mirror of
https://github.com/MillironX/XAM.jl.git
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Merge branch 'master' into develop
This commit is contained in:
commit
32a2b129e1
7 changed files with 113 additions and 8 deletions
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@ -1,7 +1,7 @@
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name = "XAM"
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uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
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authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
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version = "0.2.2"
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version = "0.2.3"
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[deps]
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Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
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@ -58,6 +58,7 @@ In-place reading reuses a pre-allocated object for every record and less memory
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reader = open(BAM.Reader, "data.bam")
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record = BAM.Record()
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while !eof(reader)
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empty!(record)
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read!(reader, record)
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# do something
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end
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@ -72,12 +72,11 @@ function Base.seekstart(reader::Reader)
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seek(reader.stream, reader.start_offset)
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end
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function Base.iterate(reader::Reader, rec=Record())
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if eof(reader)
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function Base.iterate(reader::Reader, nextone = Record())
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if BioGenerics.IO.tryread!(reader, nextone) === nothing
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return nothing
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end
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read!(reader, rec)
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return copy(rec), rec
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return copy(nextone), empty!(nextone)
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end
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# Initialize a BAM reader by reading the header section.
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@ -45,6 +45,19 @@ function Base.convert(::Type{Record}, data::Vector{UInt8})
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return record
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end
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function Base.:(==)(a::Record, b::Record)
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return a.block_size == b.block_size &&
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a.refid == b.refid &&
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a.pos == b.pos &&
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a.bin_mq_nl == b.bin_mq_nl &&
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a.flag_nc == b.flag_nc &&
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a.l_seq == b.l_seq &&
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a.next_refid == b.next_refid &&
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a.next_pos == b.next_pos &&
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a.tlen == b.tlen &&
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a.data[1:data_size(a)] == b.data[1:data_size(b)]
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end
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function Base.copy(record::Record)
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copy = Record()
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copy.block_size = record.block_size
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@ -63,6 +76,22 @@ function Base.copy(record::Record)
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return copy
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end
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function Base.empty!(record::Record)
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record.block_size = 0
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record.refid = 0
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record.pos = 0
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record.bin_mq_nl = 0
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record.flag_nc = 0
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record.l_seq = 0
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record.next_refid = 0
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record.next_pos = 0
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record.tlen = 0
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#Note: data will be overwritten and indexed using data_size.
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return record
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end
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function Base.show(io::IO, record::Record)
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print(io, summary(record), ':')
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if isfilled(record)
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@ -81,9 +81,20 @@ function index!(record::Record)
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return record
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end
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function Base.read!(rdr::Reader, rec::Record)
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function Base.iterate(reader::Reader, nextone::Record = Record())
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if BioGenerics.IO.tryread!(reader, nextone) === nothing
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return nothing
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end
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return copy(nextone), empty!(nextone)
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end
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empty!(rec.fields) #Note: data is pushed to the fields field, and other field data is overwritten. #TODO: distinguish for inplace reading pattern.
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"""
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read!(rdr::Reader, rec::Record)
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Read a `Record` into `rec`; overwriting or adding to existing field values.
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It is assumed that `rec` is already initialized or empty.
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"""
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function Base.read!(rdr::Reader, rec::Record)
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cs, ln, f = readrecord!(rdr.state.stream, rec, (rdr.state.state, rdr.state.linenum))
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@ -74,6 +74,23 @@ function Base.convert(::Type{Record}, str::AbstractString)
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return Record(collect(UInt8, str))
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end
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function Base.:(==)(a::Record, b::Record)
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return a.filled == b.filled &&
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a.qname == b.qname &&
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a.flag == b.flag &&
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a.rname == b.rname &&
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a.pos == b.pos &&
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a.mapq == b.mapq &&
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a.cigar == b.cigar &&
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a.rnext == b.rnext &&
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a.pnext == b.pnext &&
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a.tlen == b.tlen &&
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a.seq == b.seq &&
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a.qual == b.qual &&
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a.fields == b.fields &&
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a.data[a.filled] == b.data[b.filled]
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end
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function Base.show(io::IO, record::Record)
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print(io, summary(record), ':')
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if isfilled(record)
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@ -554,7 +571,7 @@ end
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# Helper Functions
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# ----------------
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function initialize!(record::Record)
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function Base.empty!(record::Record)
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record.filled = 1:0
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record.qname = 1:0
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record.flag = 1:0
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@ -571,6 +588,10 @@ function initialize!(record::Record)
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return record
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end
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function initialize!(record::Record) #TODO: deprecate.
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return empty!(record)
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end
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function checkfilled(record::Record)
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if !isfilled(record)
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throw(ArgumentError("unfilled SAM record"))
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@ -196,6 +196,29 @@ end
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end
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end
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end
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@testset "In-Place-Reading Pattern" begin
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file_sam = joinpath(samdir, "ce#5b.sam")
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records = open(collect, SAM.Reader, file_sam)
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reader = open(SAM.Reader, file_sam)
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record = SAM.Record()
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i = 0
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while !eof(reader)
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empty!(record) # Reset the record.
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read!(reader, record)
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i = i + 1
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@test records[i] == record
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end
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close(reader)
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end
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end
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@testset "BAM" begin
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@ -414,6 +437,27 @@ end
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end
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end
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@testset "In-Place-Reading Pattern" begin
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file_bam = joinpath(bamdir, "ce#5b.bam")
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records = open(collect, BAM.Reader, file_bam)
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reader = open(BAM.Reader, file_bam)
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record = BAM.Record()
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i = 0
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while !eof(reader)
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empty!(record) # Reset the record.
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read!(reader, record)
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i = i + 1
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@test records[i] == record
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end
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close(reader)
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end
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@testset "Random access" begin
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filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
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reader = open(BAM.Reader, filepath, index=filepath * ".bai")
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