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 <hpa...@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 > > <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.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@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 > > -- > 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: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
