Update .github files, README, pkgdown config, ran dev/04_update.R

LieberInstitute · May 7, 2023 · 9136079 · 9136079
1 parent af99b6f
commit 9136079
Show file tree

Hide file tree

Showing 20 changed files with 411 additions and 212 deletions.
diff --git a/.github/ISSUE_TEMPLATE/feature_request_template.md b/.github/ISSUE_TEMPLATE/feature_request_template.md
@@ -0,0  1,37 @@
 ---
 name: Feature Request
 about: Suggest an idea for this package
 title: "[Feature Request] A short description of the feature"
 labels: ''
 assignees: ''
 ---
 
 Please ask questions about how to use `megadepth` on the Bioconductor
 Support Site at <https://support.bioconductor.org> using the appropriate tag(s)
 including the one for this package.
 
 **Note**. Update the issue title to summarize the feature request.
 
 ## Is the feature request related to a problem?
 
 Please provide a clear and concise description of what the problem
 is. Ex. I'm always frustrated when [...]
 
 ## Describe the solution
 
 A clear and concise description of what you want to happen.
 
 ## Describe any alternatives considered
 
 A clear and concise description of any alternative solutions or
 features you've considered.
 
 ## Additional context
 
 Add any other context about the feature request here. You may include web links
 (e.g., from GitHub) to:
 
 * raw code
 * a commit
 * code inside a commit
 * code from an R package
diff --git a/.github/ISSUE_TEMPLATE/issue_template.md b/.github/ISSUE_TEMPLATE/issue_template.md
@@ -1,56  1,73 @@
 ---
-name: Bug report or feature request
-about: Describe a bug you've seen or make a case for a new feature
-title: "[BUG] Your bug or feature request"
 name: Bug Report
 about: Describe the bug in detail
 title: "[BUG] A short description of the bug"
 labels: ''
 assignees: ''
 ---
 
-Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://support.bioconductor.org/> using the appropriate tag(s) including one for this package.
 Please ask questions about how to use `megadepth` on the
 [Bioconductor Support Site](https://support.bioconductor.org) using the
 appropriate tag(s) including the one for this package.
 
-## Context
 **Note**. Update the issue title to concisely describe the bug.
 
-Provide some context for your bug report or feature request. This could be the:
 ## Describe the bug
 
-* link to raw code, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/blob/master/00-template.Rmd#L24-L28
-* link to a commit, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/commit/6aa30b22eda614d932c12997ba611ba582c435d7
-* link to a line of code inside a commit, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/commit/6aa30b22eda614d932c12997ba611ba582c435d7#diff-e265269fe4f17929940e81341b92b116R17
-* link to code from an R package, example: https://github.com/LieberInstitute/spatialLIBD/blob/master/R/run_app.R#L51-L55
 Please provide a clear and concise description of what the bug is.
 
-## Code
 ### Provide a minimally reproducible example (reprex)
 
-Include the code you ran and comments
 Provide a clear and concise description of the bug. It can be easily (but not
 necessarily) illustrated with a minimally reproducible example using the
 [`reprex` package](https://reprex.tidyverse.org/articles/learn-reprex.html).
 
-```R
-## prompt an error
-stop('hola')
 For tips on creating a reprex, see this
 [StackOverflow link](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example).
 
-## check the error trace
-traceback()
-```
 ## Expected behavior
 
-## Small reproducible example
 A clear and concise description of what you expected to happen.
 
-If you copy the lines of code that lead to your error, you can then run [`reprex::reprex()`](https://reprex.tidyverse.org/reference/reprex.html) which will create a small website with code you can then easily copy-paste here in a way that will be easy to work with later on.
 ## R Session Information
 
-```R
-## prompt an error
-stop('hola')
-#> Error in eval(expr, envir, enclos): hola
 Please report the output of either `sessionInfo()` or
 `sessioninfo::session_info()` here.
 
 <details>
 
-## check the error trace
-traceback()
-#> No traceback available
 ```R
 options(width = 120)
 ## insert session info here
 # sessioninfo::session_info() ## provides GitHub, pandoc, and other details
 # sessionInfo() ## base R function in case you don't want to install sessioninfo
 ```
 
 </details>
 
-## R session information
 Indicate whether `BiocManager::valid()` returns `TRUE`. 
 
-Remember to include your full R session information.
 - [ ] `BiocManager::valid()` is `TRUE`
 
-```R
-options(width = 120)
-sessioninfo::session_info()
-```
 **Note**. To avoid potential issues with version mixing and reproducibility, do
 not install packages from `GitHub`.
 
