WARNING_REF_DOES_NOT_MATCH_GENOME was not being calculated in some cases: Fixed.

git-svn-id: https://svn.code.sf.net/p/snpeff/code@968 3341ced4-5d85-40e2-8a85-8d6cb0b68e6b
WARNING_REF_DOES_NOT_MATCH_GENOME was not being calculated in some cases: Fixed.
Test case added.

git-svn-id: https://svn.code.sf.net/p/snpeff/code@969 3341ced4-5d85-40e2-8a85-8d6cb0b68e6b


git-svn-id: https://svn.code.sf.net/p/snpeff/code@970 3341ced4-5d85-40e2-8a85-8d6cb0b68e6b
Merge remote-tracking branch 'upstream'