Avoid fastq quality format checks for streaming remote inputs. Be more agressive with memory usage during alignment to make use of available resources
Keep genotype information with vcfallelicprimitives since output with mult-allele MNPs does not have same issues as INFO fields. Bug fixes for previous updates for checking input variation files
Download S3 files prior to alignment to avoid errors when streaming large files directly into bwa
Allow batching of pre-called variants with analyzed samples for validation. Uses identical callability regions across comparison to make pre-called and called directly comparable
Provide automated download of GEMINI on AWS instances when used for processing. Thanks to Yuri for report
Upgrade ipython-cluster-helper version to 0.3.7.

This has a fix in it to work on SLURM setups where there is
an account, but the user is not assigned to it and SLURM is
set up to not need an account passed to it.
Update ipython-cluster-helper to 0.3.8 with helpful debug message.