Flag tests

Author: Ciarán O'Mara

test/runtests.jl

@@ -30,6 +30,7 @@ end
     include("test_issues.jl")
     include("test_crosscheck.jl")
     include("test_convert.jl")
+    include("test_flags.jl")
 
     # Include doctests.
     DocMeta.setdocmeta!(XAM, :DocTestSetup, :(using XAM); recursive=true)

test/test_flags.jl

@@ -0,0 +1,48 @@
+@testset "Flags" begin
+
+    flag_tests = [
+        (XAM.ispaired, XAM.FLAG_PAIRED),
+        (XAM.isproperpair, XAM.FLAG_PROPER_PAIR),
+        (XAM.isunmapped, XAM.FLAG_UNMAPPED), 
+        (XAM.ismapped, ~XAM.FLAG_UNMAPPED), 
+        (XAM.isnextunmapped, XAM.FLAG_NEXT_UNMAPPED), 
+        (XAM.isnextmapped, ~XAM.FLAG_NEXT_UNMAPPED), 
+        (XAM.isreversecomplemented, XAM.FLAG_REVERSE), 
+        (XAM.isforwardstrand, ~XAM.FLAG_REVERSE), 
+        (XAM.ispositivestrand, ~XAM.FLAG_REVERSE), 
+        (XAM.isreversestrand, XAM.FLAG_REVERSE), 
+        (XAM.isnegativestrand, XAM.FLAG_REVERSE), 
+        (XAM.isnextreversecomplemented, XAM.FLAG_NEXT_REVERSE), 
+        (XAM.isfirstsegment, XAM.FLAG_FIRST_SEGMENT), 
+        (XAM.isread1, XAM.FLAG_FIRST_SEGMENT), 
+        (XAM.islastsegment, XAM.FLAG_LAST_SEGMENT), 
+        (XAM.isread2, XAM.FLAG_LAST_SEGMENT), 
+        (XAM.issecondaryalignment, XAM.FLAG_SECONDARY), 
+        (XAM.isqcfail, XAM.FLAG_QCFAIL), 
+        (XAM.isduplicate, XAM.FLAG_DUPLICATE), 
+        (XAM.issupplementaryalignment, XAM.FLAG_SUPPLEMENTARY), 
+        (XAM.isprimaryalignment, ~0x900), 
+    ]
+
+    foreach(flag_tests) do (func, flag)
+        # SAM Record
+        io = IOBuffer()
+        write(io, string(Int(flag)))
+        bytes = take!(io)
+
+        sam_record = XAM.SAM.Record()
+        sam_record.data = bytes
+        sam_record.flags = sam_record.filled = 1:length(bytes)
+
+        @test flag == XAM.flags(sam_record)
+        @test func(sam_record)
+
+        # BAM record
+        bam_record = XAM.BAM.Record(sam_record)
+
+        @test typeof(bam_record) == XAM.BAM.Record
+        @test flag == XAM.flags(bam_record)
+        @test func(bam_record)
+    end
+
+end