mirror of
https://github.com/MillironX/XAM.jl.git
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438 lines
16 KiB
Julia
438 lines
16 KiB
Julia
using Test
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using GenomicFeatures
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using XAM
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import BioAlignments: Alignment, AlignmentAnchor, OP_START, OP_MATCH, OP_DELETE
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using FormatSpecimens
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import BGZFStreams: BGZFStream
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import BioCore.Exceptions: MissingFieldException
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import BioSequences: @dna_str, @aa_str
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import BioCore:
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header,
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isfilled,
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seqname,
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hasseqname,
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sequence,
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hassequence,
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leftposition,
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rightposition,
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hasleftposition,
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hasrightposition
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# Generate a random range within `range`.
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function randrange(range)
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x = rand(range)
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y = rand(range)
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if x < y
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return x:y
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else
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return y:x
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end
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end
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@testset "SAM" begin
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samdir = path_of_format("SAM")
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@testset "MetaInfo" begin
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metainfo = SAM.MetaInfo()
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@test !isfilled(metainfo)
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@test occursin("not filled", repr(metainfo))
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metainfo = SAM.MetaInfo("CO", "some comment (parens)")
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@test isfilled(metainfo)
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@test string(metainfo) == "@CO\tsome comment (parens)"
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@test occursin("CO", repr(metainfo))
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@test SAM.tag(metainfo) == "CO"
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@test SAM.value(metainfo) == "some comment (parens)"
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@test_throws ArgumentError keys(metainfo)
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@test_throws ArgumentError values(metainfo)
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metainfo = SAM.MetaInfo("HD", ["VN" => "1.0", "SO" => "coordinate"])
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@test isfilled(metainfo)
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@test string(metainfo) == "@HD\tVN:1.0\tSO:coordinate"
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@test occursin("HD", repr(metainfo))
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@test SAM.tag(metainfo) == "HD"
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@test SAM.value(metainfo) == "VN:1.0\tSO:coordinate"
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@test keys(metainfo) == ["VN", "SO"]
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@test values(metainfo) == ["1.0", "coordinate"]
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@test SAM.keyvalues(metainfo) == ["VN" => "1.0", "SO" => "coordinate"]
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@test haskey(metainfo, "VN")
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@test haskey(metainfo, "SO")
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@test !haskey(metainfo, "GO")
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@test metainfo["VN"] == "1.0"
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@test metainfo["SO"] == "coordinate"
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@test_throws KeyError metainfo["GO"]
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end
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@testset "Header" begin
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header = SAM.Header()
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@test isempty(header)
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push!(header, SAM.MetaInfo("@HD\tVN:1.0\tSO:coordinate"))
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@test !isempty(header)
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@test length(header) == 1
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push!(header, SAM.MetaInfo("@CO\tsome comment"))
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@test length(header) == 2
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@test isa(collect(header), Vector{SAM.MetaInfo})
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end
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@testset "Record" begin
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record = SAM.Record()
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@test !isfilled(record)
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@test !SAM.ismapped(record)
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@test repr(record) == "XAM.SAM.Record: <not filled>"
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@test_throws ArgumentError SAM.flag(record)
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record = SAM.Record("r001\t99\tchr1\t7\t30\t8M2I4M1D3M\t=\t37\t39\tTTAGATAAAGGATACTG\t*")
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@test isfilled(record)
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@test occursin(r"^XAM.SAM.Record:\n", repr(record))
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@test SAM.ismapped(record)
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@test SAM.isprimary(record)
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@test SAM.hastempname(record)
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@test SAM.tempname(record) == "r001"
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@test SAM.hasflag(record)
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@test SAM.flag(record) === UInt16(99)
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@test SAM.hasrefname(record)
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@test SAM.refname(record) == "chr1"
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@test SAM.hasposition(record)
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@test SAM.position(record) === 7
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@test SAM.hasmappingquality(record)
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@test SAM.mappingquality(record) === UInt8(30)
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@test SAM.hascigar(record)
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@test SAM.cigar(record) == "8M2I4M1D3M"
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@test SAM.hasnextrefname(record)
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@test SAM.nextrefname(record) == "="
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@test SAM.hasnextposition(record)
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@test SAM.nextposition(record) === 37
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@test SAM.hastemplength(record)
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@test SAM.templength(record) === 39
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@test SAM.hassequence(record)
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@test SAM.sequence(record) == dna"TTAGATAAAGGATACTG"
