statistics app in Tapis

[schristley]

This app will compute a set of basic statistics. It should at least cover all of the statistics provided by the Stats API.

Basic analyses:

• [x] V allele, gene, family usage
• [x] J allele, gene, family usage
• [x] D allele, gene, family usage
• [ ] V-J gene joint distribution
• [ ] Allele frequency
• [ ] Isotype distribution
• [ ] Fraction of productive sequences

Diversity:

• [ ] Diversity at different Renyi/Hill numbers from zero (richness) and up to infinity (Berger- Parker)
• [ ] Rarefaction curves and sampling sufficiency estimates

CDR3 analyses:

• [x] CDR3 length distribution
• [ ] CDR3 nucleotide and amino acid composition
• [ ] Biochemical properties

[schristley]

One thing to consider is if we need separate apps for rearrangement vs clone statistics? The calculations have some overlap but there might be additional stats for clones.

[schristley]

Removed the biochemical properties from statistics app as that generates annotations for each rearrangement, with a corresponding AIRR TSV. We need to think how/what we want to provide for biochemical properties, and they should probably be calculated during initial sequence annotation, i.e. IgBlast.

[schristley]

The statistics app now generates all of the rearrangement statistics for the stats API

[bcorrie]

@schristley I am cleaning up Milestones, can we mark this as closed or move it to another milestone.