Implement scaling in uniwig

[donaldcampbelljr]

Original bamsitesToWig in PEPATAC scales counts within the perl script based on a float obtained from aligned_reads:

			if ($countIndex % $stepSize == 0) {
                $scaledCount = $currentCount/$scale;
				print "$countIndex\t$scaledCount\n";
			}

Original command:

            cmd = tool_path("bamSitesToWig.py")
            cmd += " -i " + rmdup_bam
            cmd += " -c " + res.chrom_sizes
            cmd += " -w " + smooth_target
            cmd += " -m " + "atac"
            cmd += " -p " + str(int(max(1, int(pm.cores) * 2/3)))
            cmd += " --variable-step"
            if not args.no_scale:
                ar = float(pm.get_stat("Aligned_reads"))
                if ar:
                    cmd += " --scale " + str(ar)