Release Notes

• 2024.12.1

  • Fix support for GRR contents file in YAML format

• 2024.12.0

  • Restore gene scores partitions REST API

  • Clean up WDAE unit tests

  • The cnv_collection does not crash on an unknown chromosome

  • Added get_region_scores to PostionScore interface

  • Change fetch_region method signature for AlleleScore

  • Switch to using JSON format for GRR contents file

  • Reorganization of GeneSetAnnotator to support multiple gene sets

  • Fis support for downloading phenotype tool report image

  • Restore usage of gene scores partitions

• 2024.11.3

  • Fix annoate_columns to create a correct tabix index

  • Fix SimpleEffectAnnotator to produce a link to the GPF documentation

  • Adjust formatting of float numbers in annotate_columns and annotate_vcf tools

  • Fix gene set annotator to include attributes in the annotation schema

  • Fix gene score annotator documentation to include aggregator

  • Add support for read-only filesystem GRR

  • Add support for liftover annotator to use source and target genomes from liftover chain genomic resource labels

  • Annonymous users can access limited functionality of phenotype tools

  • Add support for effect annotator to use reference genome from genomic resource labels, annotation pipeline preamble, and genomic context

  • Fix types produced in annotation pipeline documentation

  • Fix dataset hierarchy permissions

  • Support for wildcards in annotation pipeline resource_id annotator’s attributes

  • Fix in region splitting in annotation and reannotation tools - annotate_columns, annotate_vcf and annotate_schema2_parquet

  • Support for categorical histograms in gene scores user interface

  • Support for consistency checks in genomic scores fetch_region method

  • Minor optimizations in the genomic position table

  • Fix an infinite loop in the liftover annotator

  • Minor improvements in DuckDb genotype storage

  • Support for downloading phenotype tool report image

  • Fix in the error handling for family filters in the genotype browser

• 2024.11.2

  • Fix pheno import type inference issues

  • Improvments in phenotype data import unit testing

  • Improvements in enrichment REST API unit testing

  • Fix handling of any_user access rights in dataset hierarchy

  • Fix query cancelation in gene browser

• 2024.11.1

  • Fix pheno import type inference issues

  • Improvments in phenotype data import testing

  • Construct gene sets download ling on the frontend

  • Fix handling of frequency filters in DuckDb genotype storage

  • Bump version DuckDb to 1.1.3

  • Implementation of full re-annotation of schema2 parquet datasets

  • Factory functions for bulding genomic resources from resource ID

  • Fix query cancelation in genotype browser

  • Improvement in handling pedigrees in dataset statistics without access rights

• 2024.11.0

  • Pure python implementation of type inference for phenotype measures

  • Phenotype data import refactored

  • Support for storing gene models in GTF format

  • Support for storing gene and genomic scores histograms in JSON format

  • Fix de Novo gene sets user interface

  • Fix hanling of families and persons IDs in save/share query

• 2024.10.6

  • Bug fix in handling genomic scores with chromosome remapping

  • Workaround for pysam handling of HLA contigs regions

  • Bug fix for handling dataset description without children

• 2024.10.5

  • GPF federation refactoring to create a separate conda package gpf_federation

  • Update de Novo gene sets REST API

  • Support for restricted access of GPF tools without explicit access rights

  • Improvement and fixes in Schema2 parquet datasets re-annotation

  • Bump DuckDb version to 1.1.2

  • Support for DuckDb S3 genotype storage

  • Fix missing gene profiles state in GPFjs

• 2024.10.4

  • Refactor and fixes in support of person set collection queries

• 2024.10.3

  • Remove an exception logger from phenotype measures download in phenotype browser

