Pypgx

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

* Add new genotyping platform, ``LongRead``, to :command:`import-variants` command.
* Add new command :command:`run-long-read-pipeline`.
* Remove ``Code`` column from ``cnv-table.csv`` file. From now on, CNV codes will be generated on the fly.
* Add new method :meth:`api.core.load_cpic_table`.
* Move following errors from ``api.core`` submodule to ``sdk.utils`` submodule: :class:`AlleleNotFoundError`, :class:`GeneNotFoundError`, :class:`NotTargetGeneError`, :class:`PhenotypeNotFoundError`, :class:`VariantNotFoundError`.
* Combine optional arguments ``--bam`` and ``--fn`` into single positional argument ``bams`` for following commands: :command:`compute-control-statistics`, :command:`compute-target-depth`, :command:`prepare-depth-of-coverage`.
* Rename ``output`` argument to ``copy-number`` for :command:`compute-copy-number` command.
* Rename ``output`` argument to ``read-depth`` for :command:`compute-read-depth` command.
* Combine optional arguments ``--gene`` and ``--region`` into single positional argument ``gene`` for :command:`compute-control-statistics` command.
* Deprecate :meth:`sdk.utils.parse_input_bams` method.
* Update :meth:`api.utils.predict_alleles` method to match ``0.31.0`` version of ``fuc`` package.
* Fix bug in :command:`filter-samples` command when ``--exclude`` argument is used for archive files with SampleTable type.
* Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, CYP4F2, GSTM1, SLC22A2, SULT1A1, UGT1A4, UGT2B15, and UGT2B17.
* Add a new CNV call for CYP2D6: ``PseudogeneDeletion``.
* In CYP2E1 CNV nomenclature, ``PartialDuplication`` has been renamed to ``PartialDuplicationHet`` and a new CNV call ``PartialDuplicationHom`` has been added. Furthermore, calling algorithm for CYP2E1\*S1 allele has been updated. When partial duplication is present, from now on the algorithm requires only \*7 to call \*S1 instead of both \*7 and \*4.
* Add a new CNV call for SLC22A2: ``Intron9Deletion,Exon11Deletion``.
* Add a new CNV call for UGT1A4: ``Intron1PartialDup``.
* Add new CNV calls for UGT2B15: ``PartialDeletion3`` and ``Deletion``.
* Add a new CNV call for UGT2B17: ``Deletion,PartialDeletion2``. Additionally, several CNV calls have been renamed: ``Normal`` → ``Normal,Normal``; ``DeletionHet`` → ``Normal,Deletion``; ``DeletionHom`` → ``Deletion,Deletion``; ``PartialDeletionHet`` → ``Deletion,PartialDeletion1``.

