v7.1.0

Merge branch 'main' of https://github.com/molgenis/vip-report-template

v7.0.6

What's Changed

• fix:composed/vipC and composed/vipCS show ids instead of labels by @dennishendriksen in #338

Full Changelog: v7.0.5...v7.0.6

v7.0.5

What's Changed

• fix:flag rendering by @dennishendriksen in #336

Full Changelog: v7.0.4...v7.0.5

v7.0.4

What's Changed

• fix:variant consequence table categorical rendering by @dennishendriksen in #335

Full Changelog: v7.0.3...v7.0.4

v7.0.3

What's Changed

• Update mock clinvar metadata by @bartcharbon in #333
• fix:VariantInfoTable categorical rendering by @dennishendriksen in #334

Full Changelog: v7.0.2...v7.0.3

v7.0.2

What's Changed

• fix:FieldGenotypeStr fallback to FieldGenotypeSnvSv in case of missing requirements by @dennishendriksen in #330
• fix:variants container subtitle can show 'undefined' by @dennishendriksen in #331
• fix:vip.filter_field does not have to exist by @dennishendriksen in #332

Full Changelog: v7.0.1...v7.0.2

v7.0.1

Full Changelog: v7.0.0...v7.0.1

v7.0.0

What's Changed

• Variant views now have separate views per variant type (SNV, STR and SV/CNV)
  • Each view only displays variants of the selected type
  • Each view can display e.g. different columns and filters relevant to that variant type
  • Best view is automatically selected
  • Configuration per view can be updated without changing the report template
  • Display labels and descriptions for categorical values
• Sample variant views
  • only show variants that remain after sample decision tree filtering
  • are limited to displaying genotypes of proband/mother/father, other pedigree member genotypes are shows per variant
• Report template accepts an external configuration file
  • Configuration file contains the VIP configuration for usage in report
  • Tables in variant views can be configured
  • Filters in (sample) variants view can be configured
  • Configuration cells/filters will only display if the required metadata is available
  • Configuration cells/filters can have limited display if optional metadata is not available
• Filter changes
  • Collapsible filters
  • Integer and float filters
  • Filter on 'null' categorical values
  • Replace filter header hover with (i) icon and tooltip
  • Select all / deselect all for large categoricals
  • Filter on fixed vcf fields (chr, pos, id, ref, alt, filter, qual)
  • Remove search box in (sample) variants view
  • String filter support multiple comma-separated values
• New custom filters that are available in variant views
  • composed/allelicImbalance
  • composed/deNovo
  • composed/hpo
  • composed/inheritanceMatch
  • composed/locus
  • composed/vipC
  • composed/vipCS
  • see documentation for details
• New custom table cells that are available in variant views
  • composed/clinVar
  • composed/gene
  • composed/genotype
  • composed/genotype_maternal
  • composed/genotype_paternal
  • composed/gnomAdAf
  • composed/hpo
  • composed/inheritancePattern
  • composed/locus
  • composed/vipC
  • composed/vipCS
  • composed/vkgl
  • see documentation for details
• VIP configuration that was used to create a report is displayed in 'Help'
• Variant views: do not show sample id for format filters (implied by sample screen)
• Improved error handling
  • all errors are now shown as generic notification
  • detailed technical messages are logged on the browser console
• Improved performance (cache requests between views)
• Bump dependencies
  • Update genome browser from v3.0.4 to v3.1.0, see here
  • Update vip-report-api from 5.1.1 to 6.2.1, see here
  • Update vip-report-vcf from 2.0.3 to 3.0.8, see here
• Under the hood
  • remove console.log in production
  • fix Travis deploy using custom script
  • node requirement for development increased from 18.18.2 to 22
  • enforce correct node and pnpm (9) versions
  • added loads of unit tests
  • fail build if coverage of .ts files below 80%
  • fix reactiveness warnings (potential bugs in current report)
  • code reuse
  • decouple filters from queries
  • only view has state, all other stuff bubbles up
  • format/lint json files
  • enable TypeScript noUncheckedIndexedAccess to prevent 'array out of bounds' access
  • remove modulePreload
  • speed up build, do not reportCompressedSize

Full Changelog: v6.2.0...v7.0.0

v6.2.0

What's Changed

• Add sampletree path to variant consequence screen by @bartcharbon in #318
• Fix: #319 Report navigation broken due to the addition of a drive let… by @bartcharbon in #322
• Fix travis by @bartcharbon in #323

Full Changelog: v6.1.1...v6.2.0

v6.1.1

Full Changelog: v6.1.0...v6.1.1