TODO
4870f3f5
 *use BSGenome and Bioc dbSNP objects instead of downloading from UCSC.
 
 *globals function needs to set elements in the list returned by
  options() instead of using the globals() fun. Other wise
  HTSeqGenieBase and gmapR will both have exported globals() functions
 
 *HTSeqGenieBase needs to depend on gmapR and not contain now-redundant
  code. To to this, HTSeqGenieBase::globals() needs to have entries
  removed now in gmapR::globals()
 
 *configureGmapR.R calls buildGmapIndex, buildGmapDbSNPIndex, and
 buildRefseqSpliceSites. These are high-level functions that obtain
 hg19 data and call more generalized functions. These high-level
 functions belong in HTSeqGenieBase.