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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

[Unreleased]

Added

Removed

  • All source files for HPO information, this is instead fetched directly from source

[3.0.0]

Fixed

  • hide pedigree panel unless it exists

[1.5.1] - 2016-07-27

Fixed

  • look for both ".bam.bai" and ".bai" extensions

[1.4.0] - 2016-03-22

Added

  • support for local frequency through loqusdb
  • bunch of other stuff

[1.3.0] - 2016-02-19

Fixed

  • Update query-phenomizer and add username/password

Changed

  • Update the way a case is checked for rerun-status

Added

  • Add new button to mark a case as "checked"
  • Link to clinical variants without 1000G annotation

[1.2.2] - 2016-02-18

Fixed

  • avoid filtering out variants lacking ExAC and 1000G annotations

[1.1.3] - 2015-10-01

Fixed

  • persist (clinical) filter when clicking load more
  • fix #154 by robustly setting clinical filter func. terms

[1.1.2] - 2015-09-07

Fixed

  • avoid replacing coverage report with none
  • update SO terms, refactored

[1.1.1] - 2015-08-20

Fixed

  • fetch case based on collaborator status (not owner)

[1.1.0] - 2015-05-29

Added

  • link(s) to SNPedia based on RS-numbers
  • new Jinja filter to "humanize" decimal numbers
  • show gene panels in variant view
  • new Jinja filter for decoding URL encoding
  • add indicator to variants in list that have comments
  • add variant number threshold and rank score threshold to load function
  • add event methods to mongo adapter
  • add tests for models
  • show badge "old" if comment was written for a previous analysis

Changed

  • show cDNA change in transcript summary unless variant is exonic
  • moved compounds table further up the page
  • show dates for case uploads in ISO format
  • moved variant comments higher up on page
  • updated documentation for pages
  • read in coverage report as blob in database and serve directly
  • change OmimPhenotype to PhenotypeTerm
  • reorganize models sub-package
  • move events (and comments) to separate collection
  • only display prev/next links for the research list
  • include variant type in breadcrumbs e.g. "Clinical variants"

Removed

  • drop dependency on moment.js

Fixed

  • show the same level of detail for all frequencies on all pages
  • properly decode URL encoded symbols in amino acid/cDNA change strings
  • fixed issue with wipe permissions in MongoDB
  • include default gene lists in "variants" link in breadcrumbs

[1.0.2] - 2015-05-20

Changed

  • update case fetching function

Fixed

  • handle multiple cases with same id

[1.0.1] - 2015-04-28

Fixed

  • Fix building URL parameters in cases list Vue component

[1.0.0] - 2015-04-12

Codename: Sara Lund

Release 1.0

Added

  • Add email logging for unexpected errors
  • New command line tool for deleting case

Changed

  • Much improved logging overall
  • Updated documentation/usage guide
  • Removed non-working IGV link

Fixed

  • Show sample display name in GT call
  • Various small bug fixes
  • Make it easier to hover over popups

[0.0.2-rc1] - 2015-03-04

Added

  • add protein table for each variant
  • add many more external links
  • add coverage reports as PDFs

Changed

  • incorporate user feedback updates
  • big refactor of load scripts

[0.0.2-rc2] - 2015-03-04

Changes

  • add gene table with gene description
  • reorganize inheritance models box

Fixed

  • avoid overwriting gene list on "research" load
  • fix various bugs in external links

[0.0.2-rc3] - 2015-03-05

Added

  • Activity log feed to variant view
  • Adds protein change strings to ODM and Sanger email

Changed

  • Extract activity log component to macro

Fixes

  • Make Ensembl transcript links use archive website