Merge branch 'release/v0.2.0'

Project.toml

@@ -1,28 +1,28 @@
 name = "XAM"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "0.1.1"
+version = "0.2.0"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
 BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
 BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
-BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
 GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 Indexes = "4ffb77ac-cb80-11e8-1b35-4b78cc642f6d"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
 [compat]
 Automa = "0.7, 0.8"
 BGZFStreams = "0.3"
 BioAlignments = "2"
-BioCore = "2"
+BioGenerics = "0.1"
 BioSequences = "2"
-BufferedStreams = "1"
 GenomicFeatures = "2"
 Indexes = "0.1"
+TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
 julia = "1.1"
 
 [extras]

src/bam/auxdata.jl

@@ -72,12 +72,15 @@ function loadauxtype(data::Vector{UInt8}, p::Int)
             b == UInt8('Z') ? String :
             error("invalid type tag: '$(Char(b))'"))
     end
+
     t = data[p]
+
     if t == UInt8('B')
         return p + 2, Vector{auxtype(data[p+1])}
-    else
-        return p + 1, auxtype(t)
     end
+
+    return p + 1, auxtype(t)
+    
 end
 
 function loadauxvalue(data::Vector{UInt8}, p::Int, ::Type{T}) where T
@@ -105,14 +108,17 @@ end
 
 function findauxtag(data::Vector{UInt8}, start::Int, stop::Int, t1::UInt8, t2::UInt8)
     pos = start
+
     while pos ≤ stop && !(data[pos] == t1 && data[pos+1] == t2)
         pos = next_tag_position(data, pos)
     end
+
     if pos > stop
         return 0
-    else
-        return pos
     end
+
+    return pos
+
 end
 
 # Find the starting position of a next tag in `data` after `p`.
@@ -120,24 +126,40 @@ end
 function next_tag_position(data::Vector{UInt8}, p::Int)
     typ = Char(data[p+2])
     p += 3
+
     if typ == 'A'
-        p += 1
+        return p += 1
-    elseif typ == 'c' || typ == 'C'
+    end
-        p += 1
+
-    elseif typ == 's' || typ == 'S'
+    if typ == 'c' || typ == 'C'
-        p += 2
+        return p += 1
-    elseif typ == 'i' || typ == 'I'
+    end
-        p += 4
+
-    elseif typ == 'f'
+    if typ == 's' || typ == 'S'
-        p += 4
+        return p += 2
-    elseif typ == 'd'
+    end
-        p += 8
+
-    elseif typ == 'Z' || typ == 'H'
+    if typ == 'i' || typ == 'I'
+        return p += 4
+    end
+
+    if typ == 'f'
+        return p += 4
+    end
+
+    if typ == 'd'
+        return p += 8
+    end
+
+    if typ == 'Z' || typ == 'H'
         while data[p] != 0x00  # NULL-terminalted string
             p += 1
         end
-        p += 1
+        return p += 1
-    elseif typ == 'B'
+
+    end
+
+    if typ == 'B'
         eltyp = Char(data[p])
         elsize = eltyp == 'c' || eltyp == 'C'                 ? 1 :
                  eltyp == 's' || eltyp == 'S'                 ? 2 :
@@ -145,9 +167,9 @@ function next_tag_position(data::Vector{UInt8}, p::Int)
                  error("invalid type tag: '$(Char(eltyp))'")
         p += 1
         n = unsafe_load(Ptr{Int32}(pointer(data, p)))
-        p += 4 + elsize * n
+        return p += 4 + elsize * n
-    else
-        error("invalid type tag: '$(Char(typ))'")
     end
-    return p
+
+    error("invalid type tag: '$(Char(typ))'")
+
 end

src/bam/bam.jl

@@ -3,7 +3,7 @@
 
 module BAM
 
-using BioCore
+using BioGenerics
 using GenomicFeatures
 using XAM.SAM
 
@@ -11,7 +11,7 @@ import BGZFStreams
 import BioAlignments
 import Indexes
 import BioSequences
-import BioCore: isfilled, header
+import BioGenerics: isfilled, header
 
 import GenomicFeatures: eachoverlap
 

src/bam/overlap.jl

@@ -16,7 +16,7 @@ function Base.eltype(::Type{OverlapIterator{T}}) where T
 end
 
 function GenomicFeatures.eachoverlap(reader::Reader, interval::Interval)
-    return GenomicFeatures.eachoverlap(reader, interval.seqname, interval.first:interval.last)
+    return GenomicFeatures.eachoverlap(reader, GenomicFeatures.seqname(interval), GenomicFeatures.leftposition(interval):GenomicFeatures.rightposition(interval))
 end
 
