def get_chrs_from_bam(self, file_name):
        """
        Uses samtools to grab the chromosomes from the header that are contained
        in this bam file.
        """
        x = subprocess.check_output(self.tools.samtools + " view -H " + file_name + " | grep '^@SQ' | cut -f2| sed s'/SN://'", shell=True)
        # Chromosomes will be separated by newlines; split into list to return
        return x.split()
Uses samtools to grab the chromosomes from the header that are contained
        in this bam file.