Thanks, I will try and figure out if I can work this out from your
suggestions.
On Tuesday, October 27, 2015 at 8:29:07 AM UTC-6, Yichao Yu wrote:
>
> On Tue, Oct 27, 2015 at 10:08 AM, Taylor Maxwell
> <taylor....@gmail.com <javascript:>> wrote:
> > Thanks for your response. It looks like pointer(::Array) gives me the
> same
> > pointer as if I defined the base.convert call from 0.3.
> >
> > I am not passing it to a ccall. Below is an example of what i am doing.
> > The bedfreq function gets the genotype and missing counts (4
> possibilities
> > encoded in every 2 bits) where b is the UInt8 matrix and ns is the
> number of
> > individuals (this helps me figure out how far to go for each locus. The
> pj
> > variable within the function moves the pointer to the beginning of each
> > column (each locus). The ival function used to pull out the genotype or
> > missing call for each subject which is then added up in the cc matrix.
>
> I didn't look at the code close enough to rewrite the code myself but
> it seems like you could just pass the column number to ival instead.
> You could also construct a sub array for the column.
>
> This also avod some undefined behavior since the GC/codegen might get
> smarter and figure out that you are not actually using the array
> anymore after casting it to a pointer and free it while you are still
> using the pointer.
>
> >
> > I read the garbage collection safety section in documentation and and
> only
> > partially understand it. Once the b Uint8 Matrix is created, it will
> not be
> > changed or deleted while the pointer is in use. From your knowledge of
> the
> > the safe and unsafe uses of pointer to an array, is this ok (it worked
> > perfectly fine in 0.3).
>
> The separation of cconvert and unsafe_convert does not really matter
> for this case. But in general, there are cases that the conversion
> might allocate new buffers for the c function so you want to put that
> part in cconvert and only do the unsafe take-pointer part in
> unsafe_convert. I think we remove the convert method for converting to
> Ptr because you almost never want that convertion to happen
> automatically. (It's unsafe and you should be explicit if you want it,
> by calling pointer() (which should also be unnecessary in most cases),
> for example.
>
> >
> > ival(p::Ptr{UInt8},i::Integer) = i>0 ?
> > (unsafe_load(p,(i-1)>>2+1)>>(2(i-1)&0x06))&0x03 : throw(DomainError)
> >
> > function bedfreq(b::Matrix{UInt8},ns::Integer)
> > m,n = size(b)
> > div(ns+3,4) == m || error("ns = $ns should be in [$(4m-3),$(4m)] for
> > size(b) = $(size(b))")
>
> hint, we have \div operator
>
> > cc = zeros(Int, 4, n)
> > bpt = convert(Ptr{UInt8},b)
> > for j in 0:(n-1)
> > pj = bpt + j*m
> > ## the ival function is inlined explicitly
> > for i in 1:ns cc[1+ival(pj,i),1+j] += 1 end
> > end
> > cc
> > end
> >
> > Thanks!
>
