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=" ")