Access indexed sequence and sequence annotation data files via the java HTS library (aka Picard)

Original scope: Read access to a range of sequence data files could be provided via the HTS library. Typically, these would be useful when jalview is used to examine gene model predictions in the context of putative ortholog/homolog sequences, when access to original read data, coding locus or transcript may be needed, and these are stored in flat files rather than available via a standard database connection.

After 2.11 release, which added support for import of annotation via indexed VCF, need to add support for other types of HTS data.