Immunedb

* Quality strings are now properly oriented for reverse-complement sequences.
* Trees will no longer have zero-mutation roots.
* Clones can now be created with an specifiable minimum-copy number.
* Sequence exports can now optionally only include sequences assigned to clones.
* Total sequence counts in sample statistics now work with sample-level
collapsing.
* Tree creation will now emit a warning when mutation information is
unavailable.
* Multiprocess workers now emit warning when uncaught errors occur.
* VDJ alignment now uses exceptions to indicate alignment failures.
* String-fields in models are now verified to be of correct length or a
`ValueEror` is thrown.
* CDR3s are now limited to the lesser of 32 amino acids or 96 nucleotides.
* Models now consistently use `cdr3` instead of `junction` for the CDR3 region.
* Identification has been refactored to be cleaner and more efficient.
* Regression testing has been added in the `tests` directory.
* The `CloneGroup` model has been removed.
* Exporting has been refactored.

* J gene germlines are now specified by a FASTA file than hard-coded sequences.
* Clone lineages can now be created only from mutations that occur in a given
number of samples.
* Various performance enhancements to clone statistics.
* Selection pressure is pre-calculated for all mutations as well as those which
occur at least twice.
* Removed clone collapse level since it will never result in further collapsing
past the subject level.
* Delimited importing update to match new models.
* Sequences with various capitalization is now normalized.
* V identification no longer looks for hard-coded anchors.

* Versioning will now follow the [Semantic Versioning
Standard](http://semver.org).
* Major Feature: Sequences must now be collapsed at three different levels: the
sample, subject, and clone. This collapsing is to take into account Ns added
from quality filtering. Sequences that are identical except for Ns are
considered the same and will be collapsed into the highest copy-number
sequence. Equality checking ignoring Ns is written in C for efficiency.
* Feature: Fully aligned sequences with V and J assignments can now be imported
from CSV files.
* Feature: Phred quality scores can now be analyzed from FASTQ files.
* Feature: Rarefaction for samples can now be calculated with the `rarefaction`
API call.
* Feature: V-gene diversity for samples can now be calculate with the
`diversity` API call.
* Feature: Sequences can now be discarded based on number of V-ties and a
minimum identity-to-germline threshold during identification.
* Enhancement: When checking if a sequence has a similar CDR3 for clonal
assignment, only unique CDR3 amino-acid sequences are checked (24).
* Enhancement: Clone overlap in a sample-context can now be exported as a CSV
via the `clone_overlap` API call.
* Bug fix: Workers will no longer prematurely terminate due to blocking on the
task queue.
* Bug fix: Grouping of sample statistics no longer inflates distribution values.
* Bug fix: Copy numbers for duplicate sequences during `sldb_identify` are now
correct.

* [Baseline](http://selection.med.yale.edu/baseline) has now been integrated to
calculate clonal selection pressure during clone statistic calculations.
* Clone comparison now only allows one clone to be selected.
* Modification log messages now added at each pipeline stage.
* Mutations are now precalculated for all sequences and clones.
* Mutations can now be exported for both clones and samples.
* All pipeline stages now use the multiprocessing module to parallelize
processing.

* Mutations can now be filtered by occurrence frequency via the REST API.

* `sldb_sample_stats` now accepts the `--clones-only` flag which, when set, will
cause sample statistics only to be generated for clone filters. Useful for
updates to clonal assignment methods.
* Fixed a bug where exporting sequences did not return the CDR3 NTs, AAs, or
length.
* V-gene names are now lexicographically sorted when requested via the REST API.
* `sldb_clones` now accepts the `--order` flag which will sort sequences by
copy number for clonal assignment.