Fixes #91.  Sample with frameshift mutation (1 bp deletion) in RT was causing pipeline to break at csf2counts step.  Modified pileup conversion to consensus sequence so that deletions at a high frequency in the data are retained, but in-frame deletions are stripped.
Fixes #91.  Sample with frameshift mutation (1 bp deletion) in RT
was causing pipeline to break at csf2counts step.  Modified pileup
conversion to consensus sequence so that deletions at a high
frequency in the data are retained, but in-frame deletions are
stripped.

cfe-lab/MiCall,cfe-lab/MiCall,cfe-lab/MiCall