Changeo

-------------------------------------------------------------------------------

MakeDb:

+ Fixed an incompatibility with IgBLAST v1.7.0.

CreateGermlines:

+ Fixed an error that occurs when using the ``--cloned`` with an input file
containing duplicate values in ``SEQUENCE_ID`` that caused some records to
be discarded.

-------------------------------------------------------------------------------

+ Fixed an overflow error on Windows that caused tools to fatally exit.
+ All tools will now print detailed help if no arguments are provided.

-------------------------------------------------------------------------------

Fixed a bug wherein ``.tsv`` was not being recognized as a valid extension.

MakeDb:

+ Added the ``--cdr3`` argument to the igblast subcommand to extract the
CDR3 nucleotide and amino acid sequence defined by IgBLAST.
+ Updated the IMGT/HighV-QUEST parser to handle recent column name changes.
+ Fixed a bug in the igblast parser wherein some sequence identifiers were
not being processed correctly.

DefineClones:

+ Changed the way ``X`` characters are handled in the amino acid Hamming
distance model to count as a match against any character.

-------------------------------------------------------------------------------

License changed to Creative Commons Attribution-ShareAlike 4.0 International
(CC BY-SA 4.0).

CreateGermlines:

+ Added ``GERMLINE_V_CALL``, ``GERMLINE_D_CALL`` and ``GERMLINE_J_CALL``
columns to the output when the ``-cloned`` argument is specified. These
columns contain the consensus annotations when clonal groups contain
ambiguous gene assignments.
+ Fixed the error message for an invalid repo (``-r``) argument.

DefineClones:

+ Deprecated ``m1n`` and ``hs1f`` distance models, renamed them to
``m1n_compat`` and ``hs1f_compat``, and replaced them with ``hh_s1f`` and
replaced ``mk_rs1nf``, respectively.
+ Renamed the ``hs5f`` distance model to ``hh_s5f``.
+ Added the mouse specific distance model ``mk_rs5nf`` from Cui et al, 2016.

MakeDb:

+ Added compatibility for IgBLAST v1.6.
+ Added the flag ``--partial`` which tells MakeDb to pass incomplete alignment
results specified.
+ Added missing console log entries for the ihmm subcommand.
+ IMGT/HighV-QUEST, IgBLAST and iHMMune-Align parsers have been cleaned up,
better documented and moved into the iterable classes
``changeo.Parsers.IMGTReader``, ``change.Parsers.IgBLASTReader``, and
``change.Parsers.IHMMuneReader``, respectively.
+ Corrected behavior of ``D_FRAME`` annotation from the ``--junction``
argument to the imgt subcommand such that it now reports no value when no
value is reported by IMGT, rather than reporting the reading frame as 0 in
these cases.
+ Fixed parsing of ``IN_FRAME``, ``STOP``, ``D_SEQ_START`` and ``D_SEQ_LENGTH``
fields from iHMMune-Align output.
+ Removed extraneous score fields from each parser.
+ Fixed the error message for an invalid repo (``-r``) argument.

-------------------------------------------------------------------------------

Increased ``csv.field_size_limit`` in changeo.IO, ParseDb and DefineClones
to be able to handle files with larger number of UMIs in one field.

Renamed the fields ``N1_LENGTH`` to ``NP1_LENGTH`` and ``N2_LENGTH``
to ``NP2_LENGTH``.

CreateGermlines:

+ Added differentiation of the N and P regions the the ``REGION`` log field
if the N/P region info is present in the input file (eg, from the
``--junction`` argument to MakeDb-imgt). If the additional N/P region
columns are not present, then both N and P regions will be denoted by N,
as in previous versions.
+ Added the option 'regions' to the ``-g`` argument to create add the
``GERMLINE_REGIONS`` field to the output which represents the germline
positions as V, D, J, N and P characters. This is equivalent to the
``REGION`` log entry.

DefineClones:

+ Improved peformance significantly of the ``--act set`` grouping method in
the bygroup subcommand.

MakeDb:

+ Fixed a bug producing ``D_SEQ_START`` and ``J_SEQ_START`` relative to
``SEQUENCE_VDJ`` when they should be relative to ``SEQUENCE_INPUT``.
+ Added the argument ``--junction`` to the imgt subcommand to parse additional
junction information fields, including N/P region lengths and the D-segment
reading frame. This provides the following additional output fields:
``D_FRAME``, ``N1_LENGTH``, ``N2_LENGTH``, ``P3V_LENGTH``, ``P5D_LENGTH``,
``P3D_LENGTH``, ``P5J_LENGTH``.
+ The fields ``N1_LENGTH`` and ``N2_LENGTH`` have been renamed to accommodate
adding additional output from IMGT under the ``--junction`` flag. The new
names are ``NP1_LENGTH`` and ``NP2_LENGTH``.
+ Fixed a bug that caused the ``IN_FRAME``, ``MUTATED_INVARIANT`` and
``STOP`` field to be be parsed incorrectly from IMGT data.
+ Ouput from iHMMuneAlign can now be parsed via the ``ihmm`` subcommand.
Note, there is insufficient information returned by iHMMuneAlign to
reliably reconstruct germline sequences from the output using
CreateGermlines.


ParseDb:

+ Renamed the clip subcommand to baseline.

-------------------------------------------------------------------------------

Fixed a bug with installation on Windows due to old file paths lingering in
changeo.egg-info/SOURCES.txt.

Updated license from CC BY-NC-SA 3.0 to CC BY-NC-SA 4.0.

CreateGermlines:

+ Fixed a bug producing incorrect values in the ``SEQUENCE`` field on the
log file.

MakeDb:

+ Updated igblast subcommand to correctly parse records with indels. Now
igblast must be run with the argument ``outfmt "7 std qseq sseq btop"``.
+ Changed the names of the FWR and CDR output columns added with
``--regions`` to ``<region>_IMGT``.
+ Added ``V_BTOP`` and ``J_BTOP`` output when the ``--scores`` flag is
specified to the igblast subcommand.