v0.6.3

What's Changed

This release uses Hail 0.2.104

Breaking Changes

• Change type of "pc_cols" param in ancestry function from hl.expr.ArrayExpression to List[int] to help track PCs that were used in RF model by @klaricch in #448
• Add additional_samples_to_drop option to run_pca_with_relateds by @klaricch in #489

Bug fixes

• Fix to only add the error_rate annotation if fit is not supplied to assign_population_pcs by @klaricch in #453
• Modify merge_sample_qc_expr to work with the additional VDS sample QC metrics: n_singleton_ti, n_singleton_tv, and r_ti_tv_singleton by @jkgoodrich in #454
• Fix vep_or_lookup_vep to drop vep_proc_id if it exists by @konradjk in #439
• Fix to paths for VEP 101 resources in init script by @jkgoodrich in #488
• Changed tqdm to SimpleRichProgressBar in file_utils by @ch-kr in #495

New Features

• Add an n_pcs option to run_platform_pca by @jkgoodrich in #468
• Add n_partitions option to get_qc_mt before LD pruning by @klaricch in #472
• Add block_size option to get_qc_mt for LD pruning by @klaricch in #473
• Add gaussian_mixture_model_karyotype_assignment function to assign sex karyotype using Gaussian mixture models by @jkgoodrich in #478
• Add variants_filter_lcr, variants_filter_segdup and variants_snv_only options to annotate_sex to filter variants prior to variant only ploidy imputation by @jkgoodrich in #479
• Add an option compute_x_frac_variants_hom_alt to annotate_sex that computes the fraction of variants on chromosome X that are homozygous alternate per sample by @jkgoodrich in #480
• Add generic constraint functions - annotate_mutation_type(), trimer_from_heptamer(), collapse_strand(), add_most_severe_csq_to_tc_within_vep_root() by @averywpx in #474
• Add more file types to file_exists for checking '_SUCCESS' by @jkgoodrich in #486
• Add coverage_mt option to annotate_sex which takes an optional precomputed coverage MT to use for ploidy imputation instead of remaking it. by @jkgoodrich in #484
• Add function get_chr_x_hom_alt_cutoffs, add arguments to infer_sex_karyotype and get_sex_expr to use the new function and it's output. by @jkgoodrich in #492
• Add bi_allelic_only and snv_only options to get_qc_mt by @jkgoodrich in #471
• Add generic constraint functions: annotate_with_mu(), count_variants(), downsampling_counts_expr(), filter_vep_transcript_csqs(), combine_functions(), filter_x_nonpar(), and filter_y_nonpar() by @averywpx in #481

Other Changes

• Handle tags created through GitHub in publish release workflow by @nawatts in #451
• Change branch name in CI workflow configuration by @nawatts in #452

New Contributors

• @averywpx made their first contribution in #474

Full Changelog: v0.6.2...v0.6.3