wait for BOTH vcfs to be done before exiting.

Added additional or statements so that will read next variant in file A or B if other file is marked as 'done'.

Changed exit condition of while loop so will continue if either file is not done.
Removed testing prints to serr

removed counter variable and prints of that variable.
Merge pull request #25 from hardingnj/testAnnotexit

annotate genotypes change, now waits for both vcfs to be 'done'