Changelog

0.24.0 (2024-03-31)

  • Change G6PD haplotype name from *MALE to MALE, as the gene does not utilize star allele nomenclature.

  • Update G6PD haplotype nomenclature in accordance with the latest CPIC version (2024-01-07).

  • #119: Add G6PD phenotype data in accordance with the latest CPIC version (2024-01-07).

  • Update CYP4F2 haplotype nomenclature in accordance with the latest PharmVar version (2024-01-27).

0.23.0 (2023-12-24)

  • #115: Add new genes COMT and MTHFR (thanks @nbiesot).

  • #117: Fix major bug in api.utils.estimate_phase_beagle() method. The bug was introduced in version 0.22.0 (#113) and carries significant implications, especially if the user’s input VCF contains sample names that overlap with the reference panel or if there are differences in chromosome annotation compared to the reference panel (e.g. ‘chr22’ vs. ‘22’).

0.22.0 (2023-12-11)

  • #100: Add new method sdk.utils.get_bundle_path() to enable customization of the pypgx-bundle directory’s location instead of the user’s home directory.

  • #114: Fix bug in api.core.get_recommendation() method where string 'None' was treated as missing value by pandas.read_csv version 2.0 or higher.

  • #113: Fix bug in api.utils.estimate_phase_beagle() method where Beagle’s expectation-maximization algorithm estimated a parameter value that was outside the permitted range.

0.21.0 (2023-08-25)

  • #96: Fix bug in compute-copy-number command where it threw an error “Different sample sets found” when the sample name consists of only numbers with one or more leading zeros.

  • #97: Fix bug in IFNL3 genotyping where certain variants were not considered because they were located outside of the target region.

  • #99: Refresh the CPIC table for api.core.load_cpic_table() method. The table’s latest update was on February 6, 2022.

  • #63: Fix bug in api.utils.estimate_phase_beagle() method where Beagle throws an error “Window has only one position” even when multiple overlapping variants exist.

0.20.0 (2023-01-12)

  • #73: Fix bug in run-ngs-pipeline command where empty VCF (i.e. no variants were found in the target gene) was causing error when plotting allele fraction. From now on, a warning will be produced telling users to specify --do-not-plot-allele-fraction to suppress this warning.

  • #78: Fix bug in compute-copy-number command where it threw an error “Different sample sets found” when the sample name consists of only numbers.

0.19.0 (2022-09-13)

  • Add new method api.core.has_sv().

  • Update api.core.sort_alleles() method to handle 'Indeterminate' haplotype call when by='name'.

  • Update 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 api.core.load_recommendation_table() and api.core.get_recommendation().

0.18.0 (2022-08-12)

  • PyPGx now has a citation! Please refer to the publication “ClinPharmSeq: A targeted sequencing panel for clinical pharmacogenetics implementation” 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” 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. 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 run-chip-pipeline command where --impute argument is essentially ignored.

  • #68: Fix bug in api.utils.estimate_phase_beagle() method when there are no overlapping variants between input VCF and reference panel.

  • #68: Update api.utils.estimate_phase_beagle() method to warn when statistical phasing is skipped.

  • #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.

  • #68: Update 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.

  • #68: Update 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.

0.17.0 (2022-07-12)

  • #63: Fix bug in api.utils.estimate_phase_beagle() method when there is only one variant in input VCF and Beagle throws an error.

  • Update compare-genotypes command to print the entire discordant calls when --verbose is used.

  • Update compute-copy-number command to ensure that the samples in CovFrame[ReadDepth] and SampleTable[Statistics] are in the same order.

  • #64: Update 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 api.core.get_ref_allele().

0.16.0 (2022-06-08)

  • Add new optional argument --comparison-table to train-cnv-caller and test-cnv-caller commands.

  • Update sdk.utils.add_cn_samples() and sdk.utils.simulate_copy_number() methods to check input files more rigorously.

  • Update api.utils.test_cnv_caller() and 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 matplotlib.figure.Figure objects for API users (e.g. Jupyter Notebook): api.plot.plot_bam_copy_number(), api.plot.plot_bam_read_depth(), api.plot.plot_cn_af(), api.plot.plot_vcf_allele_fraction(), api.plot.plot_vcf_read_depth().

  • #61: Fix bug in commands compute-control-statistics, compute-target-depth, and 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.

  • #59: Update CNV labels.

0.15.0 (2022-05-03)

  • Add new optional arguments --genes and --exclude to prepare-depth-of-coverage command.

  • Add new command slice-bam.

  • Add new command print-data.

  • Fix typo “statistcs” to “statistics” throughout the package.

  • Update 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.

0.14.0 (2022-04-03)

  • #49: Add new gene ABCG2.

  • #50: Improve algorithm for whole gene duplication detection. This minor update will handle some rare edge cases.

  • #53: Update CYP2B6*17 variants to have synonyms. Update api.core.get_variant_synonyms() and api.utils.predict_alleles() methods to allow mapping of single variant to multiple synonyms.

