On Thu, Sep 15, 2016 at 10:08 AM, Ben Ward <[email protected]> wrote:
> Hi I have two functions and a function which calls them:
>
> @inline function expected_distance(::Type{JukesCantor69}, p::Float64)
> return -0.75 * log(1 - 4 * p / 3)
> end
>
> @inline function variance(::Type{JukesCantor69}, p::Float64, l::Int64)
> return p * (1 - p) / (((1 - 4 * p / 3) ^ 2) * l)
> end
>
> function distance{A<:NucleotideAlphabet}(::Type{JukesCantor69},
> seqs::Vector{BioSequence{A}})
> p, l = distance(Proportion{AnyMutation}, seqs)
> D = Vector{Float64}(length(p))
> V = Vector{Float64}(length(p))
> @inbounds for i in 1:length(p)
> D[i] = expected_distance(JukesCantor69, p[i])
> V[i] = variance(JukesCantor69, p[i], l[i])
> end
> return D, V
> end
>
> But I'm seeing type uncertainty:
>
> @code_warntype distance(JukesCantor69, dnas)
>
> Variables:
>
> #self#::Bio.Var.#distance
>
> #unused#::Type{Bio.Var.JukesCantor69}
>
> seqs::Array{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},1}
>
> p::Array{Float64,1}
>
> l::Array{Int64,1}
>
> #temp#@_6::Int64
>
> D::Array{Float64,1}
>
> V::Array{Float64,1}
>
> #temp#@_9::Int64
>
> i::Int64
>
>
> Body:
>
> begin
>
> SSAValue(0) = $(Expr(:invoke, LambdaInfo for
> distance(::Type{Bio.Var.Proportion{Bio.Var.AnyMutation}},
> ::Array{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},1}),
> :(Bio.Var.distance), Bio.Var.Proportion{Bio.Var.AnyMutation}, :(seqs)))
>
> #temp#@_6::Int64 = $(QuoteNode(1))
>
> SSAValue(15) =
> (Base.getfield)(SSAValue(0),1)::Union{Array{Float64,1},Array{Int64,1}}
I guess we should probably print ssavalue types to make this easier to analyse
There's likely no type instability and the warning here is just spurious
>
> SSAValue(16) = (Base.box)(Int64,(Base.add_int)(1,1))
>
> p::Array{Float64,1} = SSAValue(15)
>
> #temp#@_6::Int64 = SSAValue(16)
>
> SSAValue(17) =
> (Base.getfield)(SSAValue(0),2)::Union{Array{Float64,1},Array{Int64,1}}
>
> SSAValue(18) = (Base.box)(Int64,(Base.add_int)(2,1))
>
> l::Array{Int64,1} = SSAValue(17)
>
> #temp#@_6::Int64 = SSAValue(18) # line 314:
>
> SSAValue(7) = (Base.arraylen)(p::Array{Float64,1})::Int64
>
> D::Array{Float64,1} =
> (Core.ccall)(:jl_alloc_array_1d,(Core.apply_type)(Core.Array,Float64,1)::Type{Array{Float64,1}},(Core.svec)(Core.Any,Core.Int)::SimpleVector,Array{Float64,1},0,SSAValue(7),0)::Array{Float64,1}
> # line 315:
>
> SSAValue(9) = (Base.arraylen)(p::Array{Float64,1})::Int64
>
> V::Array{Float64,1} =
> (Core.ccall)(:jl_alloc_array_1d,(Core.apply_type)(Core.Array,Float64,1)::Type{Array{Float64,1}},(Core.svec)(Core.Any,Core.Int)::SimpleVector,Array{Float64,1},0,SSAValue(9),0)::Array{Float64,1}
> # line 316:
>
> $(Expr(:inbounds, true))
>
> SSAValue(11) = (Base.arraylen)(p::Array{Float64,1})::Int64
>
> SSAValue(19) =
> (Base.select_value)((Base.sle_int)(1,SSAValue(11))::Bool,SSAValue(11),(Base.box)(Int64,(Base.sub_int)(1,1)))::Int64
>
> #temp#@_9::Int64 = 1
>
> 22:
>
> unless (Base.box)(Base.Bool,(Base.not_int)((#temp#@_9::Int64 ===
> (Base.box)(Int64,(Base.add_int)(SSAValue(19),1)))::Bool)) goto 43
>
> SSAValue(20) = #temp#@_9::Int64
>
> SSAValue(21) = (Base.box)(Int64,(Base.add_int)(#temp#@_9::Int64,1))
>
> i::Int64 = SSAValue(20)
>
> #temp#@_9::Int64 = SSAValue(21) # line 317:
>
> SSAValue(12) = (Base.arrayref)(p::Array{Float64,1},i::Int64)::Float64
>
> $(Expr(:inbounds, false))
>
> # meta: location /Users/bward/.julia/v0.5/Bio/src/var/distances.jl
> expected_distance 69
>
> SSAValue(13) = $(Expr(:invoke, LambdaInfo for log(::Float64),
> :(Bio.Var.log),
> :((Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),(Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)((Base.box)(Float64,(Base.sitofp)(Float64,4)),SSAValue(12))),(Base.box)(Float64,(Base.sitofp)(Float64,3)))))))))
>
> # meta: pop location
>
> $(Expr(:inbounds, :pop))
>
> SSAValue(5) =
> (Base.box)(Base.Float64,(Base.mul_float)(-0.75,SSAValue(13)))
>
>
> (Base.arrayset)(D::Array{Float64,1},SSAValue(5),i::Int64)::Array{Float64,1}
> # line 318:
>
> SSAValue(14) = (Base.arrayref)(p::Array{Float64,1},i::Int64)::Float64
>
> SSAValue(6) =
> (Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)(SSAValue(14),(Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),SSAValue(14))))),(Base.box)(Base.Float64,(Base.mul_float)((Base.Math.box)(Base.Math.Float64,(Base.Math.powi_llvm)((Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),(Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)((Base.box)(Float64,(Base.sitofp)(Float64,4)),SSAValue(14))),(Base.box)(Float64,(Base.sitofp)(Float64,3)))))),(Base.box)(Int32,(Base.checked_trunc_sint)(Int32,2))))::Float64,(Base.box)(Float64,(Base.sitofp)(Float64,(Base.arrayref)(l::Array{Int64,1},i::Int64)::Int64))))))
>
>
> (Base.arrayset)(V::Array{Float64,1},SSAValue(6),i::Int64)::Array{Float64,1}
>
> 41:
>
> goto 22
>
> 43:
>
> $(Expr(:inbounds, :pop)) # line 320:
>
> return
> (Core.tuple)(D::Array{Float64,1},V::Array{Float64,1})::Tuple{Array{Float64,1},Array{Float64,1}}
>
> end::Tuple{Array{Float64,1},Array{Float64,1}}
>
>
> But I'm not sure which those lines correspond to in my code, as they're
> temporary values. I think at some point some code either results in an
> integer or a float. I wondered if it was inside the smaller function called
> by the larger one.
>
> Thanks,
> Ben.
