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v0.6.0

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@nawatts nawatts released this 06 Jan 14:58
v0.6.0
1f2d022

Released September 3rd, 2021

All resources have been moved to a requester pays bucket.

Fixed

  • Fix annotation_type_is_numeric and annotation_type_in_vcf_info (#379)

Changed

  • VersionedResource objects are no longer subclasses of BaseResource (#359)
  • gnomAD resources can now be imported from different sources (#373)
  • Replaced ht_to_vcf_mt with adjust_vcf_incompatible_types which maintains all functionality except turning the ht into a mt because it is no longer needed for use of the Hail module export_vcf (#365)
  • Modified SEXES in utils/vcf to be 'XX' and 'XY' instead of 'female' and 'male' (#381)
  • Changed module sanity_checks to validity_checks, modified functions generic_field_check, make_filters_expr_dict (previously make_filters_sanity_check_expr), and make_group_sum_expr_dict (previously sample_sum_check) (#395)

Added

  • Added function region_flag_expr to flag problematic regions (#349)
  • Added function missing_callstats_expr to create a Hail Struct with missing values that is inserted into frequency annotation arrays when data is missing (#349)
  • Added function set_female_y_metrics_to_na_expr to set Y-variant frequency callstats for female-specific metrics to missing (#349)
  • Added function make_faf_index_dict to create a look-up Dictionary for entries contained in the filter allele frequency annotation array (#349)
  • Added function make_freq_index_dict to create a look-up Dictionary for entries contained in the frequency annotation array (#349)
  • Added function remove_fields_from_constant to remove fields from a list and notify which requested fields to remove were missing (#381)
  • Added function create_label_groups to generate a list of label group dictionaries needed to populate the info dictionary for vcf export (#381)
  • Added function build_vcf_export_reference to create a subset reference based on an existing reference genome (#381)
  • Added function rekey_new_reference to re-key a Table or MatrixTable with a new reference genome (#381)
  • Added function parallel_file_exists to check whether a large number of files exist (#394)
  • Added functions summarize_variant_filters, generic_field_check_loop, compare_subset_freqs, sum_group_callstats, summarize_variants, check_raw_and_adj_callstats, check_sex_chr_metrics, compute_missingness, vcf_field_check, and validate_release_t (#395)
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