add schema changes to default create
Merge branch 'pipeline' of github.com:sanger-pathogens/vr-codebase into pipeline
Exit nicely on VCFs with wrong number of fields
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop
Merge pull request #44 from sanger-pathogens/pipeline

Mapping coverage pulled from bamcheck & db update
modified to run with update-vrtrack-schema script
tweaked SQL for new warehouse to make updates faster - using current_aliquots and indexes
SQL changed to use current_aliquots table for improved performance with new warehouse
Initial refactor of assembly pipeline
move pools if only 1, seq pipeline root in config
move seq root to data section for pipeline to use
split reads from combined pools
place lower limit on ram after num threads calculated
move split reads to the assembly class
remove database call from task
allow for abacas and descaffolding to be run
remove unused code
Allow for a single config file for a study
Prevent failing on near-empty counts_by_AF graphs.
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop