Pypgx

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

* Add new method :meth:`api.core.has_sv`.
* Update :meth:`api.core.sort_alleles` method to handle ``'Indeterminate'`` haplotype call when ``by='name'``.
* Update :meth:`api.utils.estimate_phase_beagle` method to handle situations where there are overlapping samples between input VCF and reference panel -- i.e. users are no longer required to change sample names. Before this update, the Beagle program would throw an error if there were overlapping samples (e.g. 1KGP samples). From now on, offending samples will be temporarily renamed before statistical phasing.
* Add new methods :meth:`api.core.load_recommendation_table` and :meth:`api.core.get_recommendation`.

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

* PyPGx now has a citation! Please refer to the publication "`ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation <https://doi.org/10.1371/journal.pone.0272129>`__" by Lee et al., 2022 (Steven is the first author). Fore more details, see the Citation section in README.
* Update phenotype data and star allele nomenclature for SLCO1B1 in accordance with the latest PharmVar version (v5.2.1). Note that SLCO1B1 was first formally added to PharmVar v5.1 on October 14, 2021. For more details, please refer to the publication "`PharmVar GeneFocus: SLCO1B1 <https://doi.org/10.1002/cpt.2705>`__" by Ramsey et al., 2022 (Steven is a co-author of this paper by the way) and the change log in `the PharmVar SLCO1B1 page <https://www.pharmvar.org/gene/SLCO1B1>`__. The PharmVar-developed SLCO1B1 nomenclature has been incorporated by CPIC 2022 guideline on statin-associated musculoskeletal symptoms.
* Remove duplicate DYPD entry from ``phenotype-table.csv`` file (i.e. Poor Metabolizer).
* Fix major bug in :command:`run-chip-pipeline` command where ``--impute`` argument is essentially ignored.
* :issue:`68`: Fix bug in :meth:`api.utils.estimate_phase_beagle` method when there are no overlapping variants between input VCF and reference panel.
* :issue:`68`: Update :meth:`api.utils.estimate_phase_beagle` method to warn when statistical phasing is skipped.
* :issue:`68`: Upgrade Beagle version from v5.2 (beagle.28Jun21.220.jar) to v5.4 (beagle.22Jul22.46e.jar) due to a bug in v5.2.
* :issue:`68`: Update :meth:`api.utils.estimate_phase_beagle` method to filter out variants with improper allele ('I', 'D', 'N', '.'). Note that this issue is specific to chip data.
* :issue:`68`: Update :meth:`api.utils.import_variants` method to handle input VCF with duplicate variants. Basically, it will warn the user about it and and only keep the first record. This issue seems to occur frequently with chip data.

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

* :issue:`63`: Fix bug in :meth:`api.utils.estimate_phase_beagle` method when there is only one variant in input VCF and Beagle throws an error.
* Update :command:`compare-genotypes` command to print the entire discordant calls when ``--verbose`` is used.
* Update :command:`compute-copy-number` command to ensure that the samples in CovFrame[ReadDepth] and SampleTable[Statistics] are in the same order.
* :issue:`64`: Update :meth:`api.utils.import_variants` method to 'diploidize' the input VCF when the target gene is G6PD. This is because some variant callers output haploid genotypes for males for the X chromosome, interfering with downstream analyses.
* Remove unnecessary optional argument ``assembly`` from :meth:`api.core.get_ref_allele`.

