Minimal code adjustments for working separation

- Update to use GenomicFeatures v2.
- BioAlignments v2.
- BioSequences v2.
- Indexes v0.1.

Project.toml

@@ -2,3 +2,32 @@ 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 = "0.1.0"
+
+[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"
+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"
+
+[compat]
+Automa = "0.7, 0.8"
+BGZFStreams = "0.3"
+BioAlignments = "2"
+BioCore = "2"
+BioSequences = "2"
+BufferedStreams = "1"
+GenomicFeatures = "2"
+Indexes = "0.1"
+julia = "1.1"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
+
+[targets]
+test = ["Test", "YAML"]

src/XAM.jl

@@ -1,10 +1,13 @@
 module XAM
 
 export
-    BAM,
-    SAM
+    SAM,
+    BAM
 
 include("sam/sam.jl")
 include("bam/bam.jl")
 
+using .SAM
+using .BAM
+
 end # module

src/bam/bai.jl

@@ -7,7 +7,7 @@
 # An index type for the BAM file format.
 struct BAI
     # BGZF file index
-    index::GenomicFeatures.Indexes.BGZFIndex
+    index::Indexes.BGZFIndex
 
     # number of unmapped reads
     n_no_coors::Union{Nothing, Int}
@@ -44,7 +44,7 @@ function read_bai(input::IO)
 
     # read contents
     n_refs = read(input, Int32)
-    index = GenomicFeatures.Indexes.read_bgzfindex(input, n_refs)
+    index = Indexes.read_bgzfindex(input, n_refs)
     if !eof(input)
         n_no_coors = read(input, UInt64)
     else

src/bam/bam.jl

@@ -3,11 +3,18 @@
 
 module BAM
 
+using BioCore
+using GenomicFeatures
+using XAM.SAM
+
 import BGZFStreams
-import BioAlignments: BioAlignments, SAM
-import GenomicFeatures: GenomicFeatures, Interval
+import BioAlignments
+import Indexes
 import BioSequences
-import BioCore: BioCore, isfilled
+import BioCore: isfilled, header
+
+import GenomicFeatures: eachoverlap
+
 
 include("bai.jl")
 include("auxdata.jl")

src/bam/overlap.jl

@@ -36,7 +36,7 @@ mutable struct OverlapIteratorState
     refindex::Int
 
     # possibly overlapping chunks
-    chunks::Vector{GenomicFeatures.Indexes.Chunk}
+    chunks::Vector{Indexes.Chunk}
 
     # current chunk index
     chunkid::Int
@@ -51,7 +51,7 @@ function Base.iterate(iter::OverlapIterator)
         throw(ArgumentError("sequence name $(iter.refname) is not found in the header"))
     end
     @assert iter.reader.index !== nothing
-    chunks = GenomicFeatures.Indexes.overlapchunks(iter.reader.index.index, refindex, iter.interval)
+    chunks = Indexes.overlapchunks(iter.reader.index.index, refindex, iter.interval)
     if !isempty(chunks)
         seek(iter.reader, first(chunks).start)
     end

src/bam/reader.jl

@@ -66,10 +66,6 @@ function header(reader::Reader; fillSQ::Bool=false)::SAM.Header
     return header
 end
 
-function BioCore.header(reader::Reader)
-    return header(reader)
-end
-
 function Base.seek(reader::Reader, voffset::BGZFStreams.VirtualOffset)
     seek(reader.stream, voffset)
 end

src/bam/record.jl

@@ -477,11 +477,11 @@ function hastemplength(record::Record)
 end
 
 """
-    sequence(record::Record)::BioSequences.DNASequence
+    sequence(record::Record)::BioSequences.LongDNASeq
 
 Get the segment sequence of `record`.
 """
-function sequence(record::Record)::BioSequences.DNASequence
+function sequence(record::Record)::BioSequences.LongDNASeq
     checkfilled(record)
     seqlen = seqlength(record)
     data = Vector{UInt64}(undef, cld(seqlen, 16))
@@ -491,7 +491,7 @@ function sequence(record::Record)::BioSequences.DNASequence
         x = unsafe_load(src, i)
         data[i] = (x & 0x0f0f0f0f0f0f0f0f) << 4 | (x & 0xf0f0f0f0f0f0f0f0) >> 4
     end
-    return BioSequences.DNASequence(data, 1:seqlen, false)
+    return BioSequences.LongDNASeq(data, 1:seqlen, false)
 end
 
 function hassequence(record::Record)

src/sam/reader.jl

@@ -38,10 +38,6 @@ function header(reader::Reader)::Header
     return reader.header
 end
 
