Immunedb

* Minor fix for sequences with indels in `immunedb_modify ... combine-samples`

* Collapsing sequences imported from AIRR format now uses substantially less
memory.

* CDR3 indels are now supported for AIRR formatted input.
* Clonal assignment has been greatly enhanced by allowing sequences with
different V-gene and J-gene calls but similar CDR3 nucleotide sequences to be
combined. This is helpful in highly mutated populations where gene
assignments may be incorrect for some sequences.
* Clones with less than or equal to 4 (default) nucleotide differences are
automatically combined. You can tweak this behavior in `immunedb_clones`
with the `--reduce-difference` flag.

* `immunedb_import` for IgBLAST results in AIRR format has been greatly
improved both in performance and accuracy.
* Short-read edge case for J-alignment now assigns proper gene.
* `immunedb_identify` now requires the `--ties` flag to be specified to enable
V-tie calculations. By default simply the highest-identity gene is assigned.
* `immunedb_clone_trees` defaults to only include the V-gene in lineage
construction. To use full sequences, specify the `--full-seq` flag.
* `immunedb_clones` now implements hierarchical clustering with the `cluster`
method.
* The `lineage` method for `immunedb_clones` has been removed.
* `immunedb_clones` now defaults to resetting existing clones. To avoid this
behavior specify the `--skip-regen` flag.
* `immunedb_clones` now automatically combines clones with the same V, J, and
CDR3 AA sequence. To avoid this behavior specify the `--skip-reduce` flag.
* `immunedb_clones` now defaults to assigning sub-clones.

* Importing is now supported for only IgBLAST in AIRR format.
* Database configuration can now be specified with environment variables.
`IMMUNEDB_DB`, `IMMUNEDB_PASS`, `IMMUNEDB_USER` are required to be set and
`IMMUNEDB_HOST` is optional (defaults to `localhost`). When using
environment variables, the common first parameter to all commands,
`db_config` should be excluded.
* Sample export now includes average clonal V-identity and CDR3 length as
columns.

* J-assignment fix for reverse-complement sequences.