Changeo

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MakeDb:

+ Fixed bug wherein the imgt subcommand was not properly recognizing an
extracted folder as input to the ``-i`` argument.

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Conversion to a proper Python package which uses pip and setuptools for
installation.

The package now requires Python 3.4. Python 2.7 is not longer supported.

The required dependency versions have been bumped to numpy 1.9, scipy 0.14,
pandas 0.16 and biopython 1.65.

DbCore:

+ Divided DbCore functionality into the separate modules: Defaults, Distance,
IO, Multiprocessing and Receptor.

IgCore:

+ Remove IgCore in favor of dependency on pRESTO >= 0.5.0.

AnalyzeAa:

+ This tool was removed. This functionality has been migrated to the alakazam
R package.

DefineClones:

+ Added ``--sf`` flag to specify sequence field to be used to calculate
distance between sequences.
+ Fixed bug in wherein sequences with missing data in grouping columns
were being assigned into a single group and clustered. Sequences with
missing grouping variables will now be failed.
+ Fixed bug where sequences with "None" junctions were grouped together.

GapRecords:

+ This tool was removed in favor of adding IMGT gapping support to igblast
subcommand of MakeDb.

MakeDb:

+ Updated IgBLAST parser to create an IMGT gapped sequence and infer the
junction region as defined by IMGT.
+ Added the ``--regions`` flag which adds extra columns containing FWR and CDR
regions as defined by IMGT.
+ Added support to imgt subcommand for the new IMGT/HighV-QUEST compression
scheme (.txz files).

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CreateGermlines:

+ Removed default '-r' repository and added informative error messages when
invalid germline repositories are provided.
+ Updated '-r' flag to take list of folders and/or fasta files with germlines.

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MakeDb:

+ Fixed a bug wherein N1 and N2 region indexing was off by one nucleotide
for the igblast subcommand (leading to incorrect SEQUENCE_VDJ values).

ParseDb:

+ Fixed a bug wherein specifying the ``-f`` argument to the index subcommand
would cause an error.

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DefineClones:

+ Fixed a typo in the default normalization setting of the bygroup subcommand,
which was being interpreted as 'none' rather than 'len'.
+ Changed the 'hs5f' model of the bygroup subcommand to be centered -log10 of
the targeting probability.
+ Added the ``--sym`` argument to the bygroup subcommand which determines how
asymmetric distances are handled.

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CreateGermlines:

+ Germline creation now works for IgBLAST output parsed with MakeDb. The
argument ``--sf SEQUENCE_VDJ`` must be provided to generate germlines from
IgBLAST output. The same reference database used for the IgBLAST alignment
must be specified with the ``-r`` flag.
+ Fixed a bug with determination of N1 and N2 region positions.

MakeDb:

+ Combined the ``-z`` and ``-f`` flags of the imgt subcommand into a single flag,
``-i``, which autodetects the input type.
+ Added requirement that IgBLAST input be generated using the
``-outfmt "7 std qseq"`` argument to igblastn.
+ Modified SEQUENCE_VDJ output from IgBLAST parser to include gaps inserted
during alignment.
+ Added correction for IgBLAST alignments where V/D, D/J or V/J segments are
assigned overlapping positions.
+ Corrected N1_LENGTH and N2_LENGTH calculation from IgBLAST output.
+ Added the ``--scores`` flag which adds extra columns containing alignment
scores from IMGT and IgBLAST output.