work in progress for version 2.0; fixed test; still todo : merge tests with those from version 1.9.6

version 2.0_beta where PE reads are processed separately and selected or removed from the cms if at least one of the PE has a median coverage below threshold.

Added checking that make distcheck works well.

fixed unit and non regression test; changed non regression test for the -q option; fully commented the handling of undef files