|
||||
metainfo.actions[:enter] = [:mark]
|
||||
metainfo.actions[:exit] = [:metainfo]
|
||||
|
||||
record = let
|
||||
qname = re"[!-?A-~]+"
|
||||
qname.actions[:enter] = [:pos]
|
||||
qname.actions[:exit] = [:record_qname]
|
||||
|
||||
flag = re"[0-9]+"
|
||||
flag.actions[:enter] = [:pos]
|
||||
flag.actions[:exit] = [:record_flag]
|
||||
|
||||
rname = re"\*|[!-()+-<>-~][!-~]*"
|
||||
rname.actions[:enter] = [:pos]
|
||||
rname.actions[:exit] = [:record_rname]
|
||||
|
||||
pos = re"[0-9]+"
|
||||
pos.actions[:enter] = [:pos]
|
||||
pos.actions[:exit] = [:record_pos]
|
||||
|
||||
mapq = re"[0-9]+"
|
||||
mapq.actions[:enter] = [:pos]
|
||||
mapq.actions[:exit] = [:record_mapq]
|
||||
|
||||
cigar = re"\*|([0-9]+[MIDNSHPX=])+"
|
||||
cigar.actions[:enter] = [:pos]
|
||||
cigar.actions[:exit] = [:record_cigar]
|
||||
|
||||
rnext = re"\*|=|[!-()+-<>-~][!-~]*"
|
||||
rnext.actions[:enter] = [:pos]
|
||||
rnext.actions[:exit] = [:record_rnext]
|
||||
|
||||
pnext = re"[0-9]+"
|
||||
pnext.actions[:enter] = [:pos]
|
||||
pnext.actions[:exit] = [:record_pnext]
|
||||
|
||||
tlen = re"[-+]?[0-9]+"
|
||||
tlen.actions[:enter] = [:pos]
|
||||
tlen.actions[:exit] = [:record_tlen]
|
||||
|
||||
seq = re"\*|[A-Za-z=.]+"
|
||||
seq.actions[:enter] = [:pos]
|
||||
seq.actions[:exit] = [:record_seq]
|
||||
|
||||
qual = re"[!-~]+"
|
||||
qual.actions[:enter] = [:pos]
|
||||
qual.actions[:exit] = [:record_qual]
|
||||
|
||||
field = let
|
||||
tag = re"[A-Za-z][A-Za-z0-9]"
|
||||
val = alt(
|
||||
re"A:[!-~]",
|
||||
re"i:[-+]?[0-9]+",
|
||||
re"f:[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?",
|
||||
re"Z:[ !-~]*",
|
||||
re"H:([0-9A-F][0-9A-F])*",
|
||||
re"B:[cCsSiIf](,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)+")
|
||||
|
||||
cat(tag, ':', val)
|
||||
end
|
||||
field.actions[:enter] = [:pos]
|
||||
field.actions[:exit] = [:record_field]
|
||||
|
||||
cat(
|
||||
qname, '\t',
|
||||
flag, '\t',
|
||||
rname, '\t',
|
||||
pos, '\t',
|
||||
mapq, '\t',
|
||||
cigar, '\t',
|
||||
rnext, '\t',
|
||||
pnext, '\t',
|
||||
tlen, '\t',
|
||||
seq, '\t',
|
||||
qual,
|
||||
rep(cat('\t', field)))
|
||||
end
|
||||
record.actions[:enter] = [:mark]
|
||||
record.actions[:exit] = [:record]
|
||||
|
||||
newline = let
|
||||
lf = re"\n"
|
||||
lf.actions[:enter] = [:countline]
|
||||
|
||||
cat(re"\r?", lf)
|
||||
end
|
||||
|
||||
header′ = rep(cat(metainfo, newline))
|
||||
header′.actions[:exit] = [:header]
|
||||
header = cat(header′, opt(any() \ cat('@'))) # look ahead
|
||||
|
||||
body = rep(cat(record, newline))
|
||||
body.actions[:exit] = [:body]
|
||||
|
||||
sam = cat(header, body)
|
||||
|
||||
return map(Automa.compile, (metainfo, record, header, body, sam))
|
||||
end)()
|
||||
|
||||
# write("sam_machine_metainfo.dot", Automa.machine2dot(sam_machine_metainfo))
|
||||
# run(`dot -Tsvg -o sam_machine_metainfo.svg sam_machine_metainfo.dot`)
|
||||
#
|
||||
# write("sam_machine_record.dot", Automa.machine2dot(sam_machine_record))
|
||||
# run(`dot -Tsvg -o sam_machine_record.svg sam_machine_record.dot`)
|
||||
#
|
||||
# write("sam_machine_header.dot", Automa.machine2dot(sam_machine_header))
|
||||
# run(`dot -Tsvg -o sam_machine_header.svg sam_machine_header.dot`)
|
||||
#
|
||||
# write("sam_machine_body.dot", Automa.machine2dot(sam_machine_body))
|
