Commit 9de43e5e authored by van den Berg's avatar van den Berg
Browse files

Merge branch 'devel' into 'master'

Use the tools library to determine file extension

See merge request !8
parents 4a0dc089 449e555b
Pipeline #4269 failed with stages
in 41 minutes and 55 seconds
......@@ -5,6 +5,7 @@
# Copyright (c) 2015 Leiden University Medical Center <http://lumc.nl>
# All rights reserved.
library("tools")
suppressMessages(library(Gviz))
RenameEnsemblChroms <- function(annots) {
......@@ -359,7 +360,7 @@ MakePlot <- function(parsed.data, sample.name, gene.id, gene.model, genome = "hg
plot.title <- paste(c("Variant Calls - Sample '", sample.name, "'\n", gene.symbol,
" (", gene.id, ")"), collapse = "")
if (!is.null(out.file) & tolower(unlist(strsplit(out.file, "\\."))[-1]) == "png") {
if (!is.null(out.file) & file_ext(out.file) == "png") {
png(out.file, height = to.plot$height, width = to.plot$width)
Gviz::plotTracks(to.plot$tracks, chromosome = chrom, main = plot.title,
col = NULL, sizes=to.plot$sizes)
......
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