Reads the BIM file.

def _read_bim(self):
        """Reads the BIM file."""
        # Reading the BIM file and setting the values
        bim = pd.read_csv(self.bim_filename, delim_whitespace=True,
                          names=["chrom", "snp", "cm", "pos", "a1", "a2"],
                          dtype=dict(snp=str, a1=str, a2=str))

        # Saving the index as integer
        bim["i"] = bim.index

        # Checking for duplicated markers
        try:
            bim = bim.set_index("snp", verify_integrity=True)
            self._has_duplicated = False

        except ValueError as e:
            # Setting this flag to true
            self._has_duplicated = True

            # Finding the duplicated markers
            duplicated = bim.snp.duplicated(keep=False)
            duplicated_markers = bim.loc[duplicated, "snp"]
            duplicated_marker_counts = duplicated_markers.value_counts()

            # The dictionary that will contain information about the duplicated
            # markers
            self._dup_markers = {
                m: [] for m in duplicated_marker_counts.index
            }

            # Logging a warning
            logger.warning("Duplicated markers found")
            for marker, count in duplicated_marker_counts.iteritems():
                logger.warning("  - {}: {:,d} times".format(marker, count))
            logger.warning("Appending ':dupX' to the duplicated markers "
                           "according to their location in the BIM file")

            # Renaming the markers
            counter = Counter()
            for i, marker in duplicated_markers.iteritems():
                counter[marker] += 1
                new_name = "{}:dup{}".format(marker, counter[marker])
                bim.loc[i, "snp"] = new_name

                # Updating the dictionary containing the duplicated markers
                self._dup_markers[marker].append(new_name)

            # Resetting the index
            bim = bim.set_index("snp", verify_integrity=True)

        # Encoding the allele
        #   - The original 0 is the actual 2 (a1/a1)
        #   - The original 2 is the actual 1 (a1/a2)
        #   - The original 3 is the actual 0 (a2/a2)
        #   - The original 1 is the actual -1 (no call)
        allele_encoding = np.array(
            [bim.a2 * 2, bim.a1 + bim.a2, bim.a1 * 2,
             list(repeat("00", bim.shape[0]))],
            dtype="U2",
        )
        self._allele_encoding = allele_encoding.T

        # Saving the data in the object
        self._bim = bim[["chrom", "pos", "cm", "a1", "a2", "i"]]
        self._nb_markers = self._bim.shape[0]