--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mapping_quality_stats.r	Wed Jun 15 10:43:07 2022 +0000
@@ -0,0 +1,31 @@
+## Setup R error handling to go to stderr
+options(show.error.messages = FALSE,
+        error = function() {
+            cat(geterrmessage(), file = stderr())
+            q("no", 1, FALSE)
+        }
+)
+
+
+warnings()
+library(optparse)
+library(ggplot2)
+
+option_list <- list(
+    make_option(c("-i", "--input"), type = "character", help = "Path to tabular file"),
+    make_option(c("-o", "--output"), type = "character", help = "path to the pdf plot")
+    )
+
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args <- parse_args(parser)
+
+# data frame implementation
+table <- read.delim(args$input, header = TRUE)
+colnames(table) <- c("MAPQ", "Counts")
+
+
+# Barplot
+pdf(file = args$output)
+ggplot(table, aes(x = MAPQ, y = Counts)) +
+    geom_bar(stat = "identity")
+devname <- dev.off()