uniquify vcfs on combine [ci skip]
ref guided diversity [ci skip]
more trimming of ends on assembly refinement (up from 20bp to 55bp) -- see bug described here: http://virological.org/t/early-release-16-new-ebov-genomes-from-sierra-leone/72/3
some cleaning/reorg of modify_contig
REAL indel fixing in refine1 and refine2 steps
change the replay_deletions stuff to be optional
oops, in unit test, retrieve first element of iterator in a py27 safe way
separate out each rule set a bit more and make the library->sample merging optional [ci skip]
descriptive comments and errors [ci skip]
rename consensus.py to assembly.py
dont always assume LB is in the RG header
pull seq_run_date from file instead of dir
consensus.py -> assembly.py in snakemake too [ci skip]
Merge pull request #52 from broadinstitute/dp-indels

reorganize, document, tune defaults