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

* Add new optional argument ``--comparison-table`` to :command:`train-cnv-caller` and :command:`test-cnv-caller` commands.
* Update :meth:`sdk.utils.add_cn_samples` and :meth:`sdk.utils.simulate_copy_number` methods to check input files more rigorously.
* Update :meth:`api.utils.test_cnv_caller` and :meth:`api.utils.train_cnv_caller` methods to accept the latest format of SampleTable[CNVCalls] as input.
* Update plotting methods to optionally return a list of :class:`matplotlib.figure.Figure` objects for API users (e.g. Jupyter Notebook): :meth:`api.plot.plot_bam_copy_number`, :meth:`api.plot.plot_bam_read_depth`, :meth:`api.plot.plot_cn_af`, :meth:`api.plot.plot_vcf_allele_fraction`, :meth:`api.plot.plot_vcf_read_depth`.
* :issue:`61`: Fix bug in commands :command:`compute-control-statistics`, :command:`compute-target-depth`, and :command:`prepare-depth-of-coverage` when a BED file is provided by user.
* Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, GSTM1, SLC22A2, SULT1A1, UGT1A4, UGT2B15, UGT2B17.
* Add new CNV call for CYP2A6: ``Unknown1``, ``Hybrid7``, ``Tandem2``.
* Add new CNV calls for CYP2B6: ``Tandem1``, ``PartialDup1``, ``PartialDup2``, ``ParalogWholeDel1``.
* Add new CNV call for CYP2D6: ``WholeDel1+Tandem3``. Also, remove ``PseudogeneDownstreamDel``.
* Add new CNV calls for CYP2E1: ``WholeDel1`` and ``WholeDup1+PartialDup1``.
* Add new CNV call for SLC22A2: ``NoncodingDel1Hom``.
* Add new CNV call for SULT1A1: ``Unknown2``, ``Unknown3``, ``Unknown4``.
* Add new CNV call for UGT1A4: ``NoncodingDel1Hom``.
* Add new CNV call for UGT2B15: ``PartialDup2``.
* Add new CNV call for UGT2B17: ``PartialDel2``. Also, define a new star allele ``*S3`` for ``PartialDel3``.
* :issue:`59`: Update CNV labels.

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

* Add new optional arguments ``--genes`` and ``--exclude`` to :command:`prepare-depth-of-coverage` command.
* Add new command :command:`slice-bam`.
* Add new command :command:`print-data`.
* Fix typo "statistcs" to "statistics" throughout the package.
* Update :meth:`sdk.utils.simulate_copy_number` method to automatically handle duplicate sample names.
* Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, GSTM1, SLC22A2, SULT1A1, UGT1A4, UGT2B15, UGT2B17.
* Add new CNV calls for CYP2A6: ``Deletion2Hom``, ``Hybrid5``, ``Hybrid6``, ``PseudogeneDeletion``.
* Add new CNV call for CYP2D6: ``Tandem2F``.
* Add new CNV call for GSTM1: ``Normal,Deletion2``.
* Add new CNV call for SULT1A1: ``Unknown1``.
* Add new CNV call for UGT2B17: ``Deletion,PartialDeletion3``.

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

* :issue:`49`: Add new gene ABCG2.
* :issue:`50`: Improve algorithm for whole gene duplication detection. This minor update will handle some rare edge cases.
* :issue:`53`: Update CYP2B6\*17 variants to have synonyms. Update :meth:`api.core.get_variant_synonyms` and :meth:`api.utils.predict_alleles` methods to allow mapping of single variant to multiple synonyms.
* :issue:`54`: Add new command :command:`create-input-vcf`.
* Fix minor error in ``gene-table.csv``. Two control genes EGFR and VDR incorrectly had ``TRUE`` for ``Variants`` column. They were changed to ``FALSE``.
* Change the three paralogs in ``gene-table.csv`` (CYP2A7, CYP2B7, and CYP2D7) to have ``FALSE`` for ``SV`` column.
* Add new optional arguments to :command:`create-regions-bed` command: ``--target-genes``, ``--var-genes``, ``--genes``, ``--exclude``.
* Improve CNV caller for CYP2A6, CYP2B6, CYP2D6, CYP2E1, GSTM1, SLC22A2, SULT1A1, UGT1A4, UGT2B15, UGT2B17.
* Add new CNV calls for CYP2A6: ``Hybrid2Hom``, ``Hybrid4``, ``Tandem``.
* Add new CNV calls for CYP2D6: ``Tandem4``, ``PseudogeneDownstreamDel``, ``Unknown2``.
* Add a new CNV call for CYP2E1: ``Multiplication2``.
* Add new CNV calls for GSTM1: ``PartialDuplication`` and ``DeletionHet,Deletion2``.
* Add a new CNV call for SLC22A2: ``PartialDuplication``.
* Add a new CNV call for SULT1A1: ``DeletionHom``.
* Add new CNV calls for UGT2B15: ``Deletion2``, ``Duplication``, ``PartialDuplication``.
* Add a new CNV call for UGT2B17: ``Normal,PartialDeletion3``.