[Bioc-devel] Long-form documentation for DelayedArray?

[Francesco Napolitano]

Oh, I forgot an important point. Does the seed class need to contain
"Array"? What about "array"? I just remembered that I changed it to
"array" because I have no "Array" in my namespace.

On Mon, Oct 30, 2017 at 11:24 AM, Francesco Napolitano
<franapoli at gmail.com> wrote:
>
>
> Il 29/10/2017 22:45, Hervé Pagès ha scritto:
>
> In particular, I'd like to read more about how to create a backend for
> DelayedArray. Is there any documentation available beyond the
> reference manual?
>
>
> I'm guilty. I plan to remedy this ASAP. In the mean time I'll be glad
> to help. Note that other people are already working (or planning to
> work) on other backends:
>
> Backend for remote HDF5 data:
>
>   https://github.com/vjcitn/RemoteArray
>
>   See issues #1, #2, #3 for some discussion about this.
>
> Backend for GDS files:
>
>   https://github.com/Bioconductor/VariantExperiment/issues/1
>
>
> Thank you, Hervé. Maybe I could use some help than! Discussions in issue #2
> seems useful for my case. I have a specific question: when I create a
> DelayedArray with my backend, it seems that subset_seed_as_array() is
> called, which is not really intuitive. Is this normal? What is this first
> call supposed to do? In my case it fails with dimensionality problems (the
> array is empty).
>
> I did look into HDF5Array code, but I'm not sure I understand what the
> following is doing:
>
> .subset_HDF5ArraySeed_as_array <- function(seed, index)
> {
>     ans_dim <- DelayedArray:::get_Nindex_lengths(index, dim(seed))
>     if (any(ans_dim == 0L)) {
>         ans <- seed at first_val[0]
>         dim(ans) <- ans_dim
>     } else {
>         ans <- h5read2(seed at file, seed at name, index)
>     }
>     ans
> }
>
> In particular, I'm not sure how to interpret the index variable, which seems
> to be a list. Each element "i" is a vector of indices for the i-th
> dimension? And what does seed at first_val[0] do? And the first_val attribute
> in general.
>
> Thank you very much for your help,
> francesco