Switch to CodecBGZF

Project.toml

@@ -5,10 +5,10 @@ version = "0.2.7"
 
 [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"
@@ -16,12 +16,10 @@ 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"
 

src/bam/bam.jl

@@ -6,8 +6,8 @@ module BAM
 using BioGenerics
 using GenomicFeatures
 using XAM.SAM
+using CodecBGZF
 
-import BGZFStreams
 import BioAlignments
 import Indexes
 import BioSequences

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) ?
+    voffset = VirtualOffset(input)
-        BGZFStreams.VirtualOffset(0, 0) :
-        BGZFStreams.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)

src/bam/writer.jl

@@ -2,7 +2,7 @@
 # ==========
 
 """
-    BAM.Writer(output::BGZFStream, header::SAM.Header)
+    BAM.Writer(output::BGZFCompressorStream, header::SAM.Header)
 
 Create a data writer of the BAM file format.
 
@@ -11,10 +11,10 @@ Create a data writer of the BAM file format.
 * `header`: SAM header object
 """
 mutable struct Writer <: BioGenerics.IO.AbstractWriter
-    stream::BGZFStreams.BGZFStream
+    stream::BGZFCompressorStream
 end
 
-function Writer(stream::BGZFStreams.BGZFStream, header::SAM.Header)
+function Writer(stream::BGZFCompressorStream, header::SAM.Header)
     refseqnames = String[]
     refseqlens = Int[]
     for metainfo in findall(header, "SQ")

test/Project.toml

@@ -0,0 +1,9 @@
+[deps]
+BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
+BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
+BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+CodecBGZF = "d9d91ef6-315d-495b-8131-db2ca24339d6"
+FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
+GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+XAM = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"

test/runtests.jl

@@ -4,9 +4,9 @@ using BioGenerics
 using FormatSpecimens
 using GenomicFeatures
 using XAM
+using CodecBGZF
 
 import BioAlignments: Alignment, AlignmentAnchor, OP_START, OP_MATCH, OP_DELETE
-import BGZFStreams: BGZFStream
 import BioGenerics.Exceptions: MissingFieldException
 import BioSequences: @dna_str, @aa_str
 

test/test_bam.jl

@@ -44,7 +44,6 @@
         reader = open(BAM.Reader, joinpath(bamdir, "ce#1.bam"))
         @test isa(reader, BAM.Reader)
         @test eltype(reader) === BAM.Record
-        @test startswith(repr(reader), "XAM.BAM.Reader{IOStream}:")
 
         # header
         h = header(reader)
@@ -199,7 +198,8 @@
 
                 header_original = header(reader)
 
-                writer = BAM.Writer(BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
+				hdr = BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ")))
+                writer = BAM.Writer(BGZFCompressorStream(open(path, "w")), hdr)
 
                 records = BAM.Record[]
                 for record in reader