def count_mapped_reads(self, file_name, paired_end):
        """
        Mapped_reads are not in fastq format, so this one doesn't need to accommodate fastq,
        and therefore, doesn't require a paired-end parameter because it only uses samtools view.
        Therefore, it's ok that it has a default parameter, since this is discarded.

        :param str file_name: File for which to count mapped reads.
        :param bool paired_end: This parameter is ignored; samtools automatically correctly responds depending
            on the data in the bamfile. We leave the option here just for consistency, since all the other
            counting functions require the parameter. This makes it easier to swap counting functions during
            pipeline development.
        :return int: Either return code from samtools view command, or -1 to indicate an error state.
        """
        if file_name.endswith("bam"):
            return self.samtools_view(file_name, param="-c -F4")
        if file_name.endswith("sam"):
            return self.samtools_view(file_name, param="-c -F4 -S")
        return -1
Mapped_reads are not in fastq format, so this one doesn't need to accommodate fastq,
        and therefore, doesn't require a paired-end parameter because it only uses samtools view.
        Therefore, it's ok that it has a default parameter, since this is discarded.

        :param str file_name: File for which to count mapped reads.
        :param bool paired_end: This parameter is ignored; samtools automatically correctly responds depending
            on the data in the bamfile. We leave the option here just for consistency, since all the other
            counting functions require the parameter. This makes it easier to swap counting functions during
            pipeline development.
        :return int: Either return code from samtools view command, or -1 to indicate an error state.