fix graph ann, requires uncompressed VCF

Update Java version

Quality_Assessment now generates a combined png image of all FASTQC p…

…lots

Clarify error messages for Adapter_Trimming and Read_Mapping
RTC and Indel_Realigner now support fixing quality scores that are too high
Automatically check for .bai indexing in Haplotype_Caller, RTC, and Indel_Realigner

Clarify ALTERNATE_SAMPLES