Devon Ryan

Since there has been little need for such a tool in the past ~7 years I'm not aware of a good alternative. Why do you think you need this? Library...

Sounds like you're looking for deepStats: https://github.com/gtrichard/deepStats

Usually this is an installation issue of some dependency. Maybe try a clean install?

For single-end reads the fragment length is the read length.

Yes, this indicates a formatting issue with your BED file.

The .mat.gz file that's used as input into plotHeatmap is just a compressed text file that's (more or less) human readable. I'm pretty sure the name of the feature is...

I can't reproduce this using 0.11.2 on Galaxy (18.05, not that that should matter) with a slurm (17.02.9) cluster. I've tried using both 20 cores and 1 core (in case...

Same here, on the command line it's trying to run the following: bash -c "block_align outdir/229.tmp 'outdir/alignment.maf' ''" It seems likely that this is the source of the error

This is caused by https://github.com/medvedevgroup/SibeliaZ/blob/master/SibeliaZ-LCB/sibeliaz#L129 `$DIR` is set to "", which ends up causing problems due to https://github.com/medvedevgroup/SibeliaZ/blob/master/SibeliaZ-LCB/sibeliaz#L77 , since `$4` is actually now in `$3`. Since spoa is somewhere...

You mean you want all of them for a given region or just to have a list of the stats that could be returned? It's always just been the 6...