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

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This will help a lot, thank you.
Francesco

Il giorno mer, 22/11/2017 alle 15.34 -0800, Hervé Pagès ha scritto:
> 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.co
> > > m_vjcitn_RemoteArray&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeA
> > > vimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9ibHAtmTeiiRRSpiI10_Mz7cTUx
> > > XmyzMMIp1Qv4N16M&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.co
> > > m_Bioconductor_VariantExperiment_issues_1&d=DwIFaQ&c=eRAMFD45gAfq
> > > t84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=9ibHAt
> > > mTeiiRRSpiI10_Mz7cTUxXmyzMMIp1Qv4N16M&s=D7Qo7O5ahMaq4IeBWp7TVD8zw
> > > hvhmDrxrlTBz8K4d9g&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
> 
>