Latest revision as of 16:05, 26 February 2015

If you encounter bugs etc, open an issue on github, or send en email thorfinn@binf.ku.dk

Limitation

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-=Contact=
+If you encounter bugs etc, open an issue on github, or send en email thorfinn@binf.ku.dk
-Please don't hesitate to write if you have bugs.
+=Limitation=
-=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
-* 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
-* Problems opening indexfile: smallNA06985.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam.bai