Merge in changes from ZeldaAnalysis

Changes in various files:
* CountAllReads:
   - Allow command line options for alternate directory
* PlotUtils:
   - svg_heatmap takes an "index" option for relabelling the rows (I
     think)
   - fixed an alignment bug
* configure:
   - Redo the handling of yeast files to deal with merged slices
   - Specify an optional RunConfig file