disambiguate isMismatchBase(), other small cleanups
Factor out SnpTable, fix crash in SNP handling
Add tests for reference position and fix refpos position off-by-one-error
Merge pull request #40 from arahuja/referenceend

Fixing reference position from offset implementation
Print a log message on startup to more easily tell runs apart
Improve BQSR performance by reducing GC pressure
Rename 'offset' to 'readOffset' and 'position' to 'referencePosition'
Merge pull request #38 from jey/bqsr

Small bugfixes and cleanups to BQSR