Changes to stdin input handling

git-svn-id: https://svn.code.sf.net/p/vcftools/code@931 19d466ce-640d-45be-954f-fad4d9839663
Edits for BCF2.2 compatibility
End of vector byte

git-svn-id: https://svn.code.sf.net/p/vcftools/code@932 19d466ce-640d-45be-954f-fad4d9839663
Merge remote-tracking branch 'upstream'