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 > > <franap...@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@first_val[0] > > > dim(ans) <- ans_dim > > > } else { > > > ans <- h5read2(seed@file, seed@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@first_val[0] do? And the first_val > > > attribute > > > in general. > > > > > > Thank you very much for your help, > > > francesco > >
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