vcf-phased-join: Do not choke on haploid genotypes and PARs. On behalf of Shane.

git-svn-id: https://svn.code.sf.net/p/vcftools/code@911 19d466ce-640d-45be-954f-fad4d9839663
Bug fixes for diff functions

git-svn-id: https://svn.code.sf.net/p/vcftools/code@912 19d466ce-640d-45be-954f-fad4d9839663
Merge remote-tracking branch 'upstream'