updated doc

thierrygosselin · Feb 25, 2024 · 2eb1dfa · 2eb1dfa
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Showing 12 changed files with 11 additions and 16 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/.DS_Store b/.github/.DS_Store
diff --git a/R/.DS_Store b/R/.DS_Store
diff --git a/R/vcf.R b/R/vcf.R
@@ -489,6 +489,7 @@ read_vcf <- function(
   dp <- "DP" %in% detect.source$check.header$format$ID # Check that DP is valid
 
   if (!is.null(detect.source$markers.info)) markers.info <- detect.source$markers.info
+  overwrite.metadata <- NULL # by default
   if (!is.null(detect.source$overwrite.metadata)) overwrite.metadata <- detect.source$overwrite.metadata
 
   vcf_read_temp <- function(

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@ developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repo
 [![minimal R
 version](https://img.shields.io/badge/R%3E%3D-NA-6666ff.svg)](https://cran.r-project.org/)
 [![packageversion](https://img.shields.io/badge/Package%20version-1.3.0-orange.svg)](commits/master)
-[![Last-changedate](https://img.shields.io/badge/last%20change-2024--02--22-brightgreen.svg)](/commits/master)
+[![Last-changedate](https://img.shields.io/badge/last%20change-2024--02--25-brightgreen.svg)](/commits/master)
 [![R-CMD-check](https://github.com/thierrygosselin/radiator/workflows/R-CMD-check/badge.svg)](https://github.com/thierrygosselin/radiator/actions)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3687060.svg)](https://doi.org/10.5281/zenodo.3687060)
 <!-- badges: end -->

diff --git a/docs/articles/.DS_Store b/docs/articles/.DS_Store
diff --git a/docs/reference/.DS_Store b/docs/reference/.DS_Store
diff --git a/inst/.DS_Store b/inst/.DS_Store
diff --git a/man/.DS_Store b/man/.DS_Store
diff --git a/vignettes/.DS_Store b/vignettes/.DS_Store
diff --git a/vignettes/rad_genomics_computer_setup.Rmd b/vignettes/rad_genomics_computer_setup.Rmd
@@ -716,7 +716,7 @@ sudo rm -R lz4*
 
 ```{bash eval=FALSE}
 cd ~/Downloads
-curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.2.tar.gz | tar xf -
+curl -L https://github.com/facebook/zstd/archive/refs/tags/v1.5.5.tar.gz | tar xf -
 cd zstd*
 make 
 sudo make install

diff --git a/vignettes/rad_genomics_computer_setup.html b/vignettes/rad_genomics_computer_setup.html