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

[Peter Hickey]

Thank, Hervé! This is really useful and will help me finish up one such
backend.

Cheers,
Pete

On Wed, 22 Nov 2017 at 18:35 Hervé Pagès <hpages at fredhutch.org> wrote:

> Just to let you know that the process of implementing a DelayedArray
> backend is now documented:
>
>
>
> https://github.com/Bioconductor/DelayedArray/blob/master/vignettes/02-Implementing_a_backend.Rmd
>
> Feedback/questions welcome (preferably as issues on GitHub).
>
> Thanks,
> H.
>
>
> On 10/30/2017 03:27 AM, Francesco Napolitano wrote:
> > 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_vjcitn_RemoteArray&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9ibHAtmTeiiRRSpiI10_Mz7cTUxXmyzMMIp1Qv4N16M&s=pTtsQDjw-10QQfnx-yqM4Df1dO48NXxq6gQUlPaJfFk&e=
> >>
> >>    See issues #1, #2, #3 for some discussion about this.
> >>
> >> Backend for GDS files:
> >>
> >>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_VariantExperiment_issues_1&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9ibHAtmTeiiRRSpiI10_Mz7cTUxXmyzMMIp1Qv4N16M&s=D7Qo7O5ahMaq4IeBWp7TVD8zwhvhmDrxrlTBz8K4d9g&e=
> >>
> >>
> >> 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
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
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