Test for AuxException cases

src/XAMAuxData.jl

@@ -11,6 +11,7 @@ public Errors, Error
 
 # These are the numerical types supported by the BAM format.
 const AUX_NUMBER_TYPES = Union{Int8, UInt8, Int16, UInt16, Int32, UInt32, Float32}
+const BIT_INTEGERS = Union{UInt8, Int8, UInt16, Int16, UInt32, Int32, UInt64, Int64, UInt128, Int128}
 
 include("auxtag.jl")
 
@@ -80,11 +81,20 @@ function as_aux_value end
 as_sam_aux_value(x) = as_aux_value(x)
 as_bam_aux_value(x) = as_aux_value(x)
 
-as_aux_value(x::Real) = Float32(x)::Float32
+as_aux_value(x::Float32) = x
+as_aux_value(x::Float16) = Float32(x)
 
-function as_aux_value(x::AbstractChar)::Union{Char, Error}
+function as_aux_value(x::Real)
+    f = Float32(x)
+    if !isinf(x) & isinf(f)
+        throw(AuxException(Errors.InvalidFloat))
+    end
+    f
+end
+
+function as_aux_value(x::AbstractChar)::Char
     c = Char(x)::Char
-    isascii(c) ? c : throw(AuxException(Errors.InvalidChar))
+    is_printable_char(c) ? c : throw(AuxException(Errors.InvalidChar))
 end
 
 as_aux_value(x::Hex) = x
@@ -180,6 +190,7 @@ const ELTYPE_DICT = Dict(
 )
 
 is_printable_char(x::UInt8) = in(x, UInt8('!'):UInt8('~'))
+is_printable_char(c::Char) = '!' ≤ c ≤ '~'
 
 """
     Errors

src/auxtag.jl

@@ -71,10 +71,10 @@ function try_auxtag(x::Union{String, SubString{String}})
     try_auxtag(cu1, cu2)
 end
 
-function try_auxtag(x::AbstractString)
-    (x, s) = @something iterate(x) return nothing
-    (y, s) = @something iterate(x, s) return nothing
-    isnothing(iterate(x, s)) || return nothing
+function try_auxtag(str::AbstractString)
+    (x, s) = @something iterate(str) return nothing
+    (y, s) = @something iterate(str, s) return nothing
+    isnothing(iterate(str, s)) || return nothing
     try_auxtag(Char(x)::Char, Char(y)::Char)
 end
 

src/bam.jl

@@ -266,8 +266,9 @@ function bytes_needed(x::AbstractVector{<:AUX_NUMBER_TYPES})
 end
 
 as_bam_aux_value(x::AUX_NUMBER_TYPES) = x
-as_bam_aux_value(x::Signed) = Int32(x)
-as_bam_aux_value(x::Unsigned) = UInt32(x)
+
+as_bam_aux_value(x::Signed) = Int32(x)::Int32
+as_bam_aux_value(x::Unsigned) = UInt32(x)::UInt32
 
 function Base.setindex!(aux::MutableAuxiliary, val, k)
     key = convert(AuxTag, k)

src/delimited.jl

@@ -11,7 +11,7 @@ end
 
 function DelimitedIterator(x, d::T) where {T}
     v = ImmutableMemoryView(x)
-    eltype(v) == T || error("MemoryView(x) must be of eltype T") # TODO
+    eltype(v) == T || error("MemoryView element type is different from delimiter type")
     DelimitedIterator{T}(v, d)
 end
 

src/sam.jl

@@ -13,7 +13,7 @@ import ..AuxTag, ..AbstractAuxiliary, ..ELTYPE_DICT, ..is_printable_char, ..is_p
 import ..DelimitedIterator, ..get_type_tag, ..Error, ..Errors, ..load_hex, ..validate_hex
 import ..try_auxtag, ..Unsafe, ..as_sam_aux_value, ..AUX_NUMBER_TYPES, ..hexencode!
 import ..iter_encodings, ..AbstractEncodedIterator, ..AuxException, ..striptype
-import ..is_well_formed
+import ..is_well_formed, ..BIT_INTEGERS
 
 public Auxiliary, AuxTag, Hex, Errors, Error
 
@@ -230,7 +230,21 @@ function load_auxvalue(type_tag::UInt8, mem::ImmutableMemoryView{UInt8})
     end
 end
 
