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310 lines
11 KiB
Julia
310 lines
11 KiB
Julia
@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, 0, OP_START),
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AlignmentAnchor( 27, 28, 27, OP_MATCH),
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AlignmentAnchor( 27, 29, 28, OP_DELETE),
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AlignmentAnchor(100, 102, 101, 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.l_read_name == new_record.l_read_name
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@test record.mapq == new_record.mapq
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@test record.bin == new_record.bin
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@test record.block_size == new_record.block_size
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@test record.flag == new_record.flag
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@test record.n_cigar_op == new_record.n_cigar_op
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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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# rightposition (also implicitly alignlength)
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records = collect(open(BAM.Reader, joinpath(bamdir, "ce#5b.bam")))
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@test BAM.rightposition(records[6]) == rightposition(records[6]) == 83
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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 (a, b) in zip(xs, ys)
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if !(
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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.l_read_name == b.l_read_name &&
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a.mapq == b.mapq &&
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a.bin == b.bin &&
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a.n_cigar_op == b.n_cigar_op &&
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a.flag == b.flag &&
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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:BAM.data_size(a)] == b.data[1:BAM.data_size(b)])
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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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header_original = header(reader)
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writer = BAM.Writer(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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# Check that EOF_BLOCK gets written.
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nbytes = filesize(path)
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@test BAM.BGZFStreams.EOF_BLOCK == open(path) do io
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seek(io, nbytes - length(BAM.BGZFStreams.EOF_BLOCK))
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read(io)
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end
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reader = open(BAM.Reader, path)
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@test header(reader) == header_original
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@test compare_records(collect(reader), records)
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close(reader)
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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_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 "BAI" begin
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filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
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index = BAM.BAI(filepath * ".bai")
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reader = open(BAM.Reader, filepath, index=index)
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@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
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close(reader)
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@test_throws ErrorException open(BAM.Reader, filepath, index=1234)
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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)))
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close(reader)
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end
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end
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