 ## Additional Context
 
 Provide some additional context for the bug report. You may include web links
 (e.g., from GitHub) to:
 
 * raw code
 * a commit
 * code inside a commit
 * code from an R package
 
 ## Is the package installed via bioconda? 
 
 We find that [bioconda](https://bioconda.github.io/) installations can often be
 problematic due to the nature of the setup environment and potential for version
 mixing.
 
 The preferred method for installing Bioconductor software through `BiocManager`
 and we do not support issues related to `bioconda` installations at this time.
 
-The output of `sessioninfo::session_info()` includes relevant GitHub installation information and other details that are missed by `sessionInfo()`.
diff --git a/.github/SUPPORT.md b/.github/SUPPORT.md
@@ -1,35  1,64 @@
 # Getting help with `megadepth`
 
-Thanks for using `megadepth`!
-Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
 Thank you for using `megadepth`!
 Before filing an issue, there are few things you should know to make the process
 as smooth as possible for both parties.
 
 ## Make a reprex
 
-Start by making a minimal **repr**oducible **ex**ample using the  [reprex](https://reprex.tidyverse.org/) package.
-If you haven't heard of or used reprex before, you're in for a treat!
-Seriously, reprex will make all of your R-question-asking endeavors easier (which is a pretty insane ROI for the five to ten minutes it'll take you to learn what it's all about).
-For additional reprex pointers, check out the [Get help!](https://www.tidyverse.org/help/) section of the tidyverse site.
 Start by making a minimally **repr**oducible **ex**ample, also known as a
 'reprex'. You may use the [`reprex`](https://reprex.tidyverse.org/) R package to
 create one, though it is not necessary but it does help. It will make all of
 your R-question-asking endeavors easier. Learning
 [how to use it](https://reprex.tidyverse.org/articles/learn-reprex.html) takes
 about 5 to 10 minutes.
 
-## Where to ask?
 For more tips on how to make a minimally **repr**oducible **ex**ample, see this
 [StackOverflow link](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example).
 
-Armed with your reprex, the next step is to figure out [where to ask](https://www.tidyverse.org/help/#where-to-ask). See also the [Bioconductor help](http://bioconductor.org/help/) website.
 ## Where to post it?
 
-*   If it's a question: start with [community.rstudio.com](https://community.rstudio.com/), and/or StackOverflow. If this a Bioconductor-related question, please ask it at the [Bioconductor Support Website](https://support.bioconductor.org/) using the [appropriate package tag](https://support.bioconductor.org/t/megadepth) (the website will send an automatic email to the package authors). There are more people there to answer questions.
 The [Bioconductor help](http://bioconductor.org/help/) web page gives an
 overview of places that may help answer your question.
 
-*   If it's a bug: you're in the right place, [file an issue](https://github.com/LieberInstitute/megadepth/issues/new).
 * Bioconductor software related questions, such as bug reports and feature
   requests, should be addressed in the appropriate `Bioconductor/megadepth`
   GitHub repository. Follow our bug report and feature request templates on
   GitHub. If the package does not have a GitHub repository, see the next bullet
   point.
 
-*   If you're not sure: let the community help you figure it out!
-    If your problem _is_ a bug or a feature request, you can easily return here and report it.
 * Bioconductor software usage questions should be addressed in the
   [Bioconductor Support Website](https://support.bioconductor.org/). Make sure
   to use the
   [appropriate package tag](https://support.bioconductor.org/tag/megadepth),
   otherwise the package authors will not get a notification.
 
 * General R questions can be posed at StackOverflow or at the
   [RStudio Community](https://community.rstudio.com/) website especially if they
   pertain to the `tidyverse` or the RStudio GUI or related products.
 
-Before opening a new issue, be sure to [search issues and pull requests](https://github.com/LieberInstitute/megadepth/issues) to make sure the bug hasn't been reported and/or already fixed in the development version.
-By default, the search will be pre-populated with `is:issue is:open`.
-You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/)  (e.g. `is:pr`, `is:closed`) as needed.
-For example, you'd simply remove `is:open` to search _all_ issues in the repo, open or closed.
 ## Issues or Feature Requests
 
 Before opening a new issue or feature request, be sure to
 [search issues and pull requests](https://github.com/LieberInstitute/megadepth/issues)
 to ensure that one does not already exist or has been implemented in the
 development version.
 
