resolve #59

Set an internal reference sample name to avoid polluting the CNV map table with
the reference sequence names, which can sometimes intersect with actual
sequence names (e.g. 1, 2, 3... can both be sequence names and sample names).
resolve inconsistencies in vcflib from previous commit
output ALT='.' in --report-monomorphic
Setting Release-Version v9.9.11
handle = and X in alignment cigars

The handling at present isn't intelligent, but by treating this in the same way
as 'M' we can properly parse CIGARs which have them.  Better would be to skip
some of the comparison logic during parsing.
Setting Release-Version v9.9.11
Setting Release-Version v9.9.11