 function GenomicFeatures.eachoverlap(reader::Reader, interval)
@@ -67,7 +67,8 @@ function Base.iterate(iter::OverlapIterator, state)
             c = compare_intervals(state.record, (state.refindex, iter.interval))
             if c == 0
                 return copy(state.record), state
-            elseif c > 0
+            end
+            if c > 0
                 # no more overlapping records in this chunk since records are sorted
                 break
             end
@@ -82,14 +83,18 @@ end
 
 function compare_intervals(record::Record, interval::Tuple{Int,UnitRange{Int}})
     rid = refid(record)
+
     if rid < interval[1] || (rid == interval[1] && rightposition(record) < first(interval[2]))
         # strictly left
         return -1
-    elseif rid > interval[1] || (rid == interval[1] && position(record) > last(interval[2]))
+    end
+
+    if rid > interval[1] || (rid == interval[1] && position(record) > last(interval[2]))
         # strictly right
         return +1
-    else
-        # overlapping
-        return 0
     end
+
+    # overlapping
+    return 0
+
 end

src/bam/reader.jl

@@ -10,7 +10,7 @@ Create a data reader of the BAM file format.
 * `input`: data source
 * `index=nothing`: filepath to a random access index (currently *bai* is supported)
 """
-mutable struct Reader{T} <: BioCore.IO.AbstractReader
+mutable struct Reader{T} <: BioGenerics.IO.AbstractReader
     stream::BGZFStreams.BGZFStream{T}
     header::SAM.Header
     start_offset::BGZFStreams.VirtualOffset
@@ -23,17 +23,15 @@ function Base.eltype(::Type{Reader{T}}) where T
     return Record
 end
 
-function BioCore.IO.stream(reader::Reader)
+function BioGenerics.IO.stream(reader::Reader)
     return reader.stream
 end
 
 function Reader(input::IO; index=nothing)
     if isa(index, AbstractString)
         index = BAI(index)
-    else
+    elseif index != nothing
-        if index != nothing
+        error("unrecognizable index argument")
-            error("unrecognizable index argument")
-        end
     end
     reader = init_bam_reader(input)
     reader.index = index
@@ -89,6 +87,7 @@ function init_bam_reader(input::BGZFStreams.BGZFStream)
     A = read(input, UInt8)
     M = read(input, UInt8)
     x = read(input, UInt8)
+
     if B != UInt8('B') || A != UInt8('A') || M != UInt8('M') || x != 0x01
         error("input was not a valid BAM file")
     end
@@ -98,21 +97,22 @@ function init_bam_reader(input::BGZFStreams.BGZFStream)
     samreader = SAM.Reader(IOBuffer(read(input, textlen)))
 
     # reference sequences
-    refseqnames = String[]
-    refseqlens = Int[]
     n_refs = read(input, Int32)
-    for _ in 1:n_refs
+    refseqnames = Vector{String}(undef, n_refs)
+    refseqlens = Vector{Int}(undef, n_refs)
+    @inbounds for i in 1:n_refs
         namelen = read(input, Int32)
         data = read(input, namelen)
         seqname = unsafe_string(pointer(data))
         seqlen = read(input, Int32)
-        push!(refseqnames, seqname)
+        refseqnames[i] = seqname
-        push!(refseqlens, seqlen)
+        refseqlens[i] = seqlen
     end
 
     voffset = isa(input.io, Base.AbstractPipe) ?
         BGZFStreams.VirtualOffset(0, 0) :
         BGZFStreams.virtualoffset(input)
+
     return Reader(
         input,
         samreader.header,

src/bam/record.jl

@@ -163,7 +163,8 @@ function checked_refid(record::Record)
     id = refid(record)
     if id == 0
         throw(ArgumentError("record is not mapped"))
-    elseif !isdefined(record, :reader)
+    end
+    if !isdefined(record, :reader)
         throw(ArgumentError("reader is not defined"))
     end
     return id
@@ -565,42 +566,42 @@ function Base.values(record::Record)
 end
 
 
-# BioCore Methods
+# BioGenerics Methods
 # -----------
 
-function BioCore.isfilled(record::Record)
+function BioGenerics.isfilled(record::Record)
     return record.block_size != 0
 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.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
 
