mirror of
https://github.com/MillironX/XAM.jl.git
synced 2024-12-24 05:38:19 +00:00
459 lines
17 KiB
Julia
459 lines
17 KiB
Julia
using Test
|
|
|
|
using BioGenerics
|
|
using FormatSpecimens
|
|
using GenomicFeatures
|
|
using XAM
|
|
|
|
import BioAlignments: Alignment, AlignmentAnchor, OP_START, OP_MATCH, OP_DELETE
|
|
import BGZFStreams: BGZFStream
|
|
import BioGenerics.Exceptions: MissingFieldException
|
|
import BioSequences: @dna_str, @aa_str
|
|
|
|
|
|
# Generate a random range within `range`.
|
|
function randrange(range)
|
|
x = rand(range)
|
|
y = rand(range)
|
|
if x < y
|
|
return x:y
|
|
else
|
|
return y:x
|
|
end
|
|
end
|
|
|
|
@testset "SAM" begin
|
|
samdir = path_of_format("SAM")
|
|
|
|
@testset "MetaInfo" begin
|
|
metainfo = SAM.MetaInfo()
|
|
@test !isfilled(metainfo)
|
|
@test occursin("not filled", repr(metainfo))
|
|
|
|
metainfo = SAM.MetaInfo("CO", "some comment (parens)")
|
|
@test isfilled(metainfo)
|
|
@test string(metainfo) == "@CO\tsome comment (parens)"
|
|
@test occursin("CO", repr(metainfo))
|
|
@test SAM.tag(metainfo) == "CO"
|
|
@test SAM.value(metainfo) == "some comment (parens)"
|
|
@test_throws ArgumentError keys(metainfo)
|
|
@test_throws ArgumentError values(metainfo)
|
|
|
|
metainfo = SAM.MetaInfo("HD", ["VN" => "1.0", "SO" => "coordinate"])
|
|
@test isfilled(metainfo)
|
|
@test string(metainfo) == "@HD\tVN:1.0\tSO:coordinate"
|
|
@test occursin("HD", repr(metainfo))
|
|
@test SAM.tag(metainfo) == "HD"
|
|
@test SAM.value(metainfo) == "VN:1.0\tSO:coordinate"
|
|
@test keys(metainfo) == ["VN", "SO"]
|
|
@test values(metainfo) == ["1.0", "coordinate"]
|
|
@test SAM.keyvalues(metainfo) == ["VN" => "1.0", "SO" => "coordinate"]
|
|
@test haskey(metainfo, "VN")
|
|
@test haskey(metainfo, "SO")
|
|
@test !haskey(metainfo, "GO")
|
|
@test metainfo["VN"] == "1.0"
|
|
@test metainfo["SO"] == "coordinate"
|
|
@test_throws KeyError metainfo["GO"]
|
|
end
|
|
|
|
@testset "Header" begin
|
|
header = SAM.Header()
|
|
@test isempty(header)
|
|
push!(header, SAM.MetaInfo("@HD\tVN:1.0\tSO:coordinate"))
|
|
@test !isempty(header)
|
|
@test length(header) == 1
|
|
push!(header, SAM.MetaInfo("@CO\tsome comment"))
|
|
@test length(header) == 2
|
|
@test isa(collect(header), Vector{SAM.MetaInfo})
|
|
end
|
|
|
|
@testset "Record" begin
|
|
record = SAM.Record()
|
|
@test !isfilled(record)
|
|
@test !SAM.ismapped(record)
|
|
@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"^XAM.SAM.Record:\n", repr(record))
|
|
@test SAM.ismapped(record)
|
|
@test SAM.isprimary(record)
|
|
@test SAM.hastempname(record)
|
|
@test SAM.tempname(record) == "r001"
|
|
@test SAM.hasflag(record)
|
|
@test SAM.flag(record) === UInt16(99)
|
|
@test SAM.hasrefname(record)
|
|
@test SAM.refname(record) == "chr1"
|
|
@test SAM.hasposition(record)
|
|
@test SAM.position(record) === 7
|
|
@test SAM.hasmappingquality(record)
|
|
@test SAM.mappingquality(record) === UInt8(30)
|
|
@test SAM.hascigar(record)
|
|
@test SAM.cigar(record) == "8M2I4M1D3M"
|
|
