Add support for IDX field in header entries. Remove support for GATK having different indexing.

git-svn-id: https://svn.code.sf.net/p/vcftools/code@924 19d466ce-640d-45be-954f-fad4d9839663
Create a branch of the stream version to prepare for stable release



git-svn-id: https://svn.code.sf.net/p/vcftools/code@925 19d466ce-640d-45be-954f-fad4d9839663
Merge remote-tracking branch 'upstream'