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* Update :command:`run-ngs-pipeline` command to allow users to provide a custom CNV caller.
* Update :meth:`api.core.predict_phenotype` method to not raise an error when a given star allele does not exist in the allele table. From now on, the method will output a warning about it but still produce an ``Indeterminate`` call.
* Fix minor bug with ``--samples`` argument in commands :command:`plot-bam-copy-number`, :command:`plot-bam-read-depth`, :command:`plot-vcf-allele-fraction`, and :command:`plot-vcf-read-depth`.
* Update :meth:`sdk.utils.add_cn_samples` method to accept a list of samples in addition to a file.
* Add new argument ``--fontsize`` to :command:`plot-bam-read-depth` command.
* Fix minor bug in :command:`plot-bam-read-depth` command.
* Moved 1KGP reference haplotype panels and CNV callers to the ``pypgx-bundle`` `repository <https://github.com/sbslee/pypgx-bundle>`__ (only those files were moved; other files such as ``allele-table.csv`` and ``variant-table.csv`` are intact). From now on, the user needs to clone the ``pypgx-bundle`` repository with matching PyPGx version to their home directory in order for PyPGx to correctly access the moved files. This is undoubtedly annoying, but absolutely necessary for portability reasons because PyPGx has been growing exponentially in file size due to the increasing number of genes supported and their CNV complexity, to the point where it now exceeds upload size limit for PyPI (100 Mb). After removal of those files, the size of PyPGx has reduced from >100 Mb to <1 Mb.
* Add CNV caller for G6PD (mostly for sex determination since it's located on X chromosome).
* Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, GSTM1, SULT1A1, UGT2B15, and UGT2B17.
* Add new CNV calls for CYP2A6: ``Duplication2``, ``Duplication3``, ``Deletion2Het``, ``Deletion3Het``, ``PseudogeneDuplication``, ``Hybrid2``, ``Hybrid3``. Additionally, some CNV calls have been renamed: ``Hybrid`` → ``Hybrid1``; ``Duplication`` → ``Duplication1``; ``DeletionHet`` → ``Deletion1Het``; ``DeletionHom`` → ``Deletion1Hom``.
* Add a new CNV call for CYP2B6: ``Duplication``.
* Add new CNV calls for CYP2D6: ``Unknown1``, ``Tandem1B``, ``Multiplication``. Additionally, some CNV calls have been renamed: ``Tandem1`` → ``Tandem1A``; ``DeletionHet,Tandem1`` → ``DeletionHet,Tandem1A``; ``Duplication,Tandem1`` → ``Duplication,Tandem1A``.
* Add a new CNV call for CYP2E1: ``Duplication2``. Additionally, a CNV call have been renamed: ``Duplication`` → ``Duplication1``.
* Add new CNV calls for GSTM1: ``UpstreamDeletionHet`` and ``DeletionHet,UpstreamDeletionHet``.
* Add a new CNV call for UGT2B15: ``PartialDeletion2``. Additionally, a CNV call have been renamed: ``PartialDeletion`` → ``PartialDeletion1``.
* Add a new CNV call for UGT2B17: ``PartialDeletionHet``.

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

* Fix minor bug in :command:`compute-copy-number` command.
* Update :command:`plot-cn-af` command to check input files more rigorously.
* Add new method :meth:`sdk.utils.add_cn_samples`.
* Update :command:`compare-genotypes` command to output CNV comparisonw results as well.
* Update :command:`estimate-phase-beagle` command. From now on, the 'chr' prefix in contig names (e.g. 'chr1' vs. '1') will be automatically added or removed as necessary to match the reference VCF’s contig names.
* Add index files for 1KGP reference haplotype panels.
* Add new argument ``--panel`` to :command:`run-chip-pipeline` command.
* Remove 1KGP reference haplotype panels for GSTT1 and UGT2B17 because these genes only have star alleles defined with SV.
* Change 1KGP reference haplotype panels for GRCh38. Previously, PyPGx was using the panels from `Lowy-Gallego et al., 2019 <https://wellcomeopenresearch.org/articles/4-50>`__ where the authors had aligned sequence reads against the full GRCh38 reference, including ALT contigs, decoy, and EBV/IMGT/HLA sequences. This resulted in poor phasing/imputation performance for highly polymorphic PGx genes (e.g. CYP2D6) presumably because the panels were missing haplotype information for lots of SNVs/indels as sequence reads with those variants were mapped to ALT contigs; however, the panels were still the best option at the time (definitely better than lifting over GRCh37 panels). Fortunately, `Byrska-Bishop et al., 2021 <https://www.biorxiv.org/content/10.1101/2021.02.06.430068v2>`__ from New York Genome Center has recently published a new set of GRCh38 panels which apparently has less of this problem despite still having sequence reads aligned in the presence of ALT contigs, etc. When empirically tested, these panels showed a significant increase in phasing/imputation performance. Therefore, from now on, PyPGx will use these panels for GRCh38 data.
* Update GRCh38 variant information for following alleles: CYP2D6\*35, CYP2D6\*45, CYP2D6\*46.
* Update gene region for SLC22A2 to match GRCh37 and GRCh38.
* Add CNV caller for CYP4F2 and SULT1A1.
* Improve CNV caller for CYP2A6, CYP2D6, and SLC22A2.
* Add a new CNV call for CYP2D6: ``Tandem3``.

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* Fix major bug where CNV callers are not packaged properly.

