From a636cd0d0f9d33e9e6f1764c67e058e94ad5425c Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 11 Sep 2023 14:20:23 +0200
Subject: [PATCH] kmerclust_load.R: use vroom to load csv
---
src/bin/kmerclust_load.R | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/bin/kmerclust_load.R b/src/bin/kmerclust_load.R
index f6c4b1d..235cab9 100644
--- a/src/bin/kmerclust_load.R
+++ b/src/bin/kmerclust_load.R
@@ -1,10 +1,11 @@
library(kmerclust)
+library(vroom)
args <- commandArgs(trailingOnly = TRUE)
-print(args)
-data <- readr::read_tsv(args[2], show_col_types = FALSE)
+data <- vroom::vroom(args[2], show_col_types = FALSE)
format(object.size(data), units = "Mb")
annotation <- parse_annotation(args[1])
-count <- annotate_counts(annotation, data, args[3]) %>% dplyr::ungroup()
+count <- annotate_counts(annotation, data, args[3]) %>% dplyr::ungroup() %>% dplyr::select(-c("files"))
+format(object.size(count), units = "Mb")
save(count, file = paste0(args[3], ".Rdata"))
--
GitLab