@test SAM.hasnextrefname(record)
|
|
@test SAM.nextrefname(record) == "="
|
|
@test SAM.hasnextposition(record)
|
|
@test SAM.nextposition(record) === 37
|
|
@test SAM.hastemplength(record)
|
|
@test SAM.templength(record) === 39
|
|
@test SAM.hassequence(record)
|
|
@test SAM.sequence(record) == dna"TTAGATAAAGGATACTG"
|
|
@test !SAM.hasquality(record)
|
|
@test_throws MissingFieldException SAM.quality(record)
|
|
end
|
|
|
|
@testset "Reader" begin
|
|
reader = open(SAM.Reader, joinpath(samdir, "ce#1.sam"))
|
|
@test isa(reader, SAM.Reader)
|
|
@test eltype(reader) === SAM.Record
|
|
|
|
# header
|
|
h = header(reader)
|
|
@test string.(findall(header(reader), "SQ")) == ["@SQ\tSN:CHROMOSOME_I\tLN:1009800"]
|
|
|
|
# first record
|
|
record = SAM.Record()
|
|
read!(reader, record)
|
|
@test SAM.ismapped(record)
|
|
@test SAM.refname(record) == "CHROMOSOME_I"
|
|
@test SAM.position(record) == leftposition(record) == 2
|
|
@test SAM.rightposition(record) == rightposition(record) == 102
|
|
@test SAM.tempname(record) == seqname(record) == "SRR065390.14978392"
|
|
@test SAM.sequence(record) == sequence(record) == dna"CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
|
|
@test SAM.sequence(String, record) == "CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA"
|
|
@test SAM.seqlength(record) == 100
|
|
@test SAM.quality(record) == (b"#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC" .- 33)
|
|
@test SAM.quality(String, record) == "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"
|
|
@test SAM.flag(record) == 16
|
|
@test SAM.cigar(record) == "27M1D73M"
|
|
@test SAM.alignment(record) == Alignment([
|
|
AlignmentAnchor( 0, 1, OP_START),
|
|
AlignmentAnchor( 27, 28, OP_MATCH),
|
|
AlignmentAnchor( 27, 29, OP_DELETE),
|
|
AlignmentAnchor(100, 102, OP_MATCH)])
|
|
@test record["XG"] == 1
|
|
@test record["XM"] == 5
|
|
@test record["XN"] == 0
|
|
@test record["XO"] == 1
|
|
@test record["AS"] == -18
|
|
@test record["XS"] == -18
|
|
@test record["YT"] == "UU"
|
|
@test eof(reader)
|
|
close(reader)
|
|
|
|
# rightposition (also implicitly alignlength)
|
|
records = collect(open(SAM.Reader, joinpath(samdir, "ce#5b.sam")))
|
|
@test SAM.rightposition(records[6]) == rightposition(records[6]) == 83
|
|
|
|
# iterator
|
|
@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#1.sam")))) == 1
|
|
@test length(collect(open(SAM.Reader, joinpath(samdir, "ce#2.sam")))) == 2
|
|
|
|
# IOStream
|
|
@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#1.sam"))))) == 1
|
|
@test length(collect(SAM.Reader(open(joinpath(samdir, "ce#2.sam"))))) == 2
|
|
end
|
|
|
|
@testset "Round trip" begin
|
|
function compare_records(xs, ys)
|
|
if length(xs) != length(ys)
|
|
return false
|
|
end
|
|
for (x, y) in zip(xs, ys)
|
|
if x.data[x.filled] != y.data[y.filled]
|
|
return false
|
|
end
|
|
end
|
|
return true
|
|
end
|
|
for specimen in list_valid_specimens("SAM")
|
|
filepath = joinpath(samdir, filename(specimen))
|
|
mktemp() do path, io
|
|
# copy
|
|
