Packages in this release
- Other
core
- #3525 Fix missing grid ticks in dotplot (@cmdcolin)
- #3524 Fix loading session shares that have a plus sign in the sessionId (@cmdcolin)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
core- #3494 Use transitionDuration 0 as defaultProp in theme for both popovers and menus (@cmdcolin)
- #3488 Render HTML in faceted track selector for track data/metadata (@cmdcolin)
- #3483 Add anchorOrigin/transformOrigin to default menu component (@cmdcolin)
- #3470 Variant sample grid auto-size columns and resizer (@cmdcolin)
- Other
- #3304 Faceted/data grid style track selector (@cmdcolin)
- #3477 Larger margins to add track workflow to visually clarify next button behavior (@cmdcolin)
- #3475 Bypass plugins.json download if unneeded during app startup (@cmdcolin)
- #3458 Improve auto-update of sequence track height when toggling forward/reverse/translation settings (@cmdcolin)
core- Other
- Colin Diesh (@cmdcolin)
Packages in this release
core
- Other
core
- #3448 Typescriptify some docusaurus website code (@cmdcolin)
- #3444 Human vs mouse synteny demo (@cmdcolin)
core
- Colin Diesh (@cmdcolin)
Packages in this release
core- Other
- #3419 Fix rendering base-level alignments on synteny visualizations, especially in inverted regions (@cmdcolin)
- #3416 Fix rendering alignment arcs on files that need refname renaming and add jitter setting (@cmdcolin)
- #3415 Fix circular view being rendered as a blank area if tab is opened in the background (@cmdcolin)
- Colin Diesh (@cmdcolin)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
Packages in this release
- Other
coretext-indexing
- Other
- #3407 Remove trackhub registry plugin from core plugins, moved to plugin store (@cmdcolin)
- #3406 Fix loading connection tracks from connections that don't specify assemblyNames in config (@cmdcolin)
- #3390 Fix positioning within large alignments for query->target LGV synteny navigation (@cmdcolin)
- #3388 Fix search result that matches synonyms that matches multiple locations (@cmdcolin)
core
core- Other
__mocks__,core,text-indexingcore
- Colin Diesh (@cmdcolin)
Packages in this release
- Other
- #3350 Retain feature labels in compact display mode for SVG features, and allow turning off keeping feature description without feature label (@cmdcolin)
- #3357 Allow holding shift key to create rubberband selection on LGV (@cmdcolin)
- #3363 Create remove-track CLI command (@cmdcolin)
- #3341 Add BEDPE adapter type (@cmdcolin)
core
- Other
- #3377 Fix rendering and clicking synteny features when using MainThreadRpc (@cmdcolin)
- #3375 Fix
jbrowse upgradeCLI command overwriting config.json with --branch or --nightly options (@cmdcolin) - #3370 Fix error with SNPCoverage not rendering MM tag modifications in some cases (@cmdcolin)
- #3366 Fix ability to use LGV synteny track on inverted alignments (@cmdcolin)
- #3348 Fix for
breakpoint split view and circular view issues with
<TRA>type entries in v2.2.1 (@cmdcolin)
core
coretext-indexing
Packages in this release
- Other
core- #3298 Add authentication plugin to embedded components (@garrettjstevens)
- #3329 Add ability to minimize/collapse tracks and views and move views up/down in view stack (@cmdcolin)
- #3308 Add ability to display synteny track in a normal LGV showing regions of synteny as features (@cmdcolin)
- #3317 Move ErrorBoundary so that tracks/views that have crashed can be closed more easily (@cmdcolin)
- Other
core
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
- Other
- #3296 Add option to use OAuth "state" param in internet accounts (@garrettjstevens)
- #3285 Use typescript version of @gmod/cram (@cmdcolin)
core
core- Other
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Scott Cain (@scottcain)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
- Colin Diesh (@cmdcolin)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/text-indexing | |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-arc | |
| @jbrowse/plugin-authentication | |
| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-comparative-adapters | |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark |
| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-jobs-management | |
| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-text-indexing | |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| jbrowse-predefined-sessions | |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- Other
core- #3230 Add ability to customize About dialog with callbacks and optionally hide links to data (@cmdcolin)
- #3275 Add help dialog for feature sequence panel (@cmdcolin)
- #3250 Handle alternate line endings (@garrettjstevens)
- #3252 Fix gene sequence fetching in embedded, and allow fetching genomic sequence for other feature types (@cmdcolin)
core,text-indexing
core- Other
