Bugs

New stuff

• Check auto generation of tai file
• Do downsampling
• make plink toed output. Done
• make calibration matrix
• make snpfilters. Done (partial)
• check pest prior in -realSFS documentation. Done

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. Done
• 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