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| ==New stuff==
| | If you encounter bugs etc, open an issue on github, or send en email thorfinn@binf.ku.dk |
| * Do downsampling
| | =Limitation= |
| * make plink tped output
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| * make calibration matrix
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| * make snpfilters
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| * check pest prior in -realSFS documentation
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| ==Bugs==
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| * fix queing of finished threads. MAYBE_FIXED
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| * fix numSites==0 when using regions
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| * check probs with gatk likelihoods in combination with realSFS
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| * check files are closed properly
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| 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.
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| ==Limitation==
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| * RG tags are not implemented, we doubt we will ever support this. | | * 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.
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| ==small changes that would be nice==
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| * check numSites==0 in all generals: derived classes.
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| * check if subdirs exists in outputfiles. Otherwise subtle crash.
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| * Only print the FIXED
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| ###################
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| If you have selected more than one MAF estimator we will choose in following order
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| 1. knownminor bfgs
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| 2. knownminor EM
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| 3. unknownminor bfgs
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| 4. unknownminor EM
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| 5. Posterior maf
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| ###################
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| If use has selected multple mafs estimators.
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| * write about single bam -i on wiki
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| * should rna be implemented
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| * make faster the filter output (ok yoda) FIXED >0.500
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| * make program wait for finished threads when changing chromosomes FIXED >0.500
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| * modify the chromo to the index instead of the chr* FIXED >0.500
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