Return GMS scores for complex indel variants, take the first base GMS score for the region
revert auto_rec changes
improve rmsk annotations by combining rmsk, simrep, microsat.  thanks to @chapmanb
improve rmsk annotations
Merge branch 'master' of https://github.com/arq5x/gemini
Provide basic versioning of annotation files. Versions specified in install script and checked against stored version information in YAML configuration
Merge pull request #49 from chapmanb/master

Annotation file versioning
[BUG] extra newlines for ad hoc gt* queries
Merge branch 'master' of github.com:arq5x/gemini
formatting
first pass at --gt_filter option
prefer --gt-filter
handle single values in infotag.py
affected status is an integer
[ENH] add autosomal dominant tool
[ENH] upgrade to dbSNP build 137
[ENH] upgrade to ESP 6500 samples (from 5400)
[ENH] added new de_novo mutations tool.
[DOC] Minor tweaks
[ENH] store the depth of aligned sequence for each sample.  The _genotype_'s DP column.