  • #54: Add new 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 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.

0.13.0 (2022-03-01)

  • Add new genotyping platform, LongRead, to import-variants command.

  • Add new 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 api.core.load_cpic_table().

  • Move following errors from api.core submodule to sdk.utils submodule: AlleleNotFoundError, GeneNotFoundError, NotTargetGeneError, PhenotypeNotFoundError, VariantNotFoundError.

  • Combine optional arguments --bam and --fn into single positional argument bams for following commands: compute-control-statistics, compute-target-depth, prepare-depth-of-coverage.

  • Rename output argument to copy-number for compute-copy-number command.

  • Rename output argument to read-depth for compute-read-depth command.

  • Combine optional arguments --gene and --region into single positional argument gene for compute-control-statistics command.

  • Deprecate sdk.utils.parse_input_bams() method.

  • Update api.utils.predict_alleles() method to match 0.31.0 version of fuc package.

  • Fix bug in 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.

0.12.0 (2022-01-29)

  • Update run-ngs-pipeline command to allow users to provide a custom CNV caller.

  • Update 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 plot-bam-copy-number, plot-bam-read-depth, plot-vcf-allele-fraction, and plot-vcf-read-depth.

  • Update sdk.utils.add_cn_samples() method to accept a list of samples in addition to a file.

  • Add new argument --fontsize to plot-bam-read-depth command.

  • Fix minor bug in plot-bam-read-depth command.

  • Moved 1KGP reference haplotype panels and CNV callers to the pypgx-bundle repository (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.

0.11.0 (2022-01-01)

  • Fix minor bug in compute-copy-number command.

  • Update plot-cn-af command to check input files more rigorously.

  • Add new method sdk.utils.add_cn_samples().

  • Update compare-genotypes command to output CNV comparisonw results as well.

  • Update 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 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 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 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.

0.10.1 (2021-12-20)

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

0.10.0 (2021-12-19)

  • #32: Update 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 sdk.utils.Archive.check_type() method to be able to test more than one semantic type at once.

  • Update api.plot.plot_vcf_allele_fraction() method to accept both VcfFrame[Imported] and VcfFrame[Consolidated].

  • #32: Update run-ngs-pipeline command to accept phased VCF as input. In this case, the command will skip statistical haplotype phasing.

  • #34: Update commands run-ngs-pipeline and 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).

  • #36: Update phenotype data for CACNA1S, CFTR, IFNL3, RYR1 (thanks @NTNguyen13).

  • #39: Add new gene F5 (thanks @NTNguyen13).

  • Update import-variants command to be able to subset/exclude specified samples.

  • Update import-read-depth command to be able to subset/exclude specified samples.

  • Rename --samples argument from compute-copy-number command to --samples-without-sv.

  • Rename --samples argument from run-ngs-pipeline command to --samples-without-sv.

  • Update run-ngs-pipeline and run-chip-pipeline commands to be able to subset/exclude specified samples.

  • Remove --fn argument from filter-samples command.

  • Update 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.

0.9.0 (2021-12-05)

  • 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 run-ngs-pipeline and 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 sdk.utils.Archive.check() method to sdk.utils.Archive.check_type().

  • Add new method sdk.utils.Archive.check_metadata().

  • Add new error sdk.utils.IncorrectMetadataError.

  • Update run-ngs-pipeline command to check input files more vigorously.

  • Add new method sdk.utils.compare_metadata().

  • Add new method api.core.get_strand().

  • Add new method api.core.get_exon_starts().

  • Add new method api.core.get_exon_ends().

  • #31: Fix minor bug in commands run-ngs-pipeline and import-read-depth (thanks @NTNguyen13).

  • Fix minor bug in api.core.predict_score() method.

  • Update variant information for following alleles: CYP2D6*27, CYP2D6*32, CYP2D6*131, CYP2D6*141.

0.8.0 (2021-11-20)

  • Update api.core.sort_alleles() method to also sort alleles by name for genes that do not use the star allele nomenclature (e.g. the DPYD gene).

  • Add new method api.core.is_legit_allele().

  • Update api.core.predict_phenotype() method to first check if the two alleles are legit.

  • Add new genes: ABCB1, CYP1A1, CYP1B1, CYP4A11, CYP4A22, CYP4B1, CYP17A1, CYP19A1, G6PD, IFNL3, POR, PTGIS, SLCO1B3, SULT1A1, TBXAS1, UGT1A4, XPC.

0.7.0 (2021-10-23)

  • Fix minor bug in api.core.predict_phenotype() when specified diplotype is not present in diplotype table.

  • Dissolve Database of Pharmacogenomic Structural Variants (DPSV) page and move its SV data to Genes page.

  • Add new method api.core.get_variant_impact().