||||
# run(`dot -Tsvg -o sam_machine_body.svg sam_machine_body.dot`)
|
||||
#
|
||||
# write("sam_machine.dot", Automa.machine2dot(sam_machine))
|
||||
# run(`dot -Tsvg -o sam_machine.svg sam_machine.dot`)
|
||||
|
||||
function appendfrom!(dst, dpos, src, spos, n)
|
||||
if length(dst) < dpos + n - 1
|
||||
resize!(dst, dpos + n - 1)
|
||||
end
|
||||
copyto!(dst, dpos, src, spos, n)
|
||||
return dst
|
||||
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 => 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_header = merge(
|
||||
sam_actions_metainfo,
|
||||
Dict(
|
||||
:countline => :(linenum += 1),
|
||||
:header => quote
|
||||
|
||||
finish_header = true
|
||||
|
||||
if !eof(stream)
|
||||
p -= 1 # cancel look-ahead
|
||||
end
|
||||
|
||||
@escape
|
||||
end
|
||||
)
|
||||
)
|
||||
|
||||
const sam_actions_record = Dict(
|
||||
:mark => :(@mark),
|
||||
:pos => :(pos = @relpos(p)),
|
||||
:record_qname => :(record.qname = pos:@relpos(p-1)),
|
||||
:record_flag => :(record.flag = pos:@relpos(p-1)),
|
||||
:record_rname => :(record.rname = pos:@relpos(p-1)),
|
||||
:record_pos => :(record.pos = pos:@relpos(p-1)),
|
||||
:record_mapq => :(record.mapq = pos:@relpos(p-1)),
|
||||
:record_cigar => :(record.cigar = pos:@relpos(p-1)),
|
||||
:record_rnext => :(record.rnext = pos:@relpos(p-1)),
|
||||
:record_pnext => :(record.pnext = pos:@relpos(p-1)),
|
||||
:record_tlen => :(record.tlen = pos:@relpos(p-1)),
|
||||
: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)
|
||||
|
||||
found_record = true
|
||||
@escape
|
||||
end
|
||||
end
|
||||
)
|
||||
|
||||
const sam_actions_body = merge(
|
||||
sam_actions_record,
|
||||
Dict(
|
||||
:countline => :(linenum += 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
|
||||
|
|
@ -514,39 +514,39 @@ end
|
|||
# Bio Methods
|
||||
# -----------
|
||||
|
||||
function BioCore.isfilled(record::Record)
|
||||
function BioGenerics.isfilled(record::Record)
|
||||
return !isempty(record.filled)
|
||||
end
|
||||
|
||||
function BioCore.seqname(record::Record)
|
||||
function BioGenerics.seqname(record::Record)
|
||||
return tempname(record)
|
||||
end
|
||||
|
||||
function BioCore.hasseqname(record::Record)
|
||||
function BioGenerics.hasseqname(record::Record)
|
||||
return hastempname(record)
|
||||
end
|
||||
|
||||
function BioCore.sequence(record::Record)
|
||||
function BioGenerics.sequence(record::Record)
|
||||
return sequence(record)
|
||||
end
|
||||
|
||||
function BioCore.hassequence(record::Record)
|
||||
function BioGenerics.hassequence(record::Record)
|
||||
return hassequence(record)
|
||||
end
|
||||
|
||||
function BioCore.rightposition(record::Record)
|
||||
function BioGenerics.rightposition(record::Record)
|
||||
return rightposition(record)
|
||||
end
|
||||
|
||||
function BioCore.hasrightposition(record::Record)
|
||||
function BioGenerics.hasrightposition(record::Record)
|
||||
return hasrightposition(record)
|
||||
end
|
||||
|
||||
function BioCore.leftposition(record::Record)
|
||||
function BioGenerics.leftposition(record::Record)
|
||||
return position(record)
|
||||
end
|
||||
|
||||
function BioCore.hasleftposition(record::Record)
|
||||
function BioGenerics.hasleftposition(record::Record)
|
||||
return hasposition(record)
