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 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).
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))")
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!
