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<h3>vcfR documentation</h3>
by
<br>
Brian J. Knaus and Niklaus J. Grünwald
</center>
</p>
<div id="header">
<h1 class="title toc-ignore">Reporting an issue</h1>
</div>
<div id="TOC">
<ul>
<li><a href="#vcfr-data" id="toc-vcfr-data">vcfR data</a></li>
<li><a href="#your-data" id="toc-your-data">Your data</a></li>
<li><a href="#reporting-the-issue"
id="toc-reporting-the-issue">Reporting the issue</a></li>
<li><a href="#the-benefits-of-reporting"
id="toc-the-benefits-of-reporting">The benefits of reporting</a></li>
</ul>
</div>
<p>If you experience some sort of unexpected behaviour it is possible
that you have discovered a bug. Ways to report a bug include contacting
me directly. If you are a GitHub user it would be better if you <a
href="https://github.com/knausb/vcfR/issues">created an issue</a>. The
success, and efficiency, of any attempt to help you will typically
depend on your ability to create a <a
href="http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example">minimal
reproducible example</a>. A minimal reproducible example is a small
amount of code that allows me, or others, to reproduce the behaviour you
are observing. Through providing a minimal reproducible example you
accomplish two things. First, it provides me with a quick way to
validate that the behaviour is repeatable on my system, confirming that
this is not something specific to your system. Second, it provides me
with an example of the reported behaviour that I can ‘poke and prod’ so
that I can (hopefully) find a solution. To create a minimal reproducible
example you will need some VCF data. Data for an example can be provided
by using example data included in vcfR or by using your own data.</p>
<div id="vcfr-data" class="section level2">
<h2>vcfR data</h2>
<p>The R package vcfR comes with some example data. This is used in the
examples and vignettes. With a little work you can modify this example
data to provide a minimal reproducible example.</p>
<pre class="r"><code>library(vcfR)</code></pre>
<pre class="r"><code>data(vcfR_test)
vcfR_test</code></pre>
<pre><code>## ***** Object of Class vcfR *****
## 3 samples
## 1 CHROMs
## 5 variants
## Object size: 0 Mb
## 0 percent missing data
## ***** ***** *****</code></pre>
<p>Any problem is likely to occur in the ‘gt’ or ‘fix’ slots. These are
matrices that can be manipulated with the square brackets ([]).</p>
<pre class="r"><code>vcfR_test@gt</code></pre>
<pre><code>## FORMAT NA00001 NA00002 NA00003
## [1,] "GT:GQ:DP:HQ" "0|0:48:1:51,51" "1|0:48:8:51,51" "1/1:43:5:.,."
## [2,] "GT:GQ:DP:HQ" "0|0:49:3:58,50" "0|1:3:5:65,3" "0/0:41:3"
## [3,] "GT:GQ:DP:HQ" "1|2:21:6:23,27" "2|1:2:0:18,2" "2/2:35:4"
## [4,] "GT:GQ:DP:HQ" "0|0:54:7:56,60" "0|0:48:4:51,51" "0/0:61:2"
## [5,] "GT:GQ:DP" "0/1:35:4" "0/2:17:2" "1/1:40:3"</code></pre>
<pre class="r"><code>vcfR_test@gt[1,]</code></pre>
<pre><code>## FORMAT NA00001 NA00002 NA00003
## "GT:GQ:DP:HQ" "0|0:48:1:51,51" "1|0:48:8:51,51" "1/1:43:5:.,."</code></pre>
<pre class="r"><code>vcfR_test@gt[1,2]</code></pre>
<pre><code>## NA00001
## "0|0:48:1:51,51"</code></pre>
<pre class="r"><code># Change the genotype
vcfR_test@gt[1,2] <- "3|4:48:1:51,51"
