feat: add output prefix assignment

This PR closes #2 (closed) .

In order to allow the assignment of the prefix to be made without changing the current behavior, a new CLI argument (--prefix) has been added and set by default to an empty string. During the prefix assignment, if the user has not provided a prefix, the input BAM file name(s) is used instead.

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