Begin crosschecks

test/runtests.jl

@@ -25,3 +25,4 @@ end
 
 include("test_sam.jl")
 include("test_bam.jl")
+include("test_crosscheck.jl")

test/test_crosscheck.jl

@@ -0,0 +1,54 @@
+@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