vcfR_test@gt</code></pre>
<pre><code>## FORMAT NA00001 NA00002 NA00003
## [1,] "GT:GQ:DP:HQ" "3|4:48:1:51,51" "1|0:48:8:51,51" "1/1:43:5:.,."
## [2,] "GT:GQ:DP:HQ" "0|0:49:3:58,50" "0|1:3:5:65,3" "0/0:41:3"
## [3,] "GT:GQ:DP:HQ" "1|2:21:6:23,27" "2|1:2:0:18,2" "2/2:35:4"
## [4,] "GT:GQ:DP:HQ" "0|0:54:7:56,60" "0|0:48:4:51,51" "0/0:61:2"
## [5,] "GT:GQ:DP" "0/1:35:4" "0/2:17:2" "1/1:40:3"</code></pre>
<p>If you can find the part of your data that reproduces the problem you
should be able to engineer an example by using this example data.</p>
</div>
<div id="your-data" class="section level2">
<h2>Your data</h2>
<p>Of course, it might just be simpler if you send me your data. Some of
you may not be comfortable with this, particularly if your data is
unpublished. But many people have been comfortable sending me their data
to troubleshoot issues. Keep in mind that VCF data ‘self documents’ in
that it includes information about what software created it and
information about the reference file used to call variants. I think this
is interesting because I get to learn a bit about all the projects
people are using vcfR with. But if you’re uncomfortable with this you
may either want to use the above option, or come up with a way of
obfuscating any information you are uncomfortable sharing.</p>
</div>
<div id="reporting-the-issue" class="section level2">
<h2>Reporting the issue</h2>
<p>Once you have some data, you should provide a few lines of code that
reproduces the issue. If you can forward this data, code, and any error
or warning messages to me (or post it as an issue) it should help me
troubleshoot this matter. Better yet, if you use <a
href="http://rmarkdown.rstudio.com/">RMarkdown</a>, sharing your *.Rmd
and its compiled output from your system illustrating the matter
(usually *.html), that would be great.</p>
<p>Lastly, it never hurts to report your session information to validate
this is not a version issue. Mine is as follows.</p>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>## R version 4.2.1 (2022-06-23)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Monterey 12.4
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] RColorBrewer_1.1-3 memuse_4.2-1 poppr_2.9.3 adegenet_2.1.9
## [5] ade4_1.7-20 pinfsc50_1.2.0 cowplot_1.1.1 ggplot2_3.3.6
## [9] reshape2_1.4.4 vcfR_1.13.0 rmarkdown_2.16
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.2 jsonlite_1.8.0 viridisLite_0.4.1 splines_4.2.1
## [5] bslib_0.4.0 shiny_1.7.2 highr_0.9 yaml_2.3.5
## [9] pegas_1.1 cowsay_0.8.0 pillar_1.8.1 lattice_0.20-45
## [13] glue_1.6.2 digest_0.6.29 promises_1.2.0.1 colorspace_2.0-3
## [17] htmltools_0.5.3 httpuv_1.6.6 Matrix_1.4-1 plyr_1.8.8
## [21] pkgconfig_2.0.3 purrr_0.3.4 xtable_1.8-4 scales_1.2.1
## [25] later_1.3.0 tibble_3.1.8 mgcv_1.8-40 generics_0.1.3
## [29] farver_2.1.1 ellipsis_0.3.2 cachem_1.0.6 withr_2.5.0
## [33] fortunes_1.5-4 cli_3.4.0 magrittr_2.0.3 crayon_1.5.1
## [37] mime_0.12 evaluate_0.16 fansi_1.0.3 nlme_3.1-157
## [41] MASS_7.3-57 vegan_2.6-2 praise_1.0.0 tools_4.2.1
## [45] formatR_1.14 lifecycle_1.0.1 stringr_1.4.1 munsell_0.5.0
## [49] cluster_2.1.3 compiler_4.2.1 jquerylib_0.1.4 rlang_1.0.5
## [53] grid_4.2.1 igraph_1.3.5 labeling_0.4.2 boot_1.3-28
## [57] gtable_0.3.1 R6_2.5.1 knitr_1.40 dplyr_1.0.10
## [61] fastmap_1.1.0 seqinr_4.2-23 utf8_1.2.2 permute_0.9-7
## [65] ape_5.6-2 stringi_1.7.8 parallel_4.2.1 polysat_1.7-7
## [69] Rcpp_1.0.9 vctrs_0.4.1 rmsfact_0.0.3 tidyselect_1.1.2
## [73] xfun_0.32</code></pre>
</div>
<div id="the-benefits-of-reporting" class="section level2">
<h2>The benefits of reporting</h2>
<p>If you have identified an issue with the vcfR code, then reporting
this issue will have at least two positive outcomes. First, I’ll
(hopefully) resolve this matter and you can continue with your research.
Second, I will probably use your example to engineer a <a
href="https://en.wikipedia.org/wiki/Unit_testing">unit test</a>. A unit
test is a bit of code that is executed every time vcfR is built and
tests that vcfR is operating correctly. My unit tests can be seen as a
collection of code that has created issues in the past. By testing these
during builds it ensures that these problems are fixed and haven’t
inadvertantly been unfixed while trying to address a different issue. So
by reporting issues, you can actually help make vcfR a better software.
Thank you!</p>
</div>
<center>
<hr class="style1">
<p>Copyright © 2017, 2018 Brian J. Knaus. All rights reserved.</p>
<p>USDA Agricultural Research Service, Horticultural Crops Research Lab.</p>
</center>
</div>
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