-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
 
@@ -612,9 +613,10 @@ end
 function data_size(record::Record)
     if isfilled(record)
         return record.block_size - FIXED_FIELDS_BYTES + sizeof(record.block_size)
-    else
-        return 0
     end
+
+    return 0
+
 end
 
 function checkfilled(record::Record)

src/bam/writer.jl

@@ -10,7 +10,7 @@ Create a data writer of the BAM file format.
 * `output`: data sink
 * `header`: SAM header object
 """
-mutable struct Writer <: BioCore.IO.AbstractWriter
+mutable struct Writer <: BioGenerics.IO.AbstractWriter
     stream::BGZFStreams.BGZFStream
 end
 
@@ -25,7 +25,7 @@ function Writer(stream::BGZFStreams.BGZFStream, header::SAM.Header)
     return Writer(stream)
 end
 
-function BioCore.IO.stream(writer::Writer)
+function BioGenerics.IO.stream(writer::Writer)
     return writer.stream
 end
 

src/sam/reader.jl

@@ -1,16 +1,22 @@
 # SAM Reader
 # =========
 
-mutable struct Reader <: BioCore.IO.AbstractReader
+mutable struct Reader{S <: TranscodingStream} <: BioGenerics.IO.AbstractReader
-    state::BioCore.Ragel.State
+    state::State{S}
     header::Header
+end
 
-    function Reader(input::BufferedStreams.BufferedInputStream)
+function Reader(state::State{S}) where {S <: TranscodingStream}
-        reader = new(BioCore.Ragel.State(sam_header_machine.start_state, input), Header())
+
-        readheader!(reader)
+    rdr = Reader(state, Header())
-        reader.state.cs = sam_body_machine.start_state
+
-        return reader
+    cs, ln, f = readheader!(rdr.state.stream, rdr.header, (sam_machine_header.start_state, rdr.state.linenum))
-    end
+
+    rdr.state.state = sam_machine_body.start_state
+    rdr.state.linenum = ln
+    rdr.state.filled = false
+
+    return rdr
 end
 
 """
@@ -22,10 +28,22 @@ Create a data reader of the SAM file format.
 * `input`: data source
 """
 function Reader(input::IO)
-    return Reader(BufferedStreams.BufferedInputStream(input))
+
+    if input isa TranscodingStream
+        return Reader(State(input, 1, 1, false))
+    end
+
+    stream = TranscodingStreams.NoopStream(input)
+
+    return Reader(State(stream, 1, 1, false))
+
 end
 
-function BioCore.IO.stream(reader::Reader)
+function Base.eltype(::Type{<:Reader})
+    return Record
+end
+
+function BioGenerics.IO.stream(reader::Reader)
     return reader.state.stream
 end
 
@@ -38,224 +56,42 @@ function header(reader::Reader)::Header
     return reader.header
 end
 
-function Base.eltype(::Type{Reader})
+function Base.close(reader::Reader)
-    return Record
+    if reader.state.stream isa IO
+        close(reader.state.stream)
+    end
+    return nothing
 end
 
-# file   = header . body
+function index!(record::MetaInfo)
-# header = metainfo*
+    stream = TranscodingStreams.NoopStream(IOBuffer(record.data))
-# body   = record*
+    found = index!(stream, record)
-isinteractive() && info("compiling SAM")
+    if !found
-const sam_metainfo_machine, sam_record_machine, sam_header_machine, sam_body_machine = (function ()
+        throw(ArgumentError("invalid SAM metadata"))
-    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] = [:mark1]
-        tag.actions[:exit]  = [:metainfo_tag]
-
-        dict = let
-            key = re"[A-Za-z][A-Za-z0-9]"
-            key.actions[:enter] = [:mark2]
-            key.actions[:exit]  = [:metainfo_dict_key]
-            val = re"[ -~]+"
-            val.actions[:enter] = [:mark2]
-            val.actions[:exit]  = [:metainfo_dict_val]
-            keyval = cat(key, ':', val)
-
-            cat(keyval, rep(cat('\t', keyval)))
-        end
-        dict.actions[:enter] = [:mark1]
-        dict.actions[:exit]  = [:metainfo_val]
-
-        co = cat("CO")
-        co.actions[:enter] = [:mark1]
-        co.actions[:exit]  = [:metainfo_tag]
-
-        comment = re"[^\r\n]*"
-        comment.actions[:enter] = [:mark1]
-        comment.actions[:exit]  = [:metainfo_val]
-
-        cat('@', alt(cat(tag, '\t', dict), cat(co, '\t', comment)))
     end
-    metainfo.actions[:enter] = [:anchor]
+    return record
-    metainfo.actions[:exit]  = [:metainfo]
+end
 
