Immunedb

* Clone stats are now properly updated when `--force` flag is passed.
* Indels are now flagged for percentage mismatch in addition to windowed
mutations.
* The `get_stats` API call now allows for stats to be grouped by any attribute
defined in the `Sample` model.
* `sldb_sample_stats` now takes a `--clones-only` flag to only regenerate clone
statistics for samples.
* CDR3 AA and CDR3 length are now properly exported.
* Lineage trees generated by neighbor joining can no longer have a
zero-mutation node as the root.
* The `v_usage` API call now provides a list of groupings for the selected
samples and sorts the returned V-genes.

* All duplicate sequences are now properly assigned an entry in the `Sequences`
table, removing cycles from `DuplicateSequences`.
* Clones can now have a different V gene assigned or gaps added manually via
the `sldb_modify_clone` command.
* Modifications via `sldb_modify_clone` are recorded and can be fetched with
the `modification_log` API call. Other manual modification should make use
of the `ModificationLog` model.
* Neighbor joining now properly calculates copy number.
* `sldb_clone_stats` can now be limited by clone ID.

* Rows summing total/unique sequences cross all samples can be included in
clone exports.
* Neighbor joining now added as a method of lineage tree creation.
* Fixed incorrect unique sequence count in clone comparison.

* V gene usage API tweak to allow for exporting via website.
* Mutation frequency is now calculated for various thresholds.
* HighV-Quest output can now be imported with the `sldb_hvquest` binary.
* Optionally, V-ties can be calculated in addition to the Vs specified
* Sequences with probable indels or misalignments are excluded from clonal
assignment by default. Override this behavior in `sldb_clones` with
`--include-indels`.
* Major data-model changes:
* Consolidated `SequenceMapping` to `Sequence` model to reduce joining.
* `SampleStatistics` changed to match updated `Sequence` model.
* Added `CloneStats` model to reduce API query time.
* Added binary `sldb_clone_stats` to populate `CloneStats` models.
* Renamed `aggregation/stats.py` to `aggregation/sample_stats.py` and
`sldb_stats` binary to `sldb_sample_stats` for new clone statistics scripts.
* Can now export both sequences and clones. Re-architected exporting classes.

* Fixed case where duplicate sequences were incorrectly inserted.

* **First stable release**
* Duplicate sequences are now detected during identification and not
re-identified.
* Metadata fallthrough to "all" block properly during identification.
* pRESTO references removed in favor of "R1+R2"
* Insertion/deletion check based on sliding window.
* V and J ties now calculated on a per-sample basis.
* Major changes and fixes to V/J identification:
* V gene alleles can now be identified and must be separated with an asterisk
(e.g. IGHV4-34*01).
* Anchors are now found using reversed frame-shifting if forward
* frame-shifting yields a no-result.
* V and J genes now match into the CDR3 based on sliding window.
* Germlines can now be specified during identification. Note each germline name
must refer to a unique sequence.