def sam_conversions(self, sam_file, depth=True):
        cmd = self.tools.samtools + " view -bS " + sam_file + " > " + sam_file.replace(".sam", ".bam") + "\n"
        cmd += self.tools.samtools + " sort " + sam_file.replace(".sam", ".bam") + " -o " + sam_file.replace(".sam", "_sorted.bam") + "\n"
        cmd += self.tools.samtools + " index " + sam_file.replace(".sam", "_sorted.bam") + "\n"
        if depth:
            cmd += self.tools.samtools + " depth " + sam_file.replace(".sam", "_sorted.bam") + " > " + sam_file.replace(".sam", "_sorted.depth") + "\n"
        return cmd