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@test !SAM.hasquality(record)
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@test_throws MissingFieldException SAM.quality(record)
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end
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@testset "Reader" begin
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reader = open(SAM.Reader, joinpath(samdir, "ce#1.sam"))
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@test isa(reader, SAM.Reader)
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@test eltype(reader) === SAM.Record
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# header
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h = header(reader)
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@test string.(findall(header(reader), "SQ")) == ["@SQ\tSN:CHROMOSOME_I\tLN:1009800"]
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# first record
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record = SAM.Record()
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read!(reader, record)
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@test SAM.ismapped(record)
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@test SAM.refname(record) == "CHROMOSOME_I"
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@test SAM.position(record) == leftposition(record) == 2
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@test SAM.rightposition(record) == rightposition(record) == 102
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@test SAM.tempname(record) == seqname(record) == "SRR065390.14978392"
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@test SAM.sequence(record) == sequence(record) == dna"CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
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@test SAM.sequence(String, record) == "CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
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@test SAM.seqlength(record) == 100
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@test SAM.quality(record) == (b"#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC" .- 33)
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@test SAM.quality(String, record) == "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
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@test SAM.flag(record) == 16
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@test SAM.cigar(record) == "27M1D73M"
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@test SAM.alignment(record) == Alignment([
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AlignmentAnchor( 0, 1, OP_START),
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AlignmentAnchor( 27, 28, OP_MATCH),
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AlignmentAnchor( 27, 29, OP_DELETE),
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AlignmentAnchor(100, 102, OP_MATCH)])
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@test record["XG"] == 1
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@test record["XM"] == 5
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@test record["XN"] == 0
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@test record["XO"] == 1
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@test record["AS"] == -18
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@test record["XS"] == -18
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@test record["YT"] == "UU"
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@test eof(reader)
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close(reader)
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# iterator
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@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#1.sam")))) == 1
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@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#2.sam")))) == 2
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# IOStream
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@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#1.sam"))))) == 1
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@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#2.sam"))))) == 2
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end
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@testset "Round trip" begin
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function compare_records(xs, ys)
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if length(xs) != length(ys)
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return false
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end
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for (x, y) in zip(xs, ys)
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if x.data[x.filled] != y.data[y.filled]
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return false
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end
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end
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return true
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end
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for specimen in list_valid_specimens("SAM")
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filepath = joinpath(samdir, filename(specimen))
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mktemp() do path, io
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# copy
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reader = open(SAM.Reader, filepath)
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writer = SAM.Writer(io, header(reader))
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records = SAM.Record[]
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for record in reader
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push!(records, record)
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write(writer, record)
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end
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close(reader)
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close(writer)
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@test compare_records(open(collect, SAM.Reader, path), records)
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end
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end
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end
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end
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@testset "BAM" begin
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bamdir = path_of_format("BAM")
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@testset "AuxData" begin
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auxdata = BAM.AuxData(UInt8[])
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@test isempty(auxdata)
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buf = IOBuffer()
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write(buf, "NM", UInt8('s'), Int16(1))
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auxdata = BAM.AuxData(take!(buf))
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@test length(auxdata) == 1
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@test auxdata["NM"] === Int16(1)
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@test collect(auxdata) == ["NM" => Int16(1)]
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buf = IOBuffer()
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write(buf, "AS", UInt8('c'), Int8(-18))
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write(buf, "NM", UInt8('s'), Int16(1))
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write(buf, "XA", UInt8('f'), Float32(3.14))
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write(buf, "XB", UInt8('Z'), "some text\0")
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write(buf, "XC", UInt8('B'), UInt8('i'), Int32(3), Int32[10, -5, 8])
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auxdata = BAM.AuxData(take!(buf))
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@test length(auxdata) == 5
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@test auxdata["AS"] === Int8(-18)
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@test auxdata["NM"] === Int16(1)
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@test auxdata["XA"] === Float32(3.14)
