Remove problem calls in output LUMPY VCF with empty alleles. Fixes #678
Update move instead of copy to work around issue on some filesystems. Fixes #677
Alternative fix for problem LUMPY calls with no reference allele -- convert to Ns instead of dropping. #678
Move disambiguation split work inside parallel framework so download and preparation occurs on worker nodes or inside Docker containers. Enables on demand download of disambiguation genomes.
Allow use of pre-aligned input files into lumpy, assuming correct bwa-mem alignment. Fixes #682
Do not keep INFO and FORMAT fields when splitting complex alleles, reverting previous change introduced in v0.8.3. vcfallelicprimitives produces invalid VCF fields not resolved by vcffixup and will take more to include in the future. Fixes #679. Fixes #675
Fix for not uploading the combined files at the end of a RNA-seq run.
Add eXpress support.

http://bio.math.berkeley.edu/eXpress/overview.html
Support pre-created variation files as S3 inputs for validation, with automatic import and tabix preparation
Avoid requiring gof3r for template based upload back to S3. Thanks to @mjafin
Enable streaming of files from buckets without access permissions. Fix for getting HiSeq X Ten data