From ec34d1b9aa292251aa0ad9d35ee9bfff0a26cfc9 Mon Sep 17 00:00:00 2001
From: deliaBlue <iris.mepa13@gmail.com>
Date: Mon, 22 Jan 2024 13:58:11 +0100
Subject: [PATCH] feat: add output prefix assignment
---
ascii_alignment_pileup.R | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/ascii_alignment_pileup.R b/ascii_alignment_pileup.R
index 89337d7..3ddb46f 100755
--- a/ascii_alignment_pileup.R
+++ b/ascii_alignment_pileup.R
@@ -124,6 +124,15 @@ option_list <- list(
help="Character to denote insertions and deletions in alignments. [default \"%default\"]",
metavar="char"
),
+ make_option(
+ "--prefix",
+ action="store",
+ type="character",
+ default="",
+ help="Prefix to be used in the output file name(s). If not provided
+ the input BAM file(s) name will be used instead,",
+ metavar="string"
+ ),
make_option(
c("-h", "--help"),
action="store_true",
@@ -154,6 +163,7 @@ fl.bam <- cli$args[2:length(cli$args)]
fl.ref <- cli$options[["reference"]]
fl.anno <- cli$options[["annotations"]]
dir.out <- cli$options[["output-directory"]]
+prefix.out <- cli$options[["prefix"]]
width.max <- cli$options[["maximum-region-width"]]
collapse <- ! cli$options[["do-not-collapse-alignments"]]
count.min <- cli$options[["minimum-count"]]
@@ -186,8 +196,8 @@ bed <- import(con=fl.query)
if (! is.null(fl.ref)) {ref <- FaFile(fl.ref)}
if (! is.null(fl.anno)) {anno <- import(con=fl.anno)}
-# Get file prefix from BAM files
-fl.prefix <- paste(basename(file_path_sans_ext(fl.bam)), collapse=".")
+# Get file prefix from BAM files or from CLI argument
+fl.prefix <- if (prefix.out != "") prefix.out else paste(basename(file_path_sans_ext(fl.bam)), collapse=".")
#---> <---#
# Print status message
--
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