Output folder

[lskatz]

The MSA folder is not an obvious output folder. Need to:

• Add an output folder in set_manage.pl --create and other places in set_manage.pl
• Add relative symlink paths into this output folder. Output files would be: pairwise, informative.fas, out.fas, out.snpmatrix.tsv, anything else?

[chrisgulvik]

Agreed MSA isn't an obvious outdir.

Maybe a summary_stats file to indicate %reads mapped for each sample (example script attached that I use for lyve-SET), % ref genome length (how to sum bed coords used for masking??), along with other metrics already calculated from 'diagnosis'?

calc_percent_reads_mapped.txt

[lskatz]

There is an output folder now. I am open to discussion on what should be in it now. Right now the to do list for output files is:

• stats file
• diagnostics file
• Make the output folder at the time of set_manage.pl --create
• Check for proj/out in set_manage.pl and whatever other else needs to be done for subfolders
• Add output folder option in launch_set.pl just like --msadir, --logdir, --readsdir, etc

[lskatz]

set_manage.pl and launch_set.pl seem to recognize the output folder correctly now