Merge pull request #2 from iainrb/devel

Improvements to Makefile and README.txt
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
Fixed buffer overrun (fencepost error) where vector indices were being
pre- rather than post-incremented.
Merge pull request #4 from keithj/devel

Fixed buffer overrun (fencepost error)
Merge pull request #1 from wtsi-npg/devel

Changes from wtsi-npg:devel in 2013-14