-as_sam_aux_value(x::Integer) = Int32(x)::Int32
+function as_sam_aux_value(x::Integer)::Int32
+    try
+        return Int32(x)::Int32
+    catch
+        throw(AuxException(Errors.InvalidInt))
+    end
+end
+
+function as_sam_aux_value(x::BIT_INTEGERS)::Int32
+    if (x < typemin(Int32)) | (x > typemax(Int32))
+        throw(AuxException(Errors.InvalidInt))
+    else
+        x % Int32
+    end
+end
 
 function setindex_nonexisting!(aux::MutableAuxiliary, val, key::AuxTag)
     v = as_sam_aux_value(val)

test/runtests.jl

@@ -35,9 +35,11 @@ end
     @test AuxTag("ac") == AuxTag('a', 'c') == AuxTag(0x61, 0x63)
     for good in ["AB", "A1", "a9", "w5"]
         @test try_auxtag(good) isa AuxTag
+        @test try_auxtag(Test.GenericString(good)) isa AuxTag
     end
     for bad in ["", "A", "ABC", "A11", "5A", "AØ", "a!"]
         @test try_auxtag(bad) === nothing
+        @test try_auxtag(Test.GenericString(bad)) === nothing
     end
 
     @test sort!(AuxTag.(["XA", "X1", "ab", "AB"])) == AuxTag.(["AB", "X1", "XA", "ab"])
@@ -83,6 +85,19 @@ end
     @test aux["hc"] == Errors.InvalidTypeTag
 end
 
+@testset "Display" begin
+    aux = SAM.Auxiliary("AB:i:242\tkV:Z:abcdef gh \tJJ:A:!\tzZ:f:-1.2")
+    buf = IOBuffer()
+    show(buf, MIME"text/plain"(), aux)
+    str = String(take!(buf))
+    @test str == """
+    4-element XAMAuxData.SAM.Auxiliary{MemoryViews.ImmutableMemoryView{UInt8}}:
+      "AB" => 242
+      "kV" => "abcdef gh "
+      "JJ" => '!'
+      "zZ" => -1.2f0"""
+end
+
 @testset "Mutating" begin
     aux = SAM.Auxiliary(UInt8[], 1)
     d = Dict{AuxTag, Any}()
@@ -340,6 +355,19 @@ end # SAM
     end
 end
 
+@testset "Display" begin
+    aux = BAM.Auxiliary("ABS\0\xf2kVZabcdef gh \0JJA!zZf\x9a\x99\x99\xbf")
+    buf = IOBuffer()
+    show(buf, MIME"text/plain"(), aux)
+    str = String(take!(buf))
+    @test str == """
+    4-element XAMAuxData.BAM.Auxiliary{MemoryViews.ImmutableMemoryView{UInt8}}:
+      "AB" => 0xf200
+      "kV" => "abcdef gh "
+      "JJ" => '!'
+      "zZ" => -1.2f0"""
+end
+
 @testset "Mutating" begin
     aux = BAM.Auxiliary(UInt8[], 1)
     d = Dict{AuxTag, Any}()
@@ -632,4 +660,63 @@ end
     end
 end
 
+@testset "Exception types" begin
+    @test_throws(
+        "Not enough bytes remaining in Aux data to encode a full field",
+        first(values(SAM.Auxiliary("\t"))),
+    )
+
+    @test_throws(
+        "Invalid AuxTag. Tags must conform to r\"^[A-Za-z][A-Za-z0-9]\$\".",
+        first(values(SAM.Auxiliary("11:i:1"))),
+    )
+
+    @test_throws(
+        "Invalid SAM tag header. Expected <AuxTag>:<type tag>:, but found no colons.",
+        first(values(SAM.Auxiliary("ABi111"))),
+    )
+
+    @test_throws(
+        "BAM string or Hex type not terminated by null byte",
+        BAM.Auxiliary("ABZabc")["AB"],
+    )
+
+    @test_throws(
+        "BAM string or Hex type not terminated by null byte",
+        BAM.Auxiliary("ABH1234")["AB"],
+    )
+
+    @test_throws(
+        "Unknown type tag in aux value.",
+        BAM.Auxiliary("ABW123")["AB"],
+    )
+
+    @test_throws(
+        "Invalid array element type tag. Valid values are CcSsIif.",
+        BAM.Auxiliary("ABBW1234")["AB"],
+    )
+
+    @test_throws(
+        "Auxiliary Char (type 'A') must be in '!':'~'.",
+        SAM.Auxiliary(UInt8[], 1)["AB"] = '\n',
+    )
+
+    @test_throws(
+        "Data in SAM Auxiliary cannot be parsed as base-ten Int32.",
+        SAM.Auxiliary(UInt8[], 1)["AB"] = typemax(Int64)
+    )
+
+    @test_throws(
+        "Data in SAM Auxiliary cannot be parsed as Float32.",
+        SAM.Auxiliary(UInt8[], 1)["AB"] = 22e304,
+    )
+    @test SAM.Auxiliary(UInt8[], 1)["AB"] = Inf64 isa Any
+    @test SAM.Auxiliary(UInt8[], 1)["AB"] = -Inf64 isa Any
+
+    @test_throws(
+        "Auxiliary String (type 'Z') can only contain bytes in re\"[ !-~]\".",
+        SAM.Auxiliary(UInt8[], 1)["AB"] = "Rødgrød med fløde"
+    )
+end
+
 end # module