mirror of
https://github.com/MillironX/XAM.jl.git
synced 2024-11-15 06:43:10 +00:00
54 lines
1.2 KiB
Julia
54 lines
1.2 KiB
Julia
@testset "Cross Check Properties" begin
|
|
|
|
Broadcast.broadcastable(x::XAM.BAM.Record) = Ref(x) #TODO: consider moving to XAM.jl.
|
|
Broadcast.broadcastable(x::XAM.SAM.Record) = Ref(x) #TODO: consider moving to XAM.jl
|
|
|
|
function crosscheck(bam::BAM.Record, sam::SAM.Record, property::Symbol)
|
|
|
|
bam_property = getproperty(XAM.BAM, property)
|
|
sam_property = getproperty(XAM.SAM, property)
|
|
|
|
if bam_property(bam) != sam_property(sam)
|
|
@warn "$property result is not the same" bam_property(bam) sam_property(sam)
|
|
return false
|
|
end
|
|
|
|
return true
|
|
end
|
|
|
|
samdir = path_of_format("SAM")
|
|
bamdir = path_of_format("BAM")
|
|
|
|
filenames = [
|
|
"ce#1",
|
|
"ce#2",
|
|
"ce#5",
|
|
"ce#5b",
|
|
"ce#unmap",
|
|
"ce#unmap1",
|
|
"ce#unmap2",
|
|
]
|
|
|
|
properties = [
|
|
:position,# POS
|
|
:tempname,# QNAME
|
|
:mappingquality,# MAPQ
|
|
:cigar, # CIGAR
|
|
:flag, # FLAG
|
|
:sequence, # SEQ
|
|
:nextposition, # PNEXT
|
|
:templength, # TLEN
|
|
]
|
|
|
|
for filename in filenames
|
|
|
|
records_bam = collect(open(BAM.Reader, joinpath(bamdir, filename * ".bam")))
|
|
records_sam = collect(open(SAM.Reader, joinpath(samdir, filename * ".sam")))
|
|
|
|
for (bam, sam) in zip(records_bam, records_sam)
|
|
@test all(crosscheck.(bam, sam, properties)) == true
|
|
end
|
|
|
|
end
|
|
|
|
end # testset Crosscheck
|