Changeo

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+ The default output in all tools is now the AIRR Rearrangement standard
(``--format airr``). Support for the legacy Change-O data standard is still
provided through the ``--format changeo`` argument to the tools.
+ License changed to AGPL-3.

AssignGenes:

+ Added the ``igblast-aa`` subcommand to run igblastp on amino acid input.

BuildTrees:

+ Adjusted ``RECORDS`` to indicate all sequences in input file.
``INITIAL_FILTER`` now shows sequence count after initial
``min_seq`` filtering.
+ Added option to skip codon masking: ``--nmask``.
+ Mask ``:``, ``,``, ``)``, and ``(`` in IDs and metadata with ``-``.
+ Can obtain germline from ``GERMLINE_IMGT`` if ``GERMLINE_IMGT_D_MASK``
not specified.
+ Can reconstruct intermediate sequences with IgPhyML using ``--asr``.

ConvertDb:

+ Fixed a bug in the ``airr`` subcommand that caused the ``junction_length``
field to be deleted from the output.
+ Fixed a bug in the ``genbank`` subcommand that caused the junction CDS
to be missing from the ASN output.

CreateGermlines:

+ Added the ``--cf`` argument to allow specification of the clone field.

MakeDb:

+ Added the ``igblast-aa`` subcommand to parse the output of igblastp.
+ Changed the log entry ``FUNCTIONAL`` to ``PRODUCTIVE`` and removed the
``IMGT_PASS`` log entry in favor of an informative ``ERROR`` entry
when sequences fail the junction region validation.
+ Add --regions argument to the ``igblast`` and ``igblast-aa`` subcommands
to allow specification of the IMGT CDR/FWR region boundaries. Currently,
the supported specifications are ``default`` (human, mouse) and
``rhesus-igl``.

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BuildTrees:

+ Added capability of running IgPhyML on outputted data (``--igphyml``) and
support for passing IgPhyML arguments through BuildTrees.
+ Added the ``--clean`` argument to force deletion of all intermediate files
after IgPhyML execution.
+ Added the ``--format`` argument to allow specification input and output of
either the Change-O standard (``changeo``) or AIRR Rearrangement standard
(``airr``).

CreateGermlines:

+ Fixed a bug causing incorrect reporting of the germline format in the
console log.

ConvertDb:

+ Removed requirement for the ``NP1_LENGTH`` and ``NP2_LENGTH`` fields from
the genbank subcommand.

DefineClones:

+ Fixed a biopython warning arising when applying ``--model aa`` to junction
sequences that are not a multiple of three. The junction will now be
padded with an appropriate number of Ns (usually resulting in a translation
to X).

MakeDb:

+ Added the ``--10x`` argument to all subcommands to support merging of
Cell Ranger annotation data, such as UMI count and C-region assignment,
with the output of the supported alignment tools.
+ Added inference of the receptor locus from the alignment data to all
subcommands, which is output in the ``LOCUS`` field.
+ Combined the extended field arguments of all subcommands (``--scores``,
``--regions``, ``--cdr3``, and ``--junction``) into a single ``--extended``
argument.
+ Removed parsing of old IgBLAST v1.5 CDR3 fields
(``CDR3_IGBLAST``, ``CDR3_IGBLAST_AA``).

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+ Slightly changed version number display in commandline help.

BuildTrees:

+ Fixed a bug that caused malformed lineages.tsv output file.

CreateGermlines:

+ Fixed a bug in the CreateGermlines log output causing incorrect missing
D gene or J gene error messages.

DefineClones:

+ Fixed a bug that caused a missing junction column to cluster sequences
together.

MakeDb:

+ Fixed a bug that caused failed germline reconstructions to be recorded as
``None``, rather than an empty string, in the ``GERMLINE_IMGT`` column.

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+ Fixed a bug causing the values of ``_start`` fields to be off by one from
the v1.2 AIRR Schema requirement when specifying ``--format airr``.

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+ Updated airr library requirement to v1.2.1 to fix empty V(D)J start
coordinate values when specifying ``--format airr`` to tools.
+ Changed pRESTO dependency to v0.5.10.

BuildTrees:

+ New tool.
+ Converts tab-delimited database files into input for
`IgPhyML <https://bitbucket.org/kbhoehn/igphyml>`_

CreateGermlines:

+ Now verifies that all files/folder passed to the ``-r`` argument exist.

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+ Updated support for the AIRR Rearrangement schema to v1.2 and added the
associated airr library dependency.

AssignGenes:

+ New tool.
+ Provides a simple IgBLAST wrapper as the ``igblast`` subcommand.

ConvertDb:

+ The ``genbank`` subcommand will perform a check for some of the required
columns in the input file and exit if they are not found.
+ Changed the behavior of the ``-y`` argument in the ``genbank`` subcommand.
This argument is now featured to sample features only, but allows
for the inclusion of any BioSample attribute.

CreateGermlines:

+ Will now perform a naive verification that the reference sequences provided
to the ``-r`` argument are IMGT-gapped. A warning will be issued to standard
error if the reference sequence fail the check.
+ Will perform a check for some of the required columns in the input file and
exit if they are not found.

MakeDb:

+ Changed the output of ``SEQUENCE_VDJ`` from the igblast subcommand to retain
insertions in the query sequence rather than delete them as is done in the
``SEQUENCE_IMGT`` field.
+ Will now perform a naive verification that the reference sequences provided
to the ``-r`` argument are IMGT-gapped. A warning will be issued to standard
error if the reference sequence fail the check.