From ba08b20f97a063e645d06ce1d817c820ec1eb0af Mon Sep 17 00:00:00 2001
From: Iris Mestres Pascual <iris.mestrespascual@unibas.ch>
Date: Mon, 22 Jan 2024 14:51:44 +0000
Subject: [PATCH] feat: add output prefix assignment
---
ascii_alignment_pileup.R | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/ascii_alignment_pileup.R b/ascii_alignment_pileup.R
index 89337d7..ff7bb87 100755
--- a/ascii_alignment_pileup.R
+++ b/ascii_alignment_pileup.R
@@ -29,7 +29,7 @@ against one or more regions specified in a BED file.\n"
author <- "Author: Alexander Kanitz"
affiliation <- "Affiliation: Biozentrum, University of Basel"
email <- "Email: alexander.kanitz@alumni.ethz.ch"
-version <- "1.1.1"
+version <- "1.2.1"
version_formatted <- paste("Version:", version, sep=" ")
requirements <- c("optparse", "rtracklayer", "GenomicAlignments", "tools")
requirements_txt <- paste("Requires:", paste(requirements, collapse=", "), sep=" ")
@@ -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=NULL,
+ 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 (! is.null(prefix.out)) prefix.out else paste(basename(file_path_sans_ext(fl.bam)), collapse=".")
#---> <---#
# Print status message
--
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