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
Merge pull request #3 from keithj/devel

Imported programs from Variation Informatics svn repository