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@test auxdata["XB"] == "some text"
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@test auxdata["XC"] == Int32[10, -5, 8]
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@test convert(Dict{String,Any}, auxdata) == Dict(
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"AS" => Int8(-18),
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"NM" => Int16(1),
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"XA" => Float32(3.14),
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"XB" => "some text",
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"XC" => Int32[10, -5, 8])
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end
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@testset "Record" begin
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record = BAM.Record()
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@test !isfilled(record)
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@test repr(record) == "XAM.BAM.Record: <not filled>"
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@test_throws ArgumentError BAM.flag(record)
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end
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@testset "Reader" begin
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reader = open(BAM.Reader, joinpath(bamdir, "ce#1.bam"))
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@test isa(reader, BAM.Reader)
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@test eltype(reader) === BAM.Record
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@test startswith(repr(reader), "XAM.BAM.Reader{IOStream}:")
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# header
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h = header(reader)
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@test isa(h, SAM.Header)
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# first record
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record = BAM.Record()
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read!(reader, record)
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@test BAM.ismapped(record)
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@test BAM.isprimary(record)
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@test ! BAM.ispositivestrand(record)
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@test BAM.refname(record) == "CHROMOSOME_I"
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@test BAM.refid(record) === 1
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@test BAM.hasnextrefid(record)
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@test BAM.nextrefid(record) === 0
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@test BAM.hasposition(record) === hasleftposition(record) === true
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@test BAM.position(record) === leftposition(record) === 2
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@test BAM.hasnextposition(record)
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@test BAM.nextposition(record) === 0
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@test rightposition(record) == 102
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@test BAM.hastempname(record) === hasseqname(record) === true
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@test BAM.tempname(record) == seqname(record) == "SRR065390.14978392"
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@test BAM.hassequence(record) === hassequence(record) === true
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@test BAM.sequence(record) == sequence(record) == dna"""
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CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCT
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AAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA
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"""
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@test BAM.seqlength(record) === 100
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@test BAM.hasquality(record)
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@test eltype(BAM.quality(record)) == UInt8
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@test BAM.quality(record) == [Int(x) - 33 for x in "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"]
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@test BAM.flag(record) === UInt16(16)
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@test BAM.cigar(record) == "27M1D73M"
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@test BAM.alignment(record) == Alignment([
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AlignmentAnchor( 0, 1, OP_START),
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AlignmentAnchor( 27, 28, OP_MATCH),
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AlignmentAnchor( 27, 29, OP_DELETE),
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AlignmentAnchor(100, 102, OP_MATCH)])
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@test record["XG"] == 1
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@test record["XM"] == 5
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@test record["XN"] == 0
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@test record["XO"] == 1
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@test record["AS"] == -18
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@test record["XS"] == -18
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@test record["YT"] == "UU"
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@test keys(record) == ["XG","XM","XN","XO","AS","XS","YT"]
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@test values(record) == [1, 5, 0, 1, -18, -18, "UU"]
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@test eof(reader)
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close(reader)
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# Test conversion from byte array to record
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dsize = BAM.data_size(record)
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array = Vector{UInt8}(undef, BAM.FIXED_FIELDS_BYTES + dsize)
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GC.@preserve array record begin
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ptr = Ptr{UInt8}(pointer_from_objref(record))
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unsafe_copyto!(pointer(array), ptr, BAM.FIXED_FIELDS_BYTES)
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unsafe_copyto!(array, BAM.FIXED_FIELDS_BYTES + 1, record.data, 1, dsize)
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end
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new_record = convert(BAM.Record, array)
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@test record.bin_mq_nl == new_record.bin_mq_nl
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@test record.block_size == new_record.block_size
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@test record.flag_nc == new_record.flag_nc
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@test record.l_seq == new_record.l_seq
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@test record.next_refid == new_record.next_refid
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@test record.next_pos == new_record.next_pos
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@test record.refid == new_record.refid
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@test record.pos == new_record.pos
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@test record.tlen == new_record.tlen
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@test record.data == new_record.data
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# iterator
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@test length(collect(open(BAM.Reader, joinpath(bamdir, "ce#1.bam")))) == 1
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@test length(collect(open(BAM.Reader, joinpath(bamdir, "ce#2.bam")))) == 2
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# IOStream
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@test length(collect(BAM.Reader(open(joinpath(bamdir, "ce#1.bam"))))) == 1
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@test length(collect(BAM.Reader(open(joinpath(bamdir, "ce#2.bam"))))) == 2
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end
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@testset "Read long CIGARs" begin