-    record = let
+function index!(record::Record)
-        qname = re"[!-?A-~]+"
+    stream = TranscodingStreams.NoopStream(IOBuffer(record.data))
-        qname.actions[:enter] = [:mark]
+    found = index!(stream, record)
-        qname.actions[:exit]  = [:record_qname]
+    if !found
-
+        throw(ArgumentError("invalid SAM record"))
-        flag = re"[0-9]+"
-        flag.actions[:enter] = [:mark]
-        flag.actions[:exit]  = [:record_flag]
-
-        rname = re"\*|[!-()+-<>-~][!-~]*"
-        rname.actions[:enter] = [:mark]
-        rname.actions[:exit]  = [:record_rname]
-
-        pos = re"[0-9]+"
-        pos.actions[:enter] = [:mark]
-        pos.actions[:exit]  = [:record_pos]
-
-        mapq = re"[0-9]+"
-        mapq.actions[:enter] = [:mark]
-        mapq.actions[:exit]  = [:record_mapq]
-
-        cigar = re"\*|([0-9]+[MIDNSHPX=])+"
-        cigar.actions[:enter] = [:mark]
-        cigar.actions[:exit]  = [:record_cigar]
-
-        rnext = re"\*|=|[!-()+-<>-~][!-~]*"
-        rnext.actions[:enter] = [:mark]
-        rnext.actions[:exit]  = [:record_rnext]
-
-        pnext = re"[0-9]+"
-        pnext.actions[:enter] = [:mark]
-        pnext.actions[:exit]  = [:record_pnext]
-
-        tlen = re"[-+]?[0-9]+"
-        tlen.actions[:enter] = [:mark]
-        tlen.actions[:exit]  = [:record_tlen]
-
-        seq = re"\*|[A-Za-z=.]+"
-        seq.actions[:enter] = [:mark]
-        seq.actions[:exit]  = [:record_seq]
-
-        qual = re"[!-~]+"
-        qual.actions[:enter] = [:mark]
-        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] = [:mark]
-        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] = [:anchor]
+    return record
-    record.actions[:exit]  = [:record]
+end
 
-    newline = let
+function Base.read!(rdr::Reader, rec::Record)
-        lf = re"\n"
-        lf.actions[:enter] = [:countline]
 
-        cat(re"\r?", lf)
+    cs, ln, f = readrecord!(rdr.state.stream, rec, (rdr.state.state, rdr.state.linenum))
+
+    rdr.state.state = cs
+    rdr.state.linenum = ln
+    rdr.state.filled = f
+
+    if !f
+        cs == 0 && throw(EOFError())
+        throw(ArgumentError("malformed SAM file"))
     end
-
+    return rec
-    header′ = rep(cat(metainfo, newline))
+end
-    header′.actions[:exit] = [:header]
-    header = cat(header′, opt(any() \ cat('@')))  # look ahead
-
-    body = rep(cat(record, newline))
-
-    return map(Automa.compile, (metainfo, record, header, body))
-end)()
-
-const sam_metainfo_actions = Dict(
-    :metainfo_tag => :(record.tag = (mark1:p-1) .- offset),
-    :metainfo_val => :(record.val = (mark1:p-1) .- offset),
-    :metainfo_dict_key => :(push!(record.dictkey, (mark2:p-1) .- offset)),
-    :metainfo_dict_val => :(push!(record.dictval, (mark2:p-1) .- offset)),
-    :metainfo => quote
-        BioCore.ReaderHelper.resize_and_copy!(record.data, data, offset+1:p-1)
-        record.filled = (offset+1:p-1) .- offset
-    end,
-    :anchor => :(),
-    :mark1  => :(mark1 = p),
-    :mark2  => :(mark2 = p))
-eval(
-    BioCore.ReaderHelper.generate_index_function(
-        MetaInfo,
-        sam_metainfo_machine,
-        :(mark1 = mark2 = offset = 0),
-        sam_metainfo_actions))
-eval(
-    BioCore.ReaderHelper.generate_readheader_function(
-        Reader,
-        MetaInfo,
-        sam_header_machine,
-        :(mark1 = mark2 = offset = 0),
-        merge(sam_metainfo_actions, Dict(
-            :metainfo => quote
-                BioCore.ReaderHelper.resize_and_copy!(record.data, data, BioCore.ReaderHelper.upanchor!(stream):p-1)
-                record.filled = (offset+1:p-1) .- offset
-                @assert isfilled(record)
-                push!(reader.header.metainfo, record)
-                BioCore.ReaderHelper.ensure_margin!(stream)
-                record = MetaInfo()
-            end,
-            :header => :(finish_header = true; @escape),
-            :countline => :(linenum += 1),
-            :anchor => :(BioCore.ReaderHelper.anchor!(stream, p); offset = p - 1))),
-        quote
-            if !eof(stream)
-                stream.position -= 1  # cancel look-ahead
-            end
-        end))
-
-const sam_record_actions = Dict(
-    :record_qname => :(record.qname = (mark:p-1) .- offset),
-    :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)
-        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
-                found_record = true
-                @escape
-            end,
-            :countline => :(linenum += 1),
-            :anchor    => :(BioCore.ReaderHelper.anchor!(stream, p); offset = p - 1)))))

