v0.8.2

What's Changed

Breaking Changes

• Update default vep version for context table resource by @ch-kr in #726
• Add coverage_metric param to allow for different metrics of coverage and cov_model_type option to allow for linear or logarithmic by @klaricch in #724
• Add get_tissues_to_exclude function to determine what tissues to exclude from transcript annotation calculations by @jkgoodrich in #729

Bug fixes

• Fix tx_filter_variants_by_csqs to correctly handle the ignore_splicing parameter by @jkgoodrich in #727

New Features

• Add retain cdf option for median calculations when computing info fields by @klaricch in #731
• Add max_grpmax option to get_summary_stats_variant_filter_expr for filtering by grpmax by @jkgoodrich in #732
• Change filter_mt_to_trios to also filter on vds by @KoalaQin in #739
• Add get_mu_annotation_expr function that prevents a shuffle from happening when annotating a HT with mutation rate and use in annotate_with_mu by @jkgoodrich in #734
• Add assemble_constraint_context_ht function to create a fully annotated context HT for computing constraint on by @jkgoodrich in #733
• Add support for filtering Hail Tables to filter_to_trios by @jkgoodrich in #741
• Generalize the freq_bin_expr function to take in a list of allele count and allele frequency cutoffs by @jkgoodrich in #745
• Add function parse_variant to create a Struct with the locus and alleles from a variant string or contig, position, ref, and alt. by @jkgoodrich in #746
• Modify filter_vep_transcript_csqs_expr so it can also accept hl.expr.StructExpression by @jkgoodrich in #748
• Filter to Gencode CDS by genes and by exon paddings by @KoalaQin in #747
• Add functions to support padding and filtering intervals: filter_by_intervals, pad_intervals, parse_locus_intervals by @jkgoodrich in #752
• Add loftee_labels and no_lof_flags parameters to filter_vep_transcript_csqs_expr for filtering by loftee labels and flags by @jkgoodrich in #753
• Add browser tables to resources by @KoalaQin in #750
• Add functions to check struct and array missingness by @klaricch in #738

Other Changes

• Add import code for GTEx v10 RSEM by @KoalaQin in #742
• Add pext and constraint resources by @KoalaQin in #743
• Bump the pip group in /docs with 2 updates by @dependabot in #715
• Bump jinja2 from 3.1.4 to 3.1.5 in /docs in the pip group across 1 directory by @dependabot in #751
• Bump virtualenv from 20.24.6 to 20.26.6 in the pip group across 1 directory by @dependabot in #754
• Update version to 0.8.2 in setup.py for release by @KoalaQin in #758
• Add gcs connector to PyPi publish by @KoalaQin in #759

Full Changelog: v0.8.1...v0.8.2