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Scott Cain (@scottcain)
Packages in this release
- Other
- #3200 Use Alert component for track messages (@garrettjstevens)
- #3229 Allow user to select local assembly to add tracks to for trackhub registry (@cmdcolin)
- #3220 Improve error reporting on SV inspector/spreadsheet view on import form (@cmdcolin)
- #3198 Improve error reporting on jbrowse-web start screen when user attempts to open a broken recent session (@carolinebridge-oicr)
core- #3223 Allow adding session tracks to embedded react component along with disableAddTracks option if unwanted (@cmdcolin)
- #3227 Add infrastructure for creating linear-genome-view sub-classes (@carolinebridge-oicr)
- #3215 Add error boundary on view, track, and drawer widget (@cmdcolin)
- #3216 Add ability to set number of bp to fetch up/down stream/inside intron in feature details (@cmdcolin)
- Other
- #3241 Fix local session failing to load copying between tabs in some cases (@cmdcolin)
- #3234 Fix circular embedded view failing to load in v2.1.3 and v2.1.4 (@cmdcolin)
- #3233 Fix legend being cutoff on multiwiggle tracks with wide window (@cmdcolin)
- #3217 Fix loading tracks from connection using assembly alias (@cmdcolin)
- #3214 Fix trackhub registry failing to load in 2.x.y versions of jbrowse (@cmdcolin)
- #3204 Fix authentication configuration on jbrowse-desktop (@cmdcolin)
core- #3231 Fix theme coloring for components that use overrides e.g. accordion summary (@garrettjstevens)
- #3193 Add desktop specific plugin tutorial (@carolinebridge-oicr)
- Other
core- #3228 Improve TypeScript for queueDialog (@garrettjstevens)
- #3224 More typescripting of plain js files (@cmdcolin)
- #3207 Hardcoded block width of 800px on static blocks (@cmdcolin)
- #3197 Use "temporaryAssemblies" to store read vs ref assemblies, and allow selecting "sessionAssemblies" in dropdown (@cmdcolin)
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
- Colin Diesh (@cmdcolin)
Packages in this release
- Other
- #3188 Add 'Open saved session' button to start screen on desktop (@cmdcolin)
- #3187 Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table (@cmdcolin)
- #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
- #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
- #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
- #3162 Add about dialog with version number for embedded components (@cmdcolin)
- #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
- #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
- #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
- #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
- #3162 Add about dialog with version number for embedded components (@cmdcolin)
- #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
core- #3180 Improve adding assemblies internally, and use the assembly displayName in more places in the UI (@garrettjstevens)
- #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
- #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
core- #3168 Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form (@cmdcolin)
- #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
- #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
- Other
- #3138 Documentation overhaul (@carolinebridge-oicr)
- #3138 Documentation overhaul (@carolinebridge-oicr)
- Other
- #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
- #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
- #3165 Use more defaults in rollup plugins (@garrettjstevens)
core- #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
- #3164 Typescript the QuickLRU module in @jbrowse/core (@cmdcolin)
- #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
- #3164 Typescript the QuickLRU module in @jbrowse/core (@cmdcolin)
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-arc | |
| @jbrowse/plugin-authentication | |
| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-comparative-adapters | |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark |
| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-jobs-management | |
| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-text-indexing | |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
- Other
- #3152 Render CSQ and ANN fields in VCF feature details as data grids (@cmdcolin)
- #3137 Make ideogram menu item similar to others (@garrettjstevens)
core- #3159 Sequence search track (@cmdcolin)
- #3132 Extend theme with module augmentation (@garrettjstevens)
- Other
- #3157 Support the "name" field on multi-wiggle adapter subadapters instead of source (@cmdcolin)
- #3154 Use the union of all the subadapter refNames for the MultiWiggleAdapter getRefNames (@cmdcolin)
- #3156 Fix for mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode (@cmdcolin)
- #3151 Fix ability to click and drag overview scale bar dragging right to left (@cmdcolin)