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -3,23 +3,73 @@
|
|||
|
||||
module SAM
|
||||
|
||||
using BioCore
|
||||
using BioGenerics
|
||||
|
||||
import Automa
|
||||
import Automa.RegExp: @re_str
|
||||
import Automa.Stream: @mark, @markpos, @relpos, @abspos
|
||||
import BioAlignments
|
||||
import BioCore.Exceptions: missingerror
|
||||
import BioCore.RecordHelper: unsafe_parse_decimal
|
||||
import BioCore: isfilled, header
|
||||
import BioGenerics: BioGenerics, isfilled, header
|
||||
import BioGenerics.Exceptions: missingerror
|
||||
import BioGenerics.Automa: State
|
||||
import BioSequences
|
||||
import BufferedStreams
|
||||
import TranscodingStreams: TranscodingStreams, TranscodingStream
|
||||
|
||||
using Printf: @sprintf
|
||||
|
||||
|
||||
#TODO: update import BioCore.RecordHelper: unsafe_parse_decimal
|
||||
# r"[0-9]+" must match `data[range]`.
|
||||
function unsafe_parse_decimal(::Type{T}, data::Vector{UInt8}, range::UnitRange{Int}) where {T<:Unsigned}
|
||||
x = zero(T)
|
||||
@inbounds for i in range
|
||||
x = Base.Checked.checked_mul(x, 10 % T)
|
||||
x = Base.Checked.checked_add(x, (data[i] - UInt8('0')) % T)
|
||||
end
|
||||
return x
|
||||
end
|
||||
|
||||
# r"[-+]?[0-9]+" must match `data[range]`.
|
||||
function unsafe_parse_decimal(::Type{T}, data::Vector{UInt8}, range::UnitRange{Int}) where {T<:Signed}
|
||||
lo = first(range)
|
||||
if data[lo] == UInt8('-')
|
||||
sign = T(-1)
|
||||
lo += 1
|
||||
elseif data[lo] == UInt8('+')
|
||||
sign = T(+1)
|
||||
lo += 1
|
||||
else
|
||||
sign = T(+1)
|
||||
end
|
||||
x = zero(T)
|
||||
@inbounds for i in lo:last(range)
|
||||
x = Base.Checked.checked_mul(x, 10 % T)
|
||||
x = Base.Checked.checked_add(x, (data[i] - UInt8('0')) % T)
|
||||
end
|
||||
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
|
||||
|
||||
# function State(initstate::Int, input::BufferedInputStream)
|
||||
# return State(input, initstate, 1, false)
|
||||
# end
|
||||
|
||||
|
||||
include("flags.jl")
|
||||
include("metainfo.jl")
|
||||
include("record.jl")
|
||||
include("header.jl")
|
||||
include("reader.jl")
|
||||
include("readrecord.jl")
|
||||
include("writer.jl")
|
||||
|
||||
end
|
||||
|
|
|
|||
|
|
@ -10,7 +10,7 @@ Create a data writer of the SAM file format.
|
|||
* `output`: data sink
|
||||
* `header=Header()`: SAM header object
|
||||
"""
|
||||
mutable struct Writer <: BioCore.IO.AbstractWriter
|
||||
mutable struct Writer <: BioGenerics.IO.AbstractWriter
|
||||
stream::IO
|
||||
|
||||
function Writer(output::IO, header::Header=Header())
|
||||
|
|
@ -20,7 +20,7 @@ mutable struct Writer <: BioCore.IO.AbstractWriter
|
|||
end
|
||||
end
|
||||
|
||||
function BioCore.IO.stream(writer::Writer)
|
||||
function BioGenerics.IO.stream(writer::Writer)
|
||||
return writer.stream
|
||||
end
|
||||
|
||||
|
|
|
|||
|
|
@ -1,25 +1,16 @@
|
|||
using Test
|
||||
|
||||
using BioGenerics
|
||||
using FormatSpecimens
|
||||
using GenomicFeatures
|
||||
using XAM
|
||||
|
||||
import BioAlignments: Alignment, AlignmentAnchor, OP_START, OP_MATCH, OP_DELETE
|
||||
using FormatSpecimens
|
||||
import BGZFStreams: BGZFStream
|
||||
import BioCore.Exceptions: MissingFieldException
|
||||
import BioGenerics.Exceptions: MissingFieldException
|
||||
import BioSequences: @dna_str, @aa_str
|
||||
|
||||
|
||||
import BioCore:
|
||||
header,
|
||||
isfilled,
|
||||
seqname,
|
||||
hasseqname,
|
||||
sequence,
|
||||
hassequence,
|
||||
leftposition,
|
||||
rightposition,
|
||||
hasleftposition,
|
||||
hasrightposition
|
||||
|
||||
# Generate a random range within `range`.
|
||||
function randrange(range)
|
||||
x = rand(range)
|
||||
|
|
|
|||
Loading…
Reference in a new issue