Added reference to LICENSE file.
REmoved reference to confluence site and added reference to doc site.
Upping version number now before I forget.
Previous commit had incorrect message.  Updated message:  Fixed unit test.  Created unit test for inconsistent variant in case where SNP is being tagged as ONP due to GATK VCF input.
Added some more messages re: GATK VCF
Added some additional checking for error reporting in the case of GATK VCF variants of equal length but not all bases changed.
Adding testdata file so unit test passes.
Merge pull request #194 from broadinstitute/issue-134-Protein_rendering_fail_on_non_primitive_variants

Issue 134 protein rendering fail on non primitive variants
Upping version
Merge branch 'release-1.2'