reader = open(SAM.Reader, filepath)
|
|
|
|
header_original = header(reader)
|
|
|
|
writer = SAM.Writer(io, header_original)
|
|
|
|
records = SAM.Record[]
|
|
for record in reader
|
|
push!(records, record)
|
|
write(writer, record)
|
|
end
|
|
|
|
close(reader)
|
|
close(writer)
|
|
|
|
reader = open(SAM.Reader, path)
|
|
|
|
@test header(reader) == header_original
|
|
@test compare_records(collect(reader), records)
|
|
|
|
close(reader)
|
|
|
|
end
|
|
end
|
|
end
|
|
end
|
|
|
|
@testset "BAM" begin
|
|
bamdir = path_of_format("BAM")
|
|
|
|
@testset "AuxData" begin
|
|
auxdata = BAM.AuxData(UInt8[])
|
|
@test isempty(auxdata)
|
|
|
|
buf = IOBuffer()
|
|
write(buf, "NM", UInt8('s'), Int16(1))
|
|
auxdata = BAM.AuxData(take!(buf))
|
|
@test length(auxdata) == 1
|
|
@test auxdata["NM"] === Int16(1)
|
|
@test collect(auxdata) == ["NM" => Int16(1)]
|
|
|
|
buf = IOBuffer()
|
|
write(buf, "AS", UInt8('c'), Int8(-18))
|
|
write(buf, "NM", UInt8('s'), Int16(1))
|
|
write(buf, "XA", UInt8('f'), Float32(3.14))
|
|
write(buf, "XB", UInt8('Z'), "some text\0")
|
|
write(buf, "XC", UInt8('B'), UInt8('i'), Int32(3), Int32[10, -5, 8])
|
|
auxdata = BAM.AuxData(take!(buf))
|
|
@test length(auxdata) == 5
|
|
@test auxdata["AS"] === Int8(-18)
|
|
@test auxdata["NM"] === Int16(1)
|
|
@test auxdata["XA"] === Float32(3.14)
|
|
@test auxdata["XB"] == "some text"
|
|
@test auxdata["XC"] == Int32[10, -5, 8]
|
|
@test convert(Dict{String,Any}, auxdata) == Dict(
|
|
"AS" => Int8(-18),
|
|
"NM" => Int16(1),
|
|
"XA" => Float32(3.14),
|
|
"XB" => "some text",
|
|
"XC" => Int32[10, -5, 8])
|
|
end
|
|
|
|
@testset "Record" begin
|
|
record = BAM.Record()
|
|
@test !isfilled(record)
|
|
@test repr(record) == "XAM.BAM.Record: <not filled>"
|
|
@test_throws ArgumentError BAM.flag(record)
|
|
end
|
|
|
|
@testset "Reader" begin
|
|
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)
|
|
@test isa(h, SAM.Header)
|
|
|
|
# first record
|
|
record = BAM.Record()
|
|
read!(reader, record)
|
|
@test BAM.ismapped(record)
|
|
@test BAM.isprimary(record)
|
|
@test ! BAM.ispositivestrand(record)
|
|
@test BAM.refname(record) == "CHROMOSOME_I"
|
|
@test BAM.refid(record) === 1
|
|
@test BAM.hasnextrefid(record)
|
|
@test BAM.nextrefid(record) === 0
|
|
@test BAM.hasposition(record) === hasleftposition(record) === true
|
|
@test BAM.position(record) === leftposition(record) === 2
|
|
@test BAM.hasnextposition(record)
|
|
@test BAM.nextposition(record) === 0
|
|
@test rightposition(record) == 102
|
|
@test BAM.hastempname(record) === hasseqname(record) === true
|
|
@test BAM.tempname(record) == seqname(record) == "SRR065390.14978392"
|
|
@test BAM.hassequence(record) === hassequence(record) === true
|
|
@test BAM.sequence(record) == sequence(record) == dna"""
|
|
CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCT
|
|
AAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA
|
|
"""
|
|
@test BAM.seqlength(record) === 100
|
|
@test BAM.hasquality(record)
|
|
@test eltype(BAM.quality(record)) == UInt8
|
