v0.8.0

What's Changed

Breaking Changes

• Add mid to FAF and grpmax calcs by @mike-w-wilson in #658
• Update POPS constant to contain a dictionary of both exomes and genomes by @klaricch in #690

Bug fixes

• Account for missingness in int64 to int32 VCF type conversion by @mike-w-wilson in #668
• Fix generic_field_check in validity_checks.py print of failed checks by @jkgoodrich in #693

New Features

• Add RSEM summary function by @jkgoodrich in #647
• Function to get expression proportion by @KoalaQin in #649
• Add GTEx import resources by @KoalaQin in #646
• Add function agg_by_strata, which is a generalized version of the compute_freq_by_strata by @jkgoodrich in #659
• Clean up compute_coverage_stats, change it to use agg_by_strata and have an optional group_membership_ht parameter by @jkgoodrich in #660
• Add densify_all_reference_sites to perform a densify at all sites in a reference HT by @jkgoodrich in #661
• Add compute_stats_per_ref_site to generalize computation of aggregate stats at all sites in a reference Table by @jkgoodrich in #662
• Functions to process, filter, annotate and aggregate variants by transcript expression (get the pext scores per variant) by @KoalaQin in #651
• Add gnomAD all sites allele number resource by @jkgoodrich in #669
• Add read_args parameter to the read functions of Resource Classes by @jkgoodrich in #672
• Add get_is_haploid_expr, get_dp_gq_adj_expr, get_adj_het_ab_expr, and some helpful parameters to agg_by_strata and compute_stats_per_ref_site by @jkgoodrich in #673
• Add sex_karyotype_field as an argument to compute_stats_per_ref_site to include sex ploidy adjustment after densify by @jkgoodrich in #677
• Add function for adding gencode annotation by @klaricch in #681
• Update vcf.py to work on joint freq release Table by @KoalaQin in #688
• Change get_downsampling_freq_indices and downsampling_counts_expr to support both 'pop' and 'gen_anc' keys in metadata by @jkgoodrich in #633

Other Changes

• Suggestions to get_expression_proportion PR by @jkgoodrich in #653
• Suggestions to tx_annotate_mt PR by @jkgoodrich in #654
• Suggestions to tx_annotate_mt by @jkgoodrich in #655
• Rearrange and enforce adj_group and group_membership being on the sam… by @mike-w-wilson in #666
• Bump jinja2 from 3.1.2 to 3.1.3 in /docs by @dependabot in #665
• Add v4 to genome release constants by @klaricch in #671
• Pull ploidy optimization into a function by @mike-w-wilson in #676
• Fix sex ploidy adjustment so XX samples still get set to missing on chrY by @jkgoodrich in #678
• Minor GKS formatting changes and addition of gnomAD flags to annotation by @theferrit32 in #617
• Add option to exclude polyphen from process consequences by @KoalaQin in #685
• Bump black from 23.7.0 to 24.3.0 by @dependabot in #686
• Add Stat Union to the info dict by @KoalaQin in #695

Full Changelog: v0.7.1...v0.8.0