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@github-actions github-actions released this 31 Oct 16:27
· 536 commits to main since this release
v0.7.0
abf42b1

This release contained a function that required Hail >= 0.2.126. Please use a newer release

What's Changed

Breaking Changes

  • Update some gnomAD resources from lists to version dictionaries by @mike-w-wilson in #522
  • Modifications to annotate_freq to improve memory use by @jkgoodrich in #577

Bug fixes

  • Add get_slope_int_relationship_expr to get relationship between a pair of samples given slope and intercepts of lines to use as cutoffs. by @jkgoodrich in #511
  • Fix access to version's SUBSETS and POPS within repo by @mike-w-wilson in #529
  • Small changes to bokeh module imports in utils.plotting that were failing with Hail update by @jkgoodrich in #540
  • Fix filter_x_nonpar and filter_y_nonpar to use reference genome by @jkgoodrich in #553
  • Fix callstats order in merge_freq_arrays by @jkgoodrich in #574
  • Avoid DeprecationWarnings from superseded hail function and import [minor] by @jmarshall in #576
  • Fix merge_freq_arrays for cases with more than two arrays by @jkgoodrich in #587
  • Fix negative values issue with 'diff' by @KoalaQin in #590
  • Fix ValueError for count_arrays in merge_freq_arrays function by @KoalaQin in #591
  • Modify apply_rf_model to use vector_to_array from pyspark.ml.functions instead of udf by @matren395 in #592
  • Fix to drop 'AS_SB' after converting to 'AS_SB_TABLE' in get_as_info_expr by @jkgoodrich in #602
  • Fix to GKS Seqloc new_temp_file by @matren395 in #612
  • Move ga4gh imports to their functions by @mike-w-wilson in #626

New Features

  • Add generic constraint function annotate_constraint_groupings() by @averywpx in #497
  • Add an option for samples that must be kept to compute_related_samples_to_drop by @jkgoodrich in #506
  • Add determine_nearest_neighbors to find nearest neighbors for each sample. Modify compute_stratified_metrics_filter to work with a comparison_sample_expr that specifies what samples to compare to for filtering, this works well with the output of determine_nearest_neighbor. by @jkgoodrich in #509
  • Add utility function to repartition HTs prior to join by @ch-kr in #512
  • Add VEP 105 init script and its docker image by @KoalaQin in #516
  • Add VEP 105 GRCh38 context HT resource by @jkgoodrich in #524
  • Add additional groupings to optional stratified allele frequencies by @KoalaQin in #523
  • Add 'strata' and 'qc_metrics' as globals on the table returned by compute_stratified_metrics_filter by @jkgoodrich in #521
  • Modify annotate_mutation_type to take optional context length as a parameter. by @jkgoodrich in #530
  • Add generic constraint functions: oe_aggregation_expr(), compute_pli(), oe_confidence_interval(), calculate_raw_z_score(), calculate_raw_z_score_sd() by @averywpx in #505
  • Add dbSNP b156 to resources for v4 by @KoalaQin in #525
  • Add pab_max_expr function and modify default_compute_info to add 'AS_pab_max' annotation by @jkgoodrich in #531
  • Add generic constraint functions: get_downsamplings(), remove_coverage_outliers(), and filter_for_mu() by @averywpx in #507
  • Add ac_filter_groups to default_compute_info allowing additional allele count groupings by @jkgoodrich in #534
  • Add global annotations for 'vep_version', 'vep_help', and 'vep_config ' to the returned Table in vep_or_lookup_vep by @jkgoodrich in #536
  • Add annotate_allele_info function to utils.annotations by @jkgoodrich in #535
  • Add validity check code of VEP annotations in protein-coding genes by @KoalaQin in #548
  • Merge freq array function and new frequency dictionary builder by @mike-w-wilson in #551
  • Add GRCh38 methylation sites resource by @jkgoodrich in #552
  • Modify comparison_sample_expr parameter of compute_stratified_metrics_filter to also accept a BooleanExpression by @jkgoodrich in #557
  • Add parameters apply_model_func and convert_model_func to assign_population_pcs so it has the ability to work with other models types by @jkgoodrich in #558
  • Add sample_list_stratification option to create_fake_pedigree function by @jkgoodrich in #564
  • Modify default_compute_info with the option to use the AS_ annotations in gvcf_info for allele specific aggregations by @jkgoodrich in #560
  • Modify annotate_adj to support LGT and LAD by @jkgoodrich in #567
  • Function to annotate downsamplings onto HT/MT by @mike-w-wilson in #570
  • Add function to merge histograms with the same bin_edges by @mike-w-wilson in #572
  • Add option to also merge an array of counts/ints in the freq array merge by @mike-w-wilson in #565
  • Update annotate_freq and qual_hists, add split_vds and compute_freq_by_strata by @mike-w-wilson in #571
  • Add function update_structured_annotations to update structured annotations on a Table by @KoalaQin in #580
  • Make naive_coalesce optional in default_compute_info by @jkgoodrich in #584
  • Add function to remove items from freq and freq_meta by @KoalaQin in #582
  • Add a select_fields option to compute_freq_by_strata by @jkgoodrich in #595
  • Modify split_info_annotation to allow for splitting an info expression that doesn't include AS_SB_TABLE by @jkgoodrich in #594
  • Update to allow for grouping and filtering by MANE transcripts by @klaricch in #605
  • Add gnomad_gks() and get_gks() for extracting gks information for a specified variant by @matren395 in #596
  • Add aggregations to variant QC evaluation for additional plots by @jkgoodrich in #609
  • Add function to get max FAF from faf_expr by @KoalaQin in #608
  • Add optional stratification parameter to coverage by @jkgoodrich in #615
  • Add methylation resource for chrX by @klaricch in #622
  • Add pop_label option to pop_max_expr, faf_expr, and gen_anc_faf_max_expr by @jkgoodrich in #623
  • Add apply_keep_to_only_items_in_filter option to filter_arrays_by_meta by @jkgoodrich in #624
  • Add pprint globals and a global/row length comparison, updates monoallelic expr in validity checks by @mike-w-wilson in #630
  • Add MANE Select filtering option to get_summary_counts by @jkgoodrich in #634
  • Add optional parameters to set_female_y_metrics_to_na_expr to use other frequency fields by @jkgoodrich in #635
  • Update resource paths by @klaricch in #642

Other Changes

New Contributors

Full Changelog: v0.6.4...v0.7.0

Contributors

jmarshall, mattsolo1, and 8 other contributors
Assets 2
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