| refs/tags/v1.4.6 | v1.4.6 | a736631 | Changes: - Legend is now a sidebar - should be easier to navigate, sort, and visually search through (#254) - Add warning for lab-specific SNV biases - Add custom ingestion pipeline for local files (#258, #259). Thanks @apetkau - Fix geographical data for Czechia & Palestine - Bug fixes (pipeline, UI) | 08 January 2021, 07:37:38 UTC |
| refs/tags/v1.4.2 | v1.4.2 | 5510c5e | Changes: * Add projects to related projects tab * Fix bugs in pipeline | 28 December 2020, 14:13:11 UTC |
| refs/tags/v1.4.1 | v1.4.1 | 2694141 | Major changes: * Provide application-wide configuration, inside `config/config_[workflow].yaml`. Configuration options are used by snakemake during the analysis steps, and injected into JS bundles by webpack to allow for configuration of the front-end interface * Refactor pipeline into "ingest" and "main analysis" steps * Provide GenBank data ingest option, in addition to existing GISAID option * Generalize sequence groupings (i.e., grouping sequences by lineage or clade). This is configured in the application-wide config.yaml file now. (In preparation for integrating more sequence groupings/lineage definitions) * Switch to compressed data formats (fa.gz and bam instead of fa and sam) * Simplify data packaging, merge some maps into metadata_map * Add automated build scripts Bug fixes: * Fix mislabeling of some AA indels (off-by-one) * More robust fasta file comparisons * Fix download of global sequencing effort data from the plot * npm security fixes | 23 December 2020, 10:39:17 UTC |
| refs/tags/v1.3.0 | v1.3.0 | e2fde69 | Changes: * Various UI bugs * Switch to new data processing system, off of manual GISAID downloads * Updates to location metadata * Capture more patient age metadata * Remove some metadata collapsing from other fields, to better preserve original intent * Fix download of aggregate data from lineages/clades | 15 December 2020, 18:11:59 UTC |
| refs/tags/v1.2.0 | v1.2.0 | e6e55a4 | Changes: * Data now downloaded from a requested file (data_package.json) instead of inlined into the JS bundle (#243, #247) * Data date coupled to downloaded data package (3469fa1, 093c683) * Add Australia S477N mutation tutorial * Fixes for building with a sparse dataset of only a few sequences (#245) * Sort co-occurring SNVs by gene/protein, then position (#237, 9ee1333) * Only show AA SNVs from the selected gene/protein name (ac17722) * Fix geographical inconsistencies in global sequencing effort plot (08a8046, 5741dfb) * Fix processing of gene/proteins with multiple ranges (80d4230, 8f7b3fc) * Code quality, code cleanup * Adjusting copy | 13 October 2020, 02:14:39 UTC |
| refs/tags/v1.0.9 | v1.0.9 | ecec114 | A couple of minor updates since launch Changes * Increase site-wide performance by performing 'Other' grouping logic at the store level (#225) * Fix data processing of indels (4fa8617) * Fix calculation of location-date counts in Vega plots (dd120ee) * Improve reactivity of legend items, vega plots with hover (e87eb5e, 4c258b8, 0f256fd) * Snakemake fixes (0caa863, bc572a8) * UI fixes for mobile (0ab54d3, #233) * Add residue coordinates and domains for genes/proteins (#233) * Exclude sequences without lineage/clade assignment (e74dd8b) * Various UI fixes * Bump data to 2020-09-01 | 03 September 2020, 03:09:07 UTC |
| refs/tags/v1.0.3 | v1.0.3 | 20980df | Changes: * Increase performance by grouping sequences into "Other" group prior to viz * Adjust data processing of indels | 28 August 2020, 11:12:29 UTC |
| refs/tags/v1.0.1 | v1.0.1 | f11cdb9 | Changes * Adjust copy * Crash fixes, performance improvements | 27 August 2020, 15:08:48 UTC |