-function BioCore.header(reader::Reader)
-    return header(reader)
-end
-
 function Base.eltype(::Type{Reader})
     return Record
 end

src/sam/record.jl

@@ -370,17 +370,17 @@ function hastemplength(record::Record)
 end
 
 """
-    sequence(record::Record)::BioSequences.DNASequence
+    sequence(record::Record)::BioSequences.LongDNASeq
 
 Get the segment sequence of `record`.
 """
-function sequence(record::Record)::BioSequences.DNASequence
+function sequence(record::Record)::BioSequences.LongDNASeq
     checkfilled(record)
     if ismissing(record, record.seq)
         missingerror(:sequence)
     end
     seqlen = length(record.seq)
-    ret = BioSequences.DNASequence(seqlen)
+    ret = BioSequences.LongDNASeq(seqlen)
     BioSequences.encode_copy!(ret, 1, record.data, first(record.seq), seqlen)
     return ret
 end

src/sam/sam.jl

@@ -3,12 +3,14 @@
 
 module SAM
 
+using BioCore
+
 import Automa
 import Automa.RegExp: @re_str
 import BioAlignments
 import BioCore.Exceptions: missingerror
 import BioCore.RecordHelper: unsafe_parse_decimal
-import BioCore: BioCore, isfilled
+import BioCore: isfilled, header
 import BioSequences
 import BufferedStreams
 using Printf: @sprintf

test/runtests.jl

@@ -1,13 +1,25 @@
 using Test
-using BioAlignments
-using BioSymbols
+using GenomicFeatures
+using XAM
+import BioAlignments: Alignment, AlignmentAnchor, OP_START, OP_MATCH, OP_DELETE
 import BGZFStreams: BGZFStream
 import BioCore.Exceptions: MissingFieldException
 import BioCore.Testing.get_bio_fmt_specimens
 import BioSequences: @dna_str, @aa_str
-import GenomicFeatures
 import YAML
 
+import BioCore:
+    header,
+    isfilled,
+    seqname,
+    hasseqname,
+    sequence,
+    hassequence,
+    leftposition,
+    rightposition,
+    hasleftposition,
+    hasrightposition
+
 # Generate a random range within `range`.
 function randrange(range)
     x = rand(range)
@@ -68,12 +80,12 @@ end
         record = SAM.Record()
         @test !isfilled(record)
         @test !SAM.ismapped(record)
-        @test repr(record) == "BioAlignments.SAM.Record: <not filled>"
+        @test repr(record) == "XAM.SAM.Record: <not filled>"
         @test_throws ArgumentError SAM.flag(record)
 
         record = SAM.Record("r001\t99\tchr1\t7\t30\t8M2I4M1D3M\t=\t37\t39\tTTAGATAAAGGATACTG\t*")
         @test isfilled(record)
-        @test occursin(r"^BioAlignments.SAM.Record:\n", repr(record))
+        @test occursin(r"^XAM.SAM.Record:\n", repr(record))
         @test SAM.ismapped(record)
         @test SAM.isprimary(record)
         @test SAM.hastempname(record)
@@ -217,7 +229,7 @@ end
     @testset "Record" begin
         record = BAM.Record()
         @test !isfilled(record)
-        @test repr(record) == "BioAlignments.BAM.Record: <not filled>"
+        @test repr(record) == "XAM.BAM.Record: <not filled>"
         @test_throws ArgumentError BAM.flag(record)
     end
 
@@ -225,7 +237,7 @@ end
         reader = open(BAM.Reader, joinpath(bamdir, "ce#1.bam"))
         @test isa(reader, BAM.Reader)
         @test eltype(reader) === BAM.Record
-        @test startswith(repr(reader), "BioAlignments.BAM.Reader{IOStream}:")
+        @test startswith(repr(reader), "XAM.BAM.Reader{IOStream}:")
 
         # header
         h = header(reader)