Fixes to make the QC summary less confusing.

1) Change report of quality format to the one specified in the
sample configuration YAML file.
2) Remove complexity flag for RNA-seq; this was an arbitrary
threshold and was confusing.
3) Rename unique_starts_per_read to Unique Starts Per Read. This
number can be used to flag outliers for RNA-seq experiments.
4) Do not report Estimated Library size from RNA-SeQC. This was
always returning 0 and I haven't been able to figure out why.
Support bgzipped input/output to snpeff effects prediction
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Update with QC summary changes.
Add JVM memory flags to picard.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Support STAR in automated tests and as part of automated genome indexing
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Add picard to qcsummary requirements

Lower memory requirements for picard.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Allow running of gemini externally without needing explicit program version information