Basic marker details loading.

            (chr, rsid, gen. dist, pos, allelel 1, allele2)

        :param map3: When true, ignore the genetic distance column
        :return: None

def load_bim(self, map3=False):
        """Basic marker details loading.

            (chr, rsid, gen. dist, pos, allelel 1, allele2)

        :param map3: When true, ignore the genetic distance column
        :return: None
        """
        cols = [0, 1, 3, 4, 5]
        if map3:
            cols = [0, 1, 2, 3, 4]
        logging.info("Loading file: %s" % self.bim_file)
        val = sys_call('wc -l %s' % (self.bim_file))[0][0].split()[0]
        marker_count = int(val)
        self.markers = numpy.zeros((marker_count, 2), dtype=int)
        self.rsids = []
        self.alleles = []

        with open(self.bim_file) as file:
            index = 0
            for line in file:
                if map3:
                    chr, rsid, pos, al1, al2 = line.strip().split()
                else:
                    chr, rsid, gd, pos, al1, al2 = line.strip().split()
                self.markers[index, 0] = int(chr)
                self.markers[index, 1] = int(pos)
                self.alleles.append([al1, al2])
                self.rsids.append(rsid)
                index += 1
        self.locus_count = self.markers.shape[0]