Implementing an easier-to-use VCF file reader API

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1550 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adding an option to not require indexes on VcfFormatConverter; adding indexes where needed for vcfFormatTest

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1551 8bce386e-0d6e-43e0-b1ca-608082c0432d
Merge remote-tracking branch 'upstream'