v0.5.0

Released April 22nd, 2021

Fixed

• Fix for error in generate_trio_stats_expr that led to an incorrect untransmitted count. (#238)
• Fix for error in compute_quantile_bin that caused incorrect binning when a single score overlapped multiple bins (#238)
• Fixed create_binned_ht because it produced a "Cannot combine expressions from different source objects error" (#238)
• Fixed handling of missing entries (not within a ref block / alt site) when computing coverage_stats in sparse_mt.py [#242]
• Fix for error in compute_stratified_sample_qc where gt_expr caused error (#259)
• Fix for error in default_lift_data caused by missing results field in new_locus (#270)
• Fix to dbSNP b154 resource (resources.grch38.reference_data) import to allow for multiple rsIDs per variant (#345)
• Fix to set_female_metrics_to_na to correctly update chrY metrics to be missing (#347)
• Fixed available versions for gnomAD v2 coverage and liftover resources (#352)
• Removed side effect of accessing gnomAD v2 coverage and liftover exome resources that would edit available versions for other resources (#352)
• Use overwrite argument for importing a BlockMatrixResource (#342)

Changed

• Removed assumption of snv annotation from compute_quantile_bin. (#238)
• Modified compute_binned_truth_sample_concordance to handle additional binning for subsets of variants. (#240)
• Updated liftover functions to be more generic (#246)
• Changed quality histograms to label histograms calculated on raw and not adj data (#247)
• Updated some VCF export constants (#249)
• Changed default DP threshold to 5 for hemi genotype calls in annotate_adj and get_adj_expr (#252)
• Updated coverage resources to version 3.0.1 [#242]
• Update to compute_last_ref_block_end, removing assumption that sparse MatrixTables are keyed only by locus by default (#279)
• Update generic_field_check to have option to show percentage of sites that fail checks. (#284)
• Modified vep_or_lookup_vep to support the use of different VEP versions (#282)
• Modified create_truth_sample_ht to add adj annotation information in the returned Table if present in the supplied MatrixTables (#300)

Added

• Added constants and functions relevant to VCF export (#241)
• Add reference genome to call of has_liftover in get_liftover_genome (#259)
• Added fix for MQ calculation in _get_info_agg_expr, switched RAW_MQ and MQ_DP in calculation (#262)
• Add importable method for filtering clinvar to pathogenic sites (#257)
• Added common variant QC functions get_rf_runs and get_run_data to random_forest.py (#278)
• Add calculation for the strand odds ratio (SOR) to get_site_info_expr and get_as_info_expr (#281)
• Added VEPed context HT to resource files and included support for versioning (#282)
• Added code to generate summary statistics (total number of variants, number of LoF variants, LOFTEE summaries) (#285)
• Added additional counts to summary statistics (added autosome/sex chromosome counts, allele counts, counts for missense and synomymous variants) (#289)
• Added function, default_generate_gene_lof_matrix, to generate gene matrix (#290)
• Added function default_generate_gene_lof_summary to summarize gene matrix results (#292)
• Add resource for v3.1.1 release (#364)

Removed

• Removed rep_on_read; this function is no longer necessary, as MatrixTables/Tables can be repartitioned on read with _n_partitions added by this hail update (#283)
• Removed compute_quantile_bin and added compute_ranked_bin as an alternative that provides more even binning. This is now used by create_binned_ht instead. (#288)
• Removed prefix parameter from to make_combo_header_text, as this was only used to check if samples were from gnomAD (#348)

v0.4.0

Released July 9th, 2020

Note gnomAD resources have been moved to a requester pays bucket.
Dataproc clusters must be configured to allow reading from it.

• Added VEP_CSQ_HEADER to generate vep description necessary for VCF export. (#230)
• Modified variant QC pipeline functions generate_trio_stats and generate_sib_stats to add filter parameter for autosomes and bi-allelic sites (#223)
• score_bin_agg now requires additional annotations ac and ac_qc_samples_unrelated_raw and no longer needs tdt (#223)
• Changed score_bin_agg to use ac_qc_samples_unrelated_raw annotation instead of unrelated_qc_callstats (#223)
• Added singleton de novo counts to variant QC pipeline function score_bin_agg (#223)
• Modified filter_mt_to_trios to no longer filter to autosomes as this should be handled during the variant QC pipeline (#223)
• Updated annotate_sex to add globals to sex_ht (#227)
• Document slack_notifications function (#228)
• Added median_impute_features to variant QC random forest module (224)
• Created training.py in variant QC and added sample_training_examples (224)
• Added variant QC pipeline function train_rf_model (224)
• Use local copy of VEP config instead of reading from bucket (#231)
• Updated gnomAD resources paths for hail tables to requester pays buckets (#233)

v0.3.0

Released April 28th, 2020

• Updated capitalization of ambiguous sex annotation (#208)
• Updated usage of included intervals in imputing sex ploidy, also updated interval parameter names (#209)
• Updated capitalization in relatedness constants (#217)
• Changed interface for Slack notifications (#219)

v0.2.0

Released April 3rd, 2020

Added

• Function to subset a MatrixTable based on a list of samples (#196)
• Function to get file size and MD5 hash (#186)
• Developer documentation (#185)
• Include RAW_MQ and AS_VQSLOD metrics in get_annotations_hists (#181)
• Functions to compute coverage stats from sparse MT (#173)

Changed

• Repo restructured - imports may need to be updated [(#207)] (#207)
• Make some arguments to get_qc_mt optional (#200)
• Fetch VEP configuration from new Hail requestor pays buckets (#197)
• Hail must be installed separately (#194)

Fixed

• Father/mother assignments now correct (were swapped before) infer_families (#203)
• Attribute assignments for VersionedPedigreeResource (#198)
• Field references in get_annotations_hists (#181)
• Use before assignment error in default_compute_info (#195)

v0.1.0

Released March 4th, 2020

Initial release