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

* :issue:`32`: Update :command:`import-variants` command to accept phased VCF as input. It will output VcfFrame[Consolidated] if the input VCF is fully phased or otherwise VcfFrame[Imported] as usual.
* Add new property ``sdk.utils.Archive.type`` to quickly access the archive's semantic type.
* Update :meth:`sdk.utils.Archive.check_type` method to be able to test more than one semantic type at once.
* Update :meth:`api.plot.plot_vcf_allele_fraction` method to accept both VcfFrame[Imported] and VcfFrame[Consolidated].
* :issue:`32`: Update :command:`run-ngs-pipeline` command to accept phased VCF as input. In this case, the command will skip statistical haplotype phasing.
* :issue:`34`: Update commands :command:`run-ngs-pipeline` and :command:`run-chip-pipeline` to load large VCF files significantly faster by allowing random access. This also means, from now on, input VCF files must be BGZF compressed (.gz) and indexed (.tbi).
* :issue:`36`: Update phenotype data for CACNA1S, CFTR, IFNL3, RYR1 (thanks `NTNguyen13 <https://github.com/NTNguyen13>`__).
* :pr:`39`: Add new gene F5 (thanks `NTNguyen13 <https://github.com/NTNguyen13>`__).
* Update :command:`import-variants` command to be able to subset/exclude specified samples.
* Update :command:`import-read-depth` command to be able to subset/exclude specified samples.
* Rename ``--samples`` argument from :command:`compute-copy-number` command to ``--samples-without-sv``.
* Rename ``--samples`` argument from :command:`run-ngs-pipeline` command to ``--samples-without-sv``.
* Update :command:`run-ngs-pipeline` and :command:`run-chip-pipeline` commands to be able to subset/exclude specified samples.
* Remove ``--fn`` argument from :command:`filter-samples` command.
* Update :meth:`api.plot.plot_cn_af` method to accept both VcfFrame[Imported] and VcfFrame[Consolidated].
* Improve CNV caller for CYP2D6, GSTM1, and UGT1A4.
* Add a new CNV call for CYP2D6: ``Tandem2C``, ``DeletionHom``.
* Add a new CNV call for UGT1A4: ``Intron1DeletionB``. Additionally, a CNV call have been renamed: ``Intron1Deletion`` → ``Intron1DeletionA``.

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* Add 1KGP reference haplotype panels for GRCh37 for the 17 recently added genes (in ``v0.8.0``).
* Add 1KGP reference haplotype panels for GRCh38 for all target genes.
* Add GRCh37 CNV caller for UGT1A4.
* Add GRCh38 CNV callers for all ten SV genes (CYP2A6, CYP2B6, CYP2D6, CYP2E1, GSTTM1, GSTT1, SLC22A2, UGT1A4, UGT2B15, UGT2B17).
* Update commands :command:`run-ngs-pipeline` and :command:`run-chip-pipeline` to support GRCh38.
* Update the **GeT-RM WGS** tutorial to include a non-SV gene (i.e. CYP3A5) and also GRCh38.
* Make the profiles (e.g. copy number) look prettier.
* Rename :meth:`sdk.utils.Archive.check` method to :meth:`sdk.utils.Archive.check_type`.
* Add new method :meth:`sdk.utils.Archive.check_metadata`.
* Add new error ``sdk.utils.IncorrectMetadataError``.
* Update :command:`run-ngs-pipeline` command to check input files more vigorously.
* Add new method :meth:`sdk.utils.compare_metadata`.
* Add new method :meth:`api.core.get_strand`.
* Add new method :meth:`api.core.get_exon_starts`.
* Add new method :meth:`api.core.get_exon_ends`.
* :pr:`31`: Fix minor bug in commands :command:`run-ngs-pipeline` and :command:`import-read-depth` (thanks `NTNguyen13 <https://github.com/NTNguyen13>`__).
* Fix minor bug in :meth:`api.core.predict_score` method.
* Update variant information for following alleles: CYP2D6\*27, CYP2D6\*32, CYP2D6\*131, CYP2D6\*141.