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

@@ -128,7 +128,7 @@ option_list <- list(
             "--prefix",
             action="store",
             type="character",
-            default="",
+            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"
@@ -197,7 +197,7 @@ 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 or from CLI argument
-fl.prefix <- if (prefix.out != "") prefix.out else paste(basename(file_path_sans_ext(fl.bam)), collapse=".")
+fl.prefix <- if (! is.null(prefix.out)) prefix.out else paste(basename(file_path_sans_ext(fl.bam)), collapse=".")
 
 #--->   <---#
 # Print status message