|
@test BAM.quality(record) == [Int(x) - 33 for x in "#############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC"]
|
|
@test BAM.flag(record) === UInt16(16)
|
|
@test BAM.cigar(record) == "27M1D73M"
|
|
@test BAM.alignment(record) == Alignment([
|
|
AlignmentAnchor( 0, 1, OP_START),
|
|
AlignmentAnchor( 27, 28, OP_MATCH),
|
|
AlignmentAnchor( 27, 29, OP_DELETE),
|
|
AlignmentAnchor(100, 102, OP_MATCH)])
|
|
@test record["XG"] == 1
|
|
@test record["XM"] == 5
|
|
@test record["XN"] == 0
|
|
@test record["XO"] == 1
|
|
@test record["AS"] == -18
|
|
@test record["XS"] == -18
|
|
@test record["YT"] == "UU"
|
|
@test keys(record) == ["XG","XM","XN","XO","AS","XS","YT"]
|
|
@test values(record) == [1, 5, 0, 1, -18, -18, "UU"]
|
|
@test eof(reader)
|
|
close(reader)
|
|
|
|
# Test conversion from byte array to record
|
|
dsize = BAM.data_size(record)
|
|
array = Vector{UInt8}(undef, BAM.FIXED_FIELDS_BYTES + dsize)
|
|
GC.@preserve array record begin
|
|
ptr = Ptr{UInt8}(pointer_from_objref(record))
|
|
unsafe_copyto!(pointer(array), ptr, BAM.FIXED_FIELDS_BYTES)
|
|
unsafe_copyto!(array, BAM.FIXED_FIELDS_BYTES + 1, record.data, 1, dsize)
|
|
end
|
|
new_record = convert(BAM.Record, array)
|
|
@test record.bin_mq_nl == new_record.bin_mq_nl
|
|
@test record.block_size == new_record.block_size
|
|
@test record.flag_nc == new_record.flag_nc
|
|
@test record.l_seq == new_record.l_seq
|
|
@test record.next_refid == new_record.next_refid
|
|
@test record.next_pos == new_record.next_pos
|
|
@test record.refid == new_record.refid
|
|
@test record.pos == new_record.pos
|
|
@test record.tlen == new_record.tlen
|
|
@test record.data == new_record.data
|
|
|
|
# rightposition (also implicitly alignlength)
|
|
records = collect(open(BAM.Reader, joinpath(bamdir, "ce#5b.bam")))
|
|
@test BAM.rightposition(records[6]) == rightposition(records[6]) == 83
|
|
|
|
# iterator
|
|
@test length(collect(open(BAM.Reader, joinpath(bamdir, "ce#1.bam")))) == 1
|
|
@test length(collect(open(BAM.Reader, joinpath(bamdir, "ce#2.bam")))) == 2
|
|
|
|
# IOStream
|
|
@test length(collect(BAM.Reader(open(joinpath(bamdir, "ce#1.bam"))))) == 1
|
|
@test length(collect(BAM.Reader(open(joinpath(bamdir, "ce#2.bam"))))) == 2
|
|
end
|
|
|
|
@testset "Read long CIGARs" begin
|
|
function get_cigar_lens(rec::BAM.Record)
|
|
cigar_ops, cigar_n = BAM.cigar_rle(rec)
|
|
field_ops, field_n = BAM.cigar_rle(rec, false)
|
|
cigar_l = length(cigar_ops)
|
|
field_l = length(field_ops)
|
|
return cigar_l, field_l
|
|
end
|
|
|
|
function check_cigar_vs_field(rec::BAM.Record)
|
|
cigar = BAM.cigar(rec)
|
|
field = BAM.cigar(rec, false)
|
|
cigar_l, field_l = get_cigar_lens(rec)
|
|
return cigar != field && cigar_l != field_l
|
|
end
|
|
|
|
function check_cigar_lens(rec::BAM.Record, field_len, cigar_len)
|
|
cigar_l, field_l = get_cigar_lens(rec)
|
|
return cigar_l == cigar_len && field_l == field_len
|
|
end
|
|
|
|
reader = open(BAM.Reader, joinpath(bamdir, "cigar-64k.bam"))
|
|
rec = BAM.Record()
|
|