| refs/tags/v1.0.0-rc9 | v1.0.0-rc9 | bfaf9c7 | Changes: * UI and copy fixes * Location plots adapt to date range * Metadata cleaning | 26 August 2020, 23:12:10 UTC |
| refs/tags/v1.0.0-rc8 | v1.0.0-rc8 | 6e4f66a | Changes: * Add React date range interaction in group stack plot * Process SNV Co-occurrences separately * Fix various interaction bugs * Update example analyses screenshots * Add N: R203K,G204R example analysis * Rework Tab UI (#216) * Copy requests from GISAID (#219) * Download data + images from Global Sequencing Coverage plot (#218) * Update data to 2020-08-23 | 26 August 2020, 10:57:08 UTC |
| refs/tags/v1.0.0-rc7 | v1.0.0-rc7 | f539326 | Changes: * New plots for SNV view, fix inconsistencies (#220) * Clear all locations button (#221) | 25 August 2020, 15:23:39 UTC |
| refs/tags/v1.0.0-rc5 | v1.0.0-rc5 | fd15738 | Changes: * Fixes to global sequencing efforts tab * Adjust copy, examples | 19 August 2020, 02:02:51 UTC |
| refs/tags/v1.0.0-rc4 | v1.0.0-rc4 | bb0ca89 | Changes: * Switch reference from Wuhan-Hu-1 to WIV04 (#170) * More copy/layout adjustment requests from GISAID | 14 August 2020, 22:56:33 UTC |
| refs/tags/v1.0.0-rc3 | v1.0.0-rc3 | 2d682f8 | Changes: * Copy adjustments * Adjust color scheme for lineages | 14 August 2020, 15:22:35 UTC |
| refs/tags/v1.0.0-rc2 | v1.0.0-rc2 | 9ae10e7 | bugfix: remove sequences with collection date past the submission date | 14 August 2020, 00:28:01 UTC |
| refs/tags/v1.0.0-rc1 | v1.0.0-rc1 | a2ee74e | Changes * Fix UI bugs on safari (#204, #101) * Add VIPR BRC to related tools * Filter out passaged sequences (#202) * Disable patient metadata filters that were mostly empty anyways (#180) * Completely randomize the Accession ID hash, now should be impossible to reverse engineer (#148) * Various copy/UI fixes | 13 August 2020, 22:43:33 UTC |
| refs/tags/v1.0.0 | v1.0.0 | e302301 | First Release!! | 26 August 2020, 23:22:14 UTC |
| refs/tags/v0.7.3 | v0.7.3 | 15e23c7 | Minor copy edits | 11 August 2020, 14:22:38 UTC |
| refs/tags/v0.7.2 | v0.7.2 | d928fbf | Changes: * Disable acknowledgements table/download, add plot data downloads (#186) * Adjust copy throughout the site (#188, #192, #197) * Add methodology tab (#153, #188) * Move other projects to separate tab (#149, #188) * Add global sequencing efforts leaderboard (#191) * Add query params for tabs (#193) * Switch color palettes (#113, #197) * Support for multiple custom coordinate ranges, add sequence matching (#198) * Add images for example analyses (4a6d9dc) | 10 August 2020, 20:30:06 UTC |
| refs/tags/v0.7.1 | v0.7.1 | 4d457fd | Changes: * Various performance improvements | 06 August 2020, 15:27:35 UTC |
| refs/tags/v0.7.0 | v0.7.0 | 455a5a0 | Changes * Update python environment, Snakefile (e4cb045, fe51481, 6d31a2d) * Add examples tab, example analyses (#146) * Performance improvements (#144) | 04 August 2020, 15:49:49 UTC |
| refs/tags/v0.6.0 | v0.6.0 | 9de6ebe | Changes * Unify python scripts with snakemake pipeline (#136) * Various UI fixes, cleanup, and add documentation in app (#139) * Move data and configuration into separate stores (#140) * Collapse low frequency groups (lineages/clades/SNVs) into "Other" group, with 3 possible strategies -- top N groups, minimum local counts, and minimum global counts (#121) * Fix possible memory leak, improve rendering performance on legend and tables (#121) * Reduce total amount of event listeners, in legend and table (#121) * Move plot settings into separate store, in preparation for examples/vignettes (#143) | 02 August 2020, 17:44:23 UTC |