src/sam/readrecord.jl

@@ -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

src/sam/record.jl

@@ -299,9 +299,10 @@ Get the alignment of `record`.
 function alignment(record::Record)::BioAlignments.Alignment
     if ismapped(record)
         return BioAlignments.Alignment(cigar(record), 1, position(record))
-    else
-        return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
     end
+
+    return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
+
 end
 
 function hasalignment(record::Record)
@@ -474,23 +475,30 @@ function Base.getindex(record::Record, tag::AbstractString)
     else
         hi = first(record.fields[i+1]) - 2
     end
+
     if typ == UInt8('A')
         @assert lo == hi
         return Char(record.data[lo])
-    elseif typ == UInt8('i')
+    end
+    if typ == UInt8('i')
         return unsafe_parse_decimal(Int, record.data, lo:hi)
-    elseif typ == UInt8('f')
+    end
+    if typ == UInt8('f')
         # TODO: Call a C function directly for speed?
         return parse(Float32, SubString(record.data[lo:hi]))
-    elseif typ == UInt8('Z')
-        return String(record.data[lo:hi])
-    elseif typ == UInt8('H')
-        return parse_hexarray(record.data, lo:hi)
-    elseif typ == UInt8('B')
-        return parse_typedarray(record.data, lo:hi)
-    else
-        throw(ArgumentError("type code '$(Char(typ))' is not defined"))
     end
+    if typ == UInt8('Z')
+        return String(record.data[lo:hi])
+    end
+    if typ == UInt8('H')
+        return parse_hexarray(record.data, lo:hi)
+    end
+    if typ == UInt8('B')
+        return parse_typedarray(record.data, lo:hi)
+    end
+
+    throw(ArgumentError("type code '$(Char(typ))' is not defined"))
+
 end
 
 function Base.keys(record::Record)
@@ -506,39 +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
 
@@ -602,21 +610,28 @@ function parse_typedarray(data::Vector{UInt8}, range::UnitRange{Int})
     xs = split(String(data[first(range)+2:last(range)]))
     if t == UInt8('c')
         return [parse(Int8, x) for x in xs]
-    elseif t == UInt8('C')
-        return [parse(UInt8, x) for x in xs]
-    elseif t == UInt8('s')
-        return [parse(Int16, x) for x in xs]
-    elseif t == UInt8('S')
-        return [parse(UInt16, x) for x in xs]
-    elseif t == UInt8('i')
-        return [parse(Int32, x) for x in xs]
-    elseif t == UInt8('I')
-        return [parse(UInt32, x) for x in xs]
-    elseif t == UInt8('f')
-        return [parse(Float32, x) for x in xs]
-    else
-        throw(ArgumentError("type code '$(Char(t))' is not defined"))
     end
+    if t == UInt8('C')
+        return [parse(UInt8, x) for x in xs]
+    end
+    if t == UInt8('s')
+        return [parse(Int16, x) for x in xs]
+    end
+    if t == UInt8('S')
+        return [parse(UInt16, x) for x in xs]
+    end
+    if t == UInt8('i')
+        return [parse(Int32, x) for x in xs]
+    end
+    if t == UInt8('I')
+        return [parse(UInt32, x) for x in xs]
+    end
+    if t == UInt8('f')
+        return [parse(Float32, x) for x in xs]
+    end
+
+    throw(ArgumentError("type code '$(Char(t))' is not defined"))
+
 end
 
 function ismissing(record::Record, range::UnitRange{Int})

src/sam/sam.jl

@@ -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 BioGenerics: BioGenerics, isfilled, header
-import BioCore.RecordHelper: unsafe_parse_decimal
+import BioGenerics.Exceptions: missingerror
-import BioCore: isfilled, header
+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

src/sam/writer.jl

@@ -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
 

test/runtests.jl

@@ -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)