  • Update api.utils.sort_alleles() method to give priority to alleles that impact protein coding when breaking ties (i.e. alleles have the same functional status and same number of variants).

  • Update CNV caller for SLC22A2 and UGT2B15 genes.

  • Rename --chr-prefix argument in create-regions-bed to --add-chr-prefix.

  • Add --samples argument to run-ngs-pipeline command.

  • Add new command compare-genotypes.

  • Update api.genotype.call_genotypes() method to assume the samples have no SV when CNV calls are not provided even if the target gene is known to have SV.

  • Add new command run-chip-pipeline.

  • Fix minor bug in estimate-phase-beagle command on not properly exiting the program even though there was an error raised by Beagle.

  • Update api.utils.create_consolidated_vcf() method to check synonymous variants as well when performing phase-extension algorithm.

  • Update run-ngs-pipeline command to output a warning when user provides CovFrame[DepthOfCoverage] even though target gene does not have any star alleles defined by SVs.

  • Add new argument --fontsize to plot-bam-copy-number command.

  • Remove --ymin and --ymax arguments from plot-vcf-allele-fraction command.

  • Update --ymin and --ymax arguments of plot-bam-copy-number command to have a default value.

  • Add new command plot-cn-af.

  • Update run-ngs-pipeline command to output a warning when user provides a VCF file even though target gene does not have any star alleles defined by SNVs/indels.

  • Update aesthetics of copy number profile and allele fraction profile.

  • Add new method api.utils.count_alleles().

  • Update variant information for following alleles: CYP2A6*35, UGT1A1*28, UGT1A1*37.

0.6.0 (2021-10-09)

  • #25: Add new extension sphinx-issues to Read the Docs.

  • #26: Add new extension sphinx.ext.linkcode to Read the Docs.

  • Add by argument to api.utils.sort_alleles() method. When by='name' it will sort star alleles by allele number.

  • Update call-genotypes command to output genotypes with number-sorted alleles (e.g. ‘*4/*10’ instead of ‘*10/*4’).

  • Add new semantic type SampleTable[Phenotypes].

  • Add new method api.utils.call_phenotypes().

  • Add new command call-phenotypes.

  • Add --phenotypes argument to combine-results command.

  • Deprecate api.utils.load_control_table() method.

  • Split api.utils submodule into two submodules api.utils and api.core.

  • Update run-ngs-pipeline command to include phenotype calling step.

  • Update plot-bam-copy-number command to run faster when --samples argument is used.

  • Change ‘Unassigned’ genotype to ‘Indeterminate’ genotype.

  • Add new method api.core.get_variant_synonyms().

  • Update api.core.list_variants() method to accept multiple star alleles.

  • Update predict-alleles command to support multiallelic variants.

  • Update api.utils.sort_alleles() method to give priority to non-reference or non-default alleles when breaking ties (i.e. alleles have the same functional status and same number of variants).

  • Update variant information for following alleles: CYP2D6*122, CYP2D6*127, CYP2D6*139.

0.5.0 (2021-10-02)

  • Update create-read-depth-tsv command to automatically detect chr string in input BAM.

  • Add sdk.utils.parse_input_bams method.

  • Add the 1000 Genomes Project reference haplotype panel for GRCh37. When estimating haplotype phase of observed variants, users are no longer needed to download and specify a panel. GRCh38 support will follow in a future release.

  • Rename command create-read-depth-tsv to prepare-depth-of-coverage.

  • Add bed argument to prepare-depth-of-coverage command.

  • Update prepare-depth-of-coverage command to output archive file instead of TSV file.

  • Update import-read-depth command to accept archive file as input instead of TSV file.

  • Add fitted argument to plot-bam-copy-number command.

  • From now on, missing copy number will be imputed with forward filling instead of column median.

  • Update predict-cnv command to support a user-defined CNV caller.

  • Add Database of Pharmacogenomic Structural Variants (DPSV) page.

  • Update predict-alleles command to output variant data even for alleles in AlternativePhase column.

  • Update create-consolidated-vcf command to mark phased variants with ‘Phased’ in INFO column in VCF.

  • Update the allele table.

  • Update api.utils.list_alleles() method to be able to only list alleles carrying specified variant(s) as a part of definition.

  • Add mode argument to api.utils.list_variants() method.

  • Update create-consolidated-vcf command to implement phase-extension algorithm.

  • Remove SO and Type columns from the variant table.

  • Update api.genotype.GSTM1Genotyper class.

  • Add NotTargetGeneError error.

  • Add new method api.utils.is_target_gene.

  • Update run-ngs-pipeline command to check whether input gene is one of the target genes before attempting to run the pipeline.

  • Update variant information for following alleles: CYP1A2*1C, CYP1A2*1F, CYP1A2*1K, CYP1A2*1L, CYP2B6*17, CYP2D6*15, CYP2D6*21, SLCO1B1*S1, SLCO1B1*S2.

0.4.1 (2021-09-21)

  • Initial release.