Rehaul BAM and SAM accessor functions

Changelog.md

@@ -0,0 +1,3 @@
+## Rehaul
+
+* [TODO: ADD STUFF]

Project.toml

@@ -5,23 +5,21 @@ version = "0.2.6"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
-BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
 BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
 BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+CodecBGZF = "d9d91ef6-315d-495b-8131-db2ca24339d6"
 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"
 BioGenerics = "0.1"
 BioSequences = "2.0.4"
 GenomicFeatures = "2"
-Indexes = "0.1"
 TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
 julia = "1"
 

TODO.md

@@ -0,0 +1,5 @@
+## SAM
+    * quality_iter
+    * no-copy auxdata
+    * Display similar to BAM
+    * convert SAM/BAM and vice versa

src/XAM.jl

@@ -4,6 +4,7 @@ export
     SAM,
     BAM
 
+include("common.jl")
 include("sam/sam.jl")
 include("bam/bam.jl")
 

src/bam/auxdata.jl

@@ -1,8 +1,8 @@
 # BAM Auxiliary Data
 # ==================
 
-struct AuxData <: AbstractDict{String,Any}
-    data::Vector{UInt8}
+struct AuxData{T <: AbstractVector{UInt8}} <: AbstractDict{String,Any}
+    data::T
 end
 
 function Base.getindex(aux::AuxData, tag::AbstractString)
@@ -48,7 +48,7 @@ function checkauxtag(tag::AbstractString)
     end
 end
 
-function getauxvalue(data::Vector{UInt8}, start::Int, stop::Int, t1::UInt8, t2::UInt8)
+function getauxvalue(data::AbstractVector{UInt8}, start::Int, stop::Int, t1::UInt8, t2::UInt8)
     pos = findauxtag(data, start, stop, t1, t2)
     if pos == 0
         throw(KeyError(String([t1, t2])))
@@ -58,7 +58,7 @@ function getauxvalue(data::Vector{UInt8}, start::Int, stop::Int, t1::UInt8, t2::
     return val
 end
 
-function loadauxtype(data::Vector{UInt8}, p::Int)
+function loadauxtype(data::AbstractVector{UInt8}, p::Int)
     function auxtype(b)
         return (
             b == UInt8('A') ? Char  :
@@ -83,30 +83,30 @@ function loadauxtype(data::Vector{UInt8}, p::Int)
 
 end
 
-function loadauxvalue(data::Vector{UInt8}, p::Int, ::Type{T}) where T
+function loadauxvalue(data::AbstractVector{UInt8}, p::Int, ::Type{T}) where T
     return p + sizeof(T), unsafe_load(Ptr{T}(pointer(data, p)))
 end
 
-function loadauxvalue(data::Vector{UInt8}, p::Int, ::Type{Char})
+function loadauxvalue(data::AbstractVector{UInt8}, p::Int, ::Type{Char})
     return p + 1, Char(unsafe_load(pointer(data, p)))
 end
 
-function loadauxvalue(data::Vector{UInt8}, p::Int, ::Type{Vector{T}}) where T
+function loadauxvalue(data::AbstractVector{UInt8}, p::Int, ::Type{Vector{T}}) where T
     n = unsafe_load(Ptr{Int32}(pointer(data, p)))
     p += 4
     xs = Vector{T}(undef, n)
     unsafe_copyto!(pointer(xs), Ptr{T}(pointer(data, p)), n)
     return p + n * sizeof(T), xs
 end
 
-function loadauxvalue(data::Vector{UInt8}, p::Int, ::Type{String})
+function loadauxvalue(data::AbstractVector{UInt8}, p::Int, ::Type{String})
     dataptr = pointer(data, p)
     endptr = ccall(:memchr, Ptr{Cvoid}, (Ptr{Cvoid}, Cint, Csize_t), dataptr, '\0', length(data) - p + 1)
     q::Int = p + (endptr - dataptr) - 1
     return q + 2, String(data[p:q])
 end
 