• 2024.10.2

  • Clean up user edit code from GPFjs

• 2024.10.1

  • Bump Angular version to 17

  • Bump DuckDb version to 1.1.1

  • Fix Impala genotype storage bugs

  • Clean up dataset statistics unit tests

• 2024.10.0

  • Bump Angular version to 16

  • Clean up of GPFjs code

  • Fix annotatoion pipeline documentation links to genomic resources

  • Support for full VEP annotation in VEP annotator plugin

  • Reorganization of de Novo gene sets API

• 2024.9.3

  • Fix phenotype measures download in phenotype browser

  • Fix searches for datasets in management user interface

  • Fix datasets permissions REST API

• 2024.9.2

  • Support search for datasets in management user interface

  • Fix denovo report generation

  • Remove duplicated large and small value labes in genomic scores histograms help modals

  • Fix bigWig genomic position table fetch method

  • Fix inmemory genomic position table handling of zero based scores

  • Fix handling of displayed_values_percent in categorical histograms

• 2024.9.1

  • Fix default number of bins in genomic scores histograms

  • Support case insensitive search in phenotype browser

  • Update links to annotators documentation in annotation pipeline documentation

  • Add missing files method in gene sets genomic resource implementation

  • Fix handling of ultra rare heuristics in DuckDb genotype storage queries

  • Clean up and imporements in wdae unit testing

  • Fix hanlding of zero based scores in inmemory genomic position table

  • Fix phenotype browser table sorting buttons state

  • Refactor and clean up of GPFjs internal state handling and transition to ngrx

• 2024.9.0

  • Performance improvements in annotation with bigWig scores resources

  • Bug fixing in wdae datasets API hierarchy

  • Phenotype data import type inference improvements

  • GPF validation runner error reporting improvements

  • BigWig genomic resources buffering Improvments

  • Phenotype data import of browser data improvements

  • Phenotype browser table improvements

  • Support for integer region bins in schema2 genotype storages

  • Schema2 Parquet loader fixes in hadling of regions

  • DuckDb genotype storage reorganization

  • Support for DuckDb genotype storage over S3

  • Separate GPF federation into a package gpf_federation

  • Revisit histogram configuration and support for user defined plot functions

  • Improvements in gpf_wdae unit testing

• 2024.8.2

  • Improvement of SQL query builder for family and summary variants in DuckDb genotype storage