read!(reader, rec)
|
|
@test !check_cigar_vs_field(rec)
|
|
read!(reader, rec)
|
|
@test check_cigar_vs_field(rec)
|
|
@test check_cigar_lens(rec, 2, 72091)
|
|
end
|
|
|
|
function compare_records(xs, ys)
|
|
if length(xs) != length(ys)
|
|
return false
|
|
end
|
|
for (x, y) in zip(xs, ys)
|
|
if !(
|
|
x.block_size == y.block_size &&
|
|
x.refid == y.refid &&
|
|
x.pos == y.pos &&
|
|
x.bin_mq_nl == y.bin_mq_nl &&
|
|
x.flag_nc == y.flag_nc &&
|
|
x.l_seq == y.l_seq &&
|
|
x.next_refid == y.next_refid &&
|
|
x.next_pos == y.next_pos &&
|
|
x.tlen == y.tlen &&
|
|
x.data[1:BAM.data_size(x)] == y.data[1:BAM.data_size(y)])
|
|
return false
|
|
end
|
|
end
|
|
return true
|
|
end
|
|
|
|
@testset "Round trip" begin
|
|
for specimen in list_valid_specimens("BAM")
|
|
filepath = joinpath(bamdir, filename(specimen))
|
|
mktemp() do path, _
|
|
# copy
|
|
if hastags(specimen) && in("bai", tags(specimen))
|
|
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
|
else
|
|
reader = open(BAM.Reader, filepath)
|
|
end
|
|
|
|
header_original = header(reader)
|
|
|
|
writer = BAM.Writer(BGZFStream(path, "w"), BAM.header(reader, fillSQ=isempty(findall(header(reader), "SQ"))))
|
|
|
|
records = BAM.Record[]
|
|
for record in reader
|
|
push!(records, record)
|
|
write(writer, record)
|
|
end
|
|
close(reader)
|
|
close(writer)
|
|
|
|
reader = open(BAM.Reader, path)
|
|
|
|
@test header(reader) == header_original
|
|
@test compare_records(collect(reader), records)
|
|
|
|
close(reader)
|
|
|
|
end
|
|
end
|
|
end
|
|
|
|
@testset "Random access" begin
|
|
filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
|
|
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
|
|
|
@test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
|
|
@test isa(eachoverlap(reader, GenomicFeatures.Interval("chr1", 1, 100)), BAM.OverlapIterator)
|
|
|
|
# expected values are counted using samtools
|
|
for (refname, interval, expected) in [
|
|
("chr1", 1_000:10000, 21),
|
|
("chr1", 8_000:10000, 20),
|
|
("chr1", 766_000:800_000, 142),
|
|
("chr1", 786_000:800_000, 1),
|
|
("chr1", 796_000:800_000, 0)]
|
|
intsect = eachoverlap(reader, refname, interval)
|
|
@test eltype(intsect) == BAM.Record
|
|
@test count(_ -> true, intsect) == expected
|
|
# check that the intersection iterator is stateless
|
|
@test count(_ -> true, intsect) == expected
|
|
end
|
|
|
|
# randomized tests
|
|
for n in 1:50
|
|
refindex = 1
|
|
refname = "chr1"
|
|
range = randrange(1:1_000_000)
|
|
seekstart(reader)
|
|
# linear scan
|
|
expected = filter(collect(reader)) do record
|
|
BAM.compare_intervals(record, (refindex, range)) == 0
|
|
end
|
|
# indexed scan
|
|
actual = collect(eachoverlap(reader, refname, range))
|
|
@test compare_records(actual, expected)
|
|
end
|
|
close(reader)
|
|
|
|
filepath = joinpath(bamdir, "R_12h_D06.uniq.q40.bam")
|
|
reader = open(BAM.Reader, filepath, index=filepath * ".bai")
|
|
@test isempty(collect(eachoverlap(reader, "chr19", 5823708:5846478)))
|
|
close(reader)
|
|
end
|
|
end
|