- #3133 Update the ref name box when assembly is changed in LGV import form (@garrettjstevens)
- #3131 Use "code" instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo (@garrettjstevens)
- #3119 Use es2015 setting for commonjs builds of packages to fix @jbrowse/img (@cmdcolin)
- #3142 Fix unicode arrow icon not rendering with some fonts in configuration editor (@garrettjstevens)
core
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
core- #3111 Create undo manager in jbrowse-web and jbrowse-desktop (@cmdcolin)
- #3115 Add warning when dotplot renders outside of it's boundaries, and create click-and-drag panning of dotplot view (@cmdcolin)
- #3102 Allow creating alternative "add track workflows" from within the "Add track" widget (@cmdcolin)
- #3043 Create MultiWiggle track type, adapter, and renderers (@cmdcolin)
- Other
- Other
- #3109 Better support for developing plugins from within yarn 2+ workspaces (include __virtual folder in build) (@garrettjstevens)
core- #3095 Add MUI exports to re-exports list (@garrettjstevens)
- #3092 Fix use of embedded components with vite 3.0 using tsc to compile @jbrowse/core (@cmdcolin)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
core- #3089 Clarify error message when adapter has no features (@garrettjstevens)
- #3084 Show a descriptive error if an adapter doesn't provide a sequence (@garrettjstevens)
- #3071 Add ability to mouseover/click on synteny feature polygons in the linear synteny view (@cmdcolin)
- Other
- Other
- #3088 Fix labels being cut-off in SVG features by rendering feature labels on main thread (@cmdcolin)
- #3085 Fix zoom to behavior being inaccurate with many displayed regions visible (@cmdcolin)
- #3082 Fix negative strand CIGAR renderings on linear synteny view (@cmdcolin)
- #3077 Fix crash opening multiple synteny track selectors launched from dotplot view (@cmdcolin)
core
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
- Other
text-indexing__mocks__,core,text-indexing
- Other
core
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/text-indexing | |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-arc | |
| @jbrowse/plugin-authentication | |
| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-comparative-adapters | |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark |
| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-jobs-management | |
| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-text-indexing | |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-trix | https://www.npmjs.com/package/@jbrowse/plugin-trix |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| jbrowse-predefined-sessions | |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
core- Other
- #2831 Update commands for sorting GFF3 for tabix (@cmdcolin)
- #3018 Add desktop specific plugin example (@cmdcolin)
- #3022 Add example using embedded components with next.js (@cmdcolin)
- Colin Diesh (@cmdcolin)
Packages in this release
- Other
- #3025 Add dotplot session spec (@cmdcolin)
- #2975 Add simplified URL format for loading synteny views (@cmdcolin)
- #3023 Add error handling in case of invalid OAuth2 configuration used. (@andrzejgrzelak)
- #3020 Allow choosing trackId when using text-index with --file with --fileId (@cmdcolin)
- #3016 Allow whitespace separated refname,start,end type locstring (@cmdcolin)
- #3006 Add string array configuration slot UI improvements (@cmdcolin)
- #2998 Avoid rendering offscreen contents in pileup renderer (@cmdcolin)
- #3000 Add reference base and correct percentage calculations to tooltip on SNPCoverage display (@cmdcolin)
core- #2981 Add simplified URL format for loading spreadsheet and SV inspector (@cmdcolin)
- #2990 Use shortened megabases (M) display when zoomed out, and option to hide the "open track selector" button (@carolinebridge-oicr)
- #3003 Add ability to run field formatters on the feature details panel (@cmdcolin)
- #3017 Add button to copy track config in About track dialog (@cmdcolin)
- #2999 Generate clickable links to track data in about track dialog (@cmdcolin)
__mocks__,core
- Other
core
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- @andrzejgrzelak
Packages in this release
core- Other
core- Other
- #2977 Respect --indexFile option when adding VCF and BED tracks (@heavywatal)
- #2974 Fix track indexing being ignored after first add track widget usage (@teresam856)
- Adam Wright (@adamjohnwright)
- Colin Diesh (@cmdcolin)
- Teresa Martinez (@teresam856)
- Watal M. Iwasaki (@heavywatal)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-legacy-jbrowse | https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- #2970 Draw indels in modifications/methylation mode (@cmdcolin)
- #2961 Add more visible pileup mismatches when zoomed out (@cmdcolin)
- #2960 Avoid performing a text index search if input looks like a locstring (@cmdcolin