  • Fix packaging of external VEP annotator plugin

  • Support for serialisation of additional attributes of family variants

  • Fix support for log-scale Y axis in categorical histograms

  • Fix loading of gene profiles search term from gene profiles state

• 2024.8.1

  • Fix caching of genotype data groups descriptions

  • Genomic position table optimization for bigWig resources

• 2024.8.0

  • Fix for pheno data import on clusters

  • Fix genomic scores histograms large and small value labels

  • Change genomic scores configuration to support column_name and column_index

  • Fix support for genomic scores with zero_based genomic position table

• 2024.7.8

  • Fix handling of bigWig resources with chromosome mapping in grr_manage

• 2024.7.7

  • Added unit tests for external VEP annotator plugin

  • Fix collection of study parents in gpf_wdae

  • Fix bigWig genomic position table fetch method

  • Fix annotation pipeline preamble

  • Fix gene browser input field behavior in GPFjs

  • Fix query cancelation on destroy of component in GPFjs

• 2024.7.6

  • Added web caching for GPF instance home and about pages

  • Fix handling of permissions for any_user` group in gpf_wdae

  • Fix gene profiles single gene search from home page

  • Clean up old dataset description cache in GPFjs

  • Fix search query cancelation in phenotype browser

  • Fix handling of description for annonymous users in GPFjs

  • Fix in dataset selector dropdown in GPFjs

• 2024.7.5

  • Performance improvements in calculation of access rights for datasets

  • Fixes in datasets routing in GPFjs

  • Added UI for resetting gene profiles state

• 2024.7.4

  • Fixes in pheno measures dropdown selector for genotype browser and pheno tool

• 2024.7.3

  • Bump versions of django dependencies

  • Fix handling of phenotype data groups

  • Fix sorting of pheno browser table

  • Gene profiles user interface state store in user profile

  • Improvement in enrichment tool results display

  • Fixes in gpf_validation_runner tool

  • Fixes for serialization of gene models in GTF format

  • Fix chromosome mapping for bigWig genomic position table

  • Fix in phenotype tool user interface controls

  • Fix in gene browser user interface coding only control

  • Fix in histogram sliders user interface

  • Fixes for handling of selected dataset in GPFjs internal state

  • New pheno measures dropdown selector for genotype browser and pheno tool

• 2024.7.2

  • Tool for drawing score resources histograms draw_score_histograms

  • Gene sets clean up and fixes

  • Fix handling of internal buffer of tabix genomic position table

• 2024.7.1

  • Improvements in genomic position table performance

  • Initial support for 0-based genomic scores in genomic position table

  • Initial support for serialization of gene models in GTF format

  • Fix in handling of saved queries in GPFjs

• 2024.7.0

  • Bump Python version to 3.11

  • Fix in gene profiles search for genes

  • Support for browser caching of GPF wdae requests

  • Support for style tag in GRR info pages resource description

  • Support for ZSTD compression of variants data blobs in schema2 parquet

  • Fixes in annotation pipeline construction

  • Fixes in support for bigWig format in genomic scores

  • Fixes in handling of selected dataset in GPFjs

  • Fixes of visual flickering of dataset selector dropdown in GPFjs

  • Fixes in handling of internal state in GPFjs

• 2024.6.6

  • Update for GRR info pages for genomic scores, gene scores, gene models and reference genome

  • Demo annotators for external tools using batch mode annotation

  • Demo annotators for external tools using using GRR resources and batch mode annotation

  • Fixes and optimization for genotype variants query over schema2 parquet loader

  • Fix handling of bigWig resources in GRR

  • Fix home page search for a gene profile

  • Fix handling of gene browser input

• 2024.6.5

  • Fix for GTF gene models parser

• 2024.6.4

  • Initial support for batch mode in annotation pipeline and annotate columns tool

  • Fix for gene profiles state handling in GPFjs

  • Clean up and improvements in searchable dropdowns in GPFjs

• 2024.6.3

  • Fix gene scores missing description in GRR info pages

  • DuckDb version bumpted to 1.0.0

  • Initial implementation of request caching in WDAE

  • Fix a minor issue in collapsable dropdown dataset selector

• 2024.6.2

  • Initial support for BigWig genomic resources

  • Bump GPF dependencies

  • Fix handling of phenotype browser images

  • Improved gene models statistics

  • Improved gene models and reference genome info pages in GRR

• 2024.6.1

  • Fix gene models GTF parser

  • Parallelization of phenotype data import tool

• 2024.6.0

  • Fix in hadling annotation pipeline preamble in annotation documentation tool

  • Imrovements in annotation documentation tool

  • Support for quering genotye variants over Schema2 parquet loader

  • Improvements in genomic scores and gene scores info packages

  • Fix in handling studies without variants in GCP Schema2 genotype storage

  • Fix in family tags counter

  • Collapsable dropdown dataset selector

  • Fix phenotype tool legend

  • Fix the layout of histogram description in scores descriptions

• 2024.5.3

  • Fix hanlding of genomic resources varsions in GRR home page

  • Support for multiple regression measures in phenotype databases

  • Resore basic liftover annotator

  • Fix in handling studies without variants in Impala Schema2 genotype storage

  • Improvments in handling annotation pipeline preamble section

  • Fix alignment of dataset names in GPF home page hierarchy

  • Fix handling of gene profiles column ordering

  • Fix families counter in dataset statistics families by pedigree page

• 2024.5.2

  • Improved styling of annotation documentation generated by annote_doc

  • Fix handling of hidden datasets in GPF home page hierarchy

  • Bug fix for loading datasets in GPFjs

• 2024.5.1

  • Annotation pipeline as genomic resource

  • Improvements in liftover annotator

  • Store column ordering in gene profiles state

  • Fix resizing of phenotype browser table

  • Source maps instrumentation of GPFjs build

• 2024.5.0

  • Support for preamble in annotation pipeline

  • Support for genotype studies without variants

  • Improvements in loading dataset hierarchy performance

  • Full parquet datasets variants loader

  • Store gene profiles visible columns to state

  • Fix handling of invalid URLs