| refs/tags/v0.5.1 | v0.5.1 | 6d8d848 | bugfix: date selection | 27 July 2020, 17:02:52 UTC |
| refs/tags/v0.5.0 | v0.5.0 | bc4e8d9 | Changes: * Add location comparison tab (#117, #114) * Add warning box for main visualization | 27 July 2020, 16:52:46 UTC |
| refs/tags/v0.4.4 | v0.4.4 | 3e20a2b | Changes: * Process sequences up to 2020-07-22 (da4d756) * Add splash screen (#107) * Snap date selections to the nearest day (#108) * Stop highlighting empty bars (#108) * Add date selection to status bar (#108) * Add comments to the stacked bar vega spec (14e2dc8) * Add plot download options (png, svg) (#110, 007b317) * Add COVID CG logo (85c9d63) * Small UI fixes * Organize components folder a bit | 25 July 2020, 15:30:01 UTC |
| refs/tags/v0.4.3 | v0.4.3 | 18cbc2f | Changes: * Add grouping by GISAID clade (#105) * Add NGINX configuration for alpha subdomain | 23 July 2020, 15:54:27 UTC |
| refs/tags/v0.4.2 | v0.4.2 | 3e4d82c | Changes: * Rewrite a lot of VegaEmbed in the new react_vega port. It should be a lot more stable, handle data more efficiently, and preserve listeners/signals between renders. * Add cumulative counts option * Add date binning, by day, week, month * Add help tooltips for legend, plot, and table * Remove sequences with unspecific dates, or dates too early (<2019-12-15) * Clean up package.json | 23 July 2020, 01:09:21 UTC |
| refs/tags/v0.4.1 | v0.4.1 | c73ace4 | Changes: * Add about page, attributions (#95) * Add metadata filtering (#98) * Add status bar, showing number of selected sequences and selected groups (lineages/snps) | 21 July 2020, 19:17:07 UTC |
| refs/tags/v0.4.0 | v0.4.0 | aa65cbe | Stacked barplots, cross-interaction between vega and react elements | 20 July 2020, 11:11:44 UTC |
| refs/tags/v0.2.0 | v0.2.0 | 8ee35bf | Version 0.2.0 Mostly changing data processing schemes for GISAID, and including much more metadata for future filtering * Hide structural viewer until complete * Add treeview, accordions to adjust UI (#84) * Fulfill GISAID requests (#85) * UI additions * Acknowledgements table below data * Anonymize Accession IDs, mask metadata values * Custom Legend element in React instead of in Vega (#82) * Explicit color assignments (#80, #81) * Add "all locations" selector, default to no sequences selected (#76) * Fix datatable sorting issues (#77) * Fix scrolling issues (#74) * Add country flag emojis (#75) * Use lineage data from GISAID instead of running pangolin on our own (dd5fa06) * Switch static server to NGINX (8305530) * Update sequences to 2020-07-06 | 08 July 2020, 22:40:39 UTC |
| refs/tags/v0.1.1 | v0.1.1 | 8c5a995 | * UI layout changes (#60) * Add loading animations for re-rendering components (#52) * Download sequence and aggregated sequence data (#62) * Add documentation (server, main README) * Add location processing code up to sequences submitted by 2020-06-12 * Various styling fixes * Cleanup of old redux files | 13 June 2020, 11:30:06 UTC |
| refs/tags/v0.1.0 | v0.1.0 | f479ffe | Changes: - Move main data processing to Web Workers, add asynchronous updates to UI (#43) - Add loading animation skeletons (#52) - Add acknowledgements processing and downloading of Accession IDs paired to Acknowlegement texts (#51) - Add Google Analytics (#42) - Update page title (b9e8236) - Update location processing code, for sequences up to 2020-06-10 (c429176) - Replace react-data-table-component with react-grid, which massively improves performance by lazy-loading cells. Also added dropdown download button, new AA colors, and "dots" mode. (#50) | 11 June 2020, 22:16:47 UTC |
| refs/tags/v0.0.1 | v0.0.1 | d80dfd8 | First release | 09 June 2020, 15:53:15 UTC |
