legal: adds a reference to the disclaimer

fix(instrument): properly init flowcell entries

reset: start over fresh 🧹

reset: start over fresh 🧹

reset: start over fresh 🧹

tests(derive/instrument): assert that read groups succeed

feat(derive): report by read group where appropriate and feasible

feat: use NonZeroUsize for Number of Records

fix(derive/endedness): complete rename from last commit

Apply suggestions from code review

stlye: Michael M. feedback

tests(derive/junction-annotation): rewrite tests more modular

chore: delete dead code

docs: filling in TODOs

style(derive/instrument): a bit of code clean up

feat: more info in JSON report. Not complete yet. Open TODOs

feat(derive/instrument): in output, report found unique names

feat(derive/instrument): more debug statements

tests: fix broken gene test

docs: fix intra links

style: prettify imports

tests(derive): all derive commands have tests

fix: lots of code cleanup

style(derive/junction-annotation): group reported junctions by contig

[WIP]: switch min_mapq to a proper MappingQuality

fix(strandedness): break when successful

refactor(derive/strandedness): separate out results from compute

refactor: make read_groups util nicer

style: much prettier code. One broken test.

feat: derive strandedness (prototype)