fix index and remove rdd arguments
Create a cache for phred -> double values instead of recalculating

Since a phred score is only a byte in size, we can create a small
cache of values instead of recalculating the probabilities on each
requeest.
add pluginDependency section and remove versions in plugin sections
Merge pull request #66 from heuermh/plugin-dependencies

add pluginDependency section and remove versions in plugin sections
Merge pull request #60 from arahuja/readidx

Bugfix for BQSR: Offset into qualityScore list was wrong
Merge pull request #65 from bigdatagenomics/matt-phredcleanup

Create a cache for phred -> double values instead of recalculating