Changeo

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+ Active development has moved from Bitbucket to GitHub (https://github.com/immcantation/changeo).
+ Documentation updates.
+ Various updates to internals to avoid deprecation warnings.
+ Updates in requirements: Python 3.7.0, biopython>=1.81 and packaging>=23.2.

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+ Various updates to internals and error messages.

AssignGenes:

+ Added support for ``.fastq`` files. If a ``.fastq`` file is input, then a
corresponding ``.fasta`` file will be created in output directory.
+ Added support for C region alignment calls provide by IgBLAST v1.18+.

MakeDb:

+ Added support for C region alignment calls provide by IgBLAST v1.18+.

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+ Updated dependencies to presto >= v0.7.0.

AssignGenes:

+ Fixed reporting of IgBLAST output counts when specifying ``--format airr``.

BuildTrees:

+ Added support for specifying fixed omega and hotness parameters at the
commandline.

CreateGermlines:

+ Will now use the first allele in the reference database when duplicate
allele names are provided. Only appears to affect mouse BCR light chains
and TCR alleles in the IMGT database when the same allele name differs by
strain.

MakeDb:

+ Added support for changes in how IMGT/HighV-QUEST v1.8.4 handles special
characters in sequence identifiers.
+ Fixed the ``imgt`` subcommand incorrectly allowing execution without
specifying the IMGT/HighV-QUEST output file at the commandline.

ParseDb:

+ Added reporting of output file sizes to the console log of the ``split``
subcommand.

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+ Fixed gene parsing for IMGT temporary designation nomenclature.
+ Updated dependencies to biopython >= v1.77, airr >= v1.3.1, PyYAML>=5.1.

MakeDb:

+ Added the ``--imgt-id-len`` argument to accommodate changes introduced in how
IMGT/HighV-QUEST truncates sequence identifiers as of v1.8.3 (May 7, 2021).
The header lines in the fasta files are now truncated to 49 characters. In
IMGT/HighV-QUEST versions older than v1.8.3, they were truncated to 50 characters.
``--imgt-id-len`` default value is 49. Users should specify ``--imgt-id-len 50``
to analyze IMGT results generated with IMGT/HighV-QUEST versions older than v1.8.3.
+ Added the ``--infer-junction`` argument to ``MakeDb igblast``, to enable the inference
of the junction sequence when not reported by IgBLAST. Should be used with data from
IgBLAST v1.6.0 or older; before igblast added the IMGT-CDR3 inference.

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AlignRecords:

+ Fixed a bug caused the program to exit when encountering missing sequence
data. It will now fail the row or group with missing data and continue.

MakeDb:

+ Added support for IgBLAST v1.17.0.

ParseDb:

+ Added a relevant error message when an input field is missing from the data.

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+ Updated to support Biopython v1.78.
+ Increased the biopython dependency to v1.71.
+ Increased the presto dependency to 0.6.2.