Fixed SNP density function to not count duplicate sites at the same position

git-svn-id: https://svn.code.sf.net/p/vcftools/code@866 19d466ce-640d-45be-954f-fad4d9839663
Edited the SNP density function to not count sites that have no alternate allele

git-svn-id: https://svn.code.sf.net/p/vcftools/code@867 19d466ce-640d-45be-954f-fad4d9839663
Merge remote-tracking branch 'upstream'