Bugs

New stuff

• Do downsampling
• make plink tped output
• make calibration matrix
• make snpfilters
• check pest prior in -realSFS documentation

Bugs

• fix queing of finished threads. MAYBE_FIXED
• fix numSites==0 when using regions
• check probs with gatk likelihoods in combination with realSFS
• check files are closed properly

The above will not have an effect on the results. For large number of samples, the -nQueueSize can be used. If memory is a problem.

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 (ok yoda) FIXED >0.500
• make program wait for finished threads when changing chromosomes FIXED >0.500
• modify the chromo to the index instead of the chr* FIXED >0.500