TODO

Welcome to the mesa wiki!

Documentation

• Add documentation for findOutliers.py

General

• make wrapper script/cmdline so its easier to use
• switch to argparser in main instead of defining in each file

star_junc_to_bed.py

• strand will never equal 0 because it gets converted to a string before it is used

constructMESA.py

• understand min/max_length junctions
• min_samp_threshold 0.1/0.01
• runCMD unncessary
• benchmarking
• testing
• finish filterJunctions correct arm

quantMESA.py

• fix drimOut usuage
• unused classes Junction and Sample
• psutil dependency usage
• runCMD2 clusterQuant
• Why do you need to know what order you seen the junctions in
• Can just use enumerate @ 170
• Add information about the bed file format from SJ
• filter out introns before they are used to avoid nans https://github.com/bsaintjo/mesa/blob/c7ff36dc19d3836a9bc681fcfd855431c1c287c1/quantMESA.py#L119
• redo how nans are created https://github.com/bsaintjo/mesa/blob/c7ff36dc19d3836a9bc681fcfd855431c1c287c1/quantMESA.py#L191 set default thresholds or keep everything and avoid filtering until later clusterMESA.py
• what does SHC do, should it be deleted