Bugs

• fix the maxsize of a chr now its 270e6 FIXED
• fix queing of finished threads. MAYBE_FIXED

Limitation

• RG tags are not implemented, we doubt we will ever support this.
• We have observed problems for rna data. This will be fixed at some point but is not a priority.

small changes that would be nice

• check numSites==0 in all generals: derived classes.

• check if subdirs exists in outputfiles. Otherwise subtle crash.

• Only print the FIXED

If you have selected more than one MAF estimator we will choose in following order
   1. knownminor bfgs
   2. knownminor EM
   3. unknownminor bfgs
   4. unknownminor EM
   5. Posterior maf

If use has selected multple mafs estimators.

• write about single bam -i on wiki
• should rna be implemented
• make faster the filter output