 **Note**. You can remove the `is:open` search term in the issues page to search
 through open and closed issues. See
 [this link to learn more](https://help.github.com/articles/searching-issues-and-pull-requests/)
 about modifying the search.
 
 ## What happens next?
 
-To be as efficient as possible, development of tidyverse packages tends to be very bursty, so you shouldn't worry if you don't get an immediate response.
-Typically we don't look at a repo until a sufficient quantity of issues accumulates, then there’s a burst of intense activity as we focus our efforts.
-That makes development more efficient because it avoids expensive context switching between problems, at the cost of taking longer to get back to you.
-This process makes a good reprex particularly important because it might be multiple months between your initial report and when we start working on it.
-If we can’t reproduce the bug, we can’t fix it!
 Our Bioconductor maintainers are limited in resources but they do strive to be
 as responsive as possible.
 
 Please do not forget to tag the appropriate maintainer in the issue with their
 GitHub username (e.g., @username).
 
 In order to make it easy as possible for Bioconductor core developers to
 remediate the issue. Provide an accurate, brief, and reproducible report
 as outlined in the issue templates.
 
 Thank you for trusting Bioconductor.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -31,7  31,7 @@ biocViews: Software, Coverage, DataImport, Transcriptomics, RNASeq,
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
 RoxygenNote: 7.2.3
 Suggests: 
     covr,
     knitr,

diff --git a/R/bam_to_bigwig.R b/R/bam_to_bigwig.R
@@ -54,11  54,12 @@
 #'     )
 #'     bw_cov
 #' }
-bam_to_bigwig <- function(bam_file,
-    prefix = file.path(tempdir(), basename(bam_file)),
-    min_unique_qual = FALSE,
-    double_count = FALSE,
-    overwrite = FALSE) {
 bam_to_bigwig <- function(
         bam_file,
         prefix = file.path(tempdir(), basename(bam_file)),
         min_unique_qual = FALSE,
         double_count = FALSE,
         overwrite = FALSE) {
     if (xfun::is_windows()) {
         warning(
             "Megadepth currently does not support creating bigWig files on ",

diff --git a/R/bam_to_junctions.R b/R/bam_to_junctions.R
@@ -45,14  45,15 @@
 #'
 #' ## Path to the output file generated by bam_to_junctions()
 #' example_jxs
-bam_to_junctions <- function(bam_file,
-    prefix = file.path(tempdir(), basename(bam_file)),
-    all_junctions = TRUE,
-    junctions = FALSE,
-    long_reads = FALSE,
-    filter_in = 65535,
-    filter_out = 260,
-    overwrite = FALSE) {
 bam_to_junctions <- function(
         bam_file,
         prefix = file.path(tempdir(), basename(bam_file)),
         all_junctions = TRUE,
         junctions = FALSE,
         long_reads = FALSE,
         filter_in = 65535,
         filter_out = 260,
         overwrite = FALSE) {
     expected_ext <- c("all_jxs.tsv", "jxs.tsv")
     if (!overwrite) prefix_exists(prefix, expected_ext)
 

diff --git a/R/get_coverage.R b/R/get_coverage.R
@@ -72,10  72,11 @@
 #'     )
 #' }
 get_coverage <-
-    function(bigwig_file,
-    op = c("sum", "mean", "max", "min"),
-    annotation,
-    prefix = file.path(tempdir(), "bw.mean")) {
     function(
         bigwig_file,
         op = c("sum", "mean", "max", "min"),
         annotation,
         prefix = file.path(tempdir(), "bw.mean")) {
         megadepth_shell2(
             bigwig_file,
             list(

diff --git a/R/install.R b/R/install.R
@@ -140,8  140,9 @@ install_megadepth_bin <- function(exec) {
 }
 
 # obtain possible locations of the megadepth executable
-bin_paths <- function(dir = "Megadepth",
-    extra_path = getOption("megadepth.dir")) {
 bin_paths <- function(
         dir = "Megadepth",
         extra_path = getOption("megadepth.dir")) {
     if (xfun::is_windows()) {
         path <- Sys.getenv("APPDATA", "")
         path <- if (fs::dir_exists(path)) {

diff --git a/R/read_junction.R b/R/read_junction.R
@@ -33,7  33,6 @@
 #'
 #' all_jxs
 read_junction_table <- function(tsv_file) {
-
     # define the expected column names and types
     if (grepl("all_jxs.tsv", tsv_file)) {
         col_names <- c(

diff --git a/README.Rmd b/README.Rmd
@@ -16,20  16,25 @@ knitr::opts_chunk$set(
 # megadepth
 
