Checked genotypes_atoi again versus original code. I misunderstood
what it was intending. However, I'm not sure that the original
algorithm is useful since it arbitrarily assigns alleles to the SNP.

Initialize missing allele in constructor, not in open method.
Punctuation
Imported the pairwise_concordance_bed and snp_af_sample_cr_bed
programs from the Variation Informatics svn repository.

Some #include fixes for change from gcc 4.3.2 to gcc 4.6.3
Allow CXXTEST_ROOT from the environment to be used, if set