Improved error reporting when finding a duplicate allele.

git-svn-id: https://svn.code.sf.net/p/vcftools/code@904 19d466ce-640d-45be-954f-fad4d9839663
Improved handling of a duplicate alleles.

git-svn-id: https://svn.code.sf.net/p/vcftools/code@905 19d466ce-640d-45be-954f-fad4d9839663
PLINK format converter is no longer specific to human chromosome numbers

git-svn-id: https://svn.code.sf.net/p/vcftools/code@906 19d466ce-640d-45be-954f-fad4d9839663
vcftools no longer throws an error when there are no sites in the file, allowing the user to output just a header

git-svn-id: https://svn.code.sf.net/p/vcftools/code@907 19d466ce-640d-45be-954f-fad4d9839663
Merge remote-tracking branch 'upstream'