 <!-- badges: start -->
-[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
-[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/megadepth.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/megadepth)
-[![BioC dev status](http://www.bioconductor.org/shields/build/devel/bioc/megadepth.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/megadepth)
-[![Codecov test coverage](https://codecov.io/gh/LieberInstitute/megadepth/branch/master/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/megadepth?branch=master)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/megadepth.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/megadepth)
 [![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/megadepth.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/megadepth)
 [![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/megadepth.svg)](http://bioconductor.org/packages/stats/bioc/megadepth/)
 [![Bioc support](https://bioconductor.org/shields/posts/megadepth.svg)](https://support.bioconductor.org/tag/megadepth)
 [![Bioc history](https://bioconductor.org/shields/years-in-bioc/megadepth.svg)](https://bioconductor.org/packages/release/bioc/html/megadepth.html#since)
 [![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/bioc/megadepth.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/megadepth/)
 [![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/megadepth.svg)](https://bioconductor.org/packages/release/bioc/html/megadepth.html#since)
 [![Codecov test coverage](https://codecov.io/gh/LieberInstitute/megadepth/branch/devel/graph/badge.svg)](https://codecov.io/gh/LieberInstitute/megadepth?branch=devel)
 [![R build status](https://github.com/LieberInstitute/megadepth/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/LieberInstitute/megadepth/actions)
-[![Support site activity, last 6 months: tagged questions/avg. answers per question/avg. comments per question/accepted answers, or 0 if no tagged posts.](http://www.bioconductor.org/shields/posts/megadepth.svg)](https://support.bioconductor.org/t/megadepth/)
 [![GitHub issues](https://img.shields.io/github/issues/LieberInstitute/megadepth)](https://github.com/LieberInstitute/megadepth/issues)
 [![GitHub pulls](https://img.shields.io/github/issues-pr/LieberInstitute/megadepth)](https://github.com/LieberInstitute/megadepth/pulls)
 <!-- badges: end -->
 
 The goal of `megadepth` is to provide an R interface to the command line tool [Megadepth](https://github.com/ChristopherWilks/megadepth) for BigWig and BAM related utilities created by [Christopher Wilks](https://twitter.com/chrisnwilks). This R package enables **fast** processing of BigWig files on downstream packages such as [dasper](https://bioconductor.org/packages/dasper) and [recount3](https://bioconductor.org/packages/recount3). The [Megadepth](https://github.com/ChristopherWilks/megadepth) software also provides utilities for processing BAM files and extracting coverage information from them.
 
 Here is an illustration on how fast `megadepth` is compared to other tools for processing local and remote BigWig files.
 
-<a href="https://github.com/LieberInstitute/megadepth/tree/master/analysis"><img src="https://raw.githubusercontent.com/LieberInstitute/megadepth/master/analysis/md_rt_pybw_runtime.png" width="800px" ></a>
 <a href="https://github.com/LieberInstitute/megadepth/tree/devel/analysis"><img src="https://raw.githubusercontent.com/LieberInstitute/megadepth/devel/analysis/md_rt_pybw_runtime.png" width="800px" ></a>
 
 Throughout the documentation we use a capital `M` to refer to the software by Christopher Wilks and a lower case `m` to refer to this R/Bioconductor package.
 
@@ -81,7  86,7 @@ bw_cov
 
 To make it easier to use, `megadepth` includes functions that simplify the number of arguments, read in the output files, and converts them into R/Bioconductor friendly objects, such as `get_coverage()` illustrated above.
 
-We hope that you'll find `megadepth` and [Megadepth](https://github.com/ChristopherWilks/megadepth) useful for your work. If you are interested in checking how **fast** `megadepth` is, check out the [**speed analysis**](https://github.com/LieberInstitute/megadepth/tree/master/analysis) comparison against other tools. Note that the size of the files used and the number of genomic regions queried will affect the speed comparisons.
 We hope that you'll find `megadepth` and [Megadepth](https://github.com/ChristopherWilks/megadepth) useful for your work. If you are interested in checking how **fast** `megadepth` is, check out the [**speed analysis**](https://github.com/LieberInstitute/megadepth/tree/devel/analysis) comparison against other tools. Note that the size of the files used and the number of genomic regions queried will affect the speed comparisons.
 
 ```{r "interface_options"}
 ## R-like interface