-function findauxtag(data::Vector{UInt8}, start::Int, stop::Int, t1::UInt8, t2::UInt8)
+function findauxtag(data::AbstractVector{UInt8}, start::Int, stop::Int, t1::UInt8, t2::UInt8)
     pos = start
 
     while pos ≤ stop && !(data[pos] == t1 && data[pos+1] == t2)
@@ -123,7 +123,7 @@ end
 
 # Find the starting position of a next tag in `data` after `p`.
 # `(data[p], data[p+1])` is supposed to be a current tag.
-function next_tag_position(data::Vector{UInt8}, p::Int)
+function next_tag_position(data::AbstractVector{UInt8}, p::Int)
     typ = Char(data[p+2])
     p += 3
 

src/bam/bam.jl

@@ -6,16 +6,16 @@ module BAM
 using BioGenerics
 using GenomicFeatures
 using XAM.SAM
+using CodecBGZF
 
-import BGZFStreams
 import BioAlignments
 import Indexes
 import BioSequences
 import BioGenerics: isfilled, header
 
 import GenomicFeatures: eachoverlap
 
-
+include("../common.jl")
 include("bai.jl")
 include("auxdata.jl")
 include("reader.jl")

src/bam/overlap.jl

@@ -62,7 +62,7 @@ end
 function Base.iterate(iter::OverlapIterator, state)
     while state.chunkid ≤ lastindex(state.chunks)
         chunk = state.chunks[state.chunkid]
-        while BGZFStreams.virtualoffset(iter.reader.stream) < chunk.stop
+        while VirtualOffset(iter.reader.stream) < chunk.stop
             read!(iter.reader, state.record)
             c = compare_intervals(state.record, (state.refindex, iter.interval))
             if c == 0

src/bam/reader.jl

@@ -11,9 +11,9 @@ Create a data reader of the BAM file format.
 * `index=nothing`: filepath to a random access index (currently *bai* is supported)
 """
 mutable struct Reader{T} <: BioGenerics.IO.AbstractReader
-    stream::BGZFStreams.BGZFStream{T}
+    stream::BGZFDecompressorStream{T}
     header::SAM.Header
-    start_offset::BGZFStreams.VirtualOffset
+    start_offset::VirtualOffset
     refseqnames::Vector{String}
     refseqlens::Vector{Int}
     index::Union{Nothing, BAI}
@@ -64,7 +64,7 @@ function header(reader::Reader; fillSQ::Bool=false)::SAM.Header
     return header
 end
 
-function Base.seek(reader::Reader, voffset::BGZFStreams.VirtualOffset)
+function Base.seek(reader::Reader, voffset::CodecBGZF.VirtualOffset)
     seek(reader.stream, voffset)
 end
 
@@ -80,7 +80,7 @@ function Base.iterate(reader::Reader, nextone = Record())
 end
 
 # Initialize a BAM reader by reading the header section.
-function init_bam_reader(input::BGZFStreams.BGZFStream)
+function init_bam_reader(input::BGZFDecompressorStream)
     # magic bytes
     B = read(input, UInt8)
     A = read(input, UInt8)
@@ -108,9 +108,7 @@ function init_bam_reader(input::BGZFStreams.BGZFStream)
         refseqlens[i] = seqlen
     end
 
-    voffset = isa(input.io, Base.AbstractPipe) ?
-        BGZFStreams.VirtualOffset(0, 0) :
-        BGZFStreams.virtualoffset(input)
+    voffset = VirtualOffset(input)
 
     return Reader(
         input,
@@ -122,7 +120,7 @@ function init_bam_reader(input::BGZFStreams.BGZFStream)
 end
 
 function init_bam_reader(input::IO)
-    return init_bam_reader(BGZFStreams.BGZFStream(input))
+    return init_bam_reader(BGZFDecompressorStream(input))
 end
 
 function _read!(reader::Reader, record)