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function get_cigar_lens(rec::BAM.Record)
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cigar_ops, cigar_n = BAM.cigar_rle(rec)
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field_ops, field_n = BAM.cigar_rle(rec, false)
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cigar_l = length(cigar_ops)
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field_l = length(field_ops)
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return cigar_l, field_l
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end
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function check_cigar_vs_field(rec::BAM.Record)
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cigar = BAM.cigar(rec)
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field = BAM.cigar(rec, false)
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cigar_l, field_l = get_cigar_lens(rec)
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return cigar != field && cigar_l != field_l
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end
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function check_cigar_lens(rec::BAM.Record, field_len, cigar_len)
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cigar_l, field_l = get_cigar_lens(rec)
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return cigar_l == cigar_len && field_l == field_len
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end
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reader = open(BAM.Reader, joinpath(bamdir, "cigar-64k.bam"))
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rec = BAM.Record()
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read!(reader, rec)
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@test !check_cigar_vs_field(rec)
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read!(reader, rec)
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@test check_cigar_vs_field(rec)
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@test check_cigar_lens(rec, 2, 72091)
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end
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function compare_records(xs, ys)
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if length(xs) != length(ys)
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return false
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end
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for (x, y) in zip(xs, ys)
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if !(
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x.block_size == y.block_size &&
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x.refid == y.refid &&
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x.pos == y.pos &&
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x.bin_mq_nl == y.bin_mq_nl &&
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x.flag_nc == y.flag_nc &&
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x.l_seq == y.l_seq &&
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x.next_refid == y.next_refid &&
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x.next_pos == y.next_pos &&
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x.tlen == y.tlen &&
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x.data[1:BAM.data_size(x)] == y.data[1:BAM.data_size(y)])
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return false
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end
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end
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return true
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end
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@testset "Round trip" begin
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for specimen in list_valid_specimens("BAM")
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filepath = joinpath(bamdir, filename(specimen))
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mktemp() do path, _
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# copy
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if hastags(specimen) && in("bai", tags(specimen))
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reader = open(BAM.Reader, filepath, index=filepath * ".bai")
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else
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reader = open(BAM.Reader, filepath)
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end
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writer = BAM.Writer(
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BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
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records = BAM.Record[]
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for record in reader
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push!(records, record)
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write(writer, record)
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end
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close(reader)
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close(writer)
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@test compare_records(open(collect, BAM.Reader, path), records)
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end
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end
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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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@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
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@test isa(eachoverlap(reader, GenomicFeatures.Interval("chr1", 1, 100)), BAM.OverlapIterator)
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# expected values are counted using samtools
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for (refname, interval, expected) in [
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("chr1", 1_000:10000, 21),
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("chr1", 8_000:10000, 20),
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("chr1", 766_000:800_000, 142),
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("chr1", 786_000:800_000, 1),
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("chr1", 796_000:800_000, 0)]
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intsect = eachoverlap(reader, refname, interval)
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@test eltype(intsect) == BAM.Record
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@test count(_ -> true, intsect) == expected
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# check that the intersection iterator is stateless
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@test count(_ -> true, intsect) == expected
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end
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# randomized tests
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for n in 1:50
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refindex = 1
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refname = "chr1"
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range = randrange(1:1_000_000)
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seekstart(reader)
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# linear scan
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expected = filter(collect(reader)) do record
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BAM.compare_intervals(record, (refindex, range)) == 0
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end
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# indexed scan
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actual = collect(eachoverlap(reader, refname, range))
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@test compare_records(actual, expected)
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end
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close(reader)
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filepath = joinpath(bamdir, "R_12h_D06.uniq.q40.bam")
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reader = open(BAM.Reader, filepath, index=filepath * ".bai")
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@test isempty(collect(eachoverlap(reader, "chr19", 5823708:5846478)))
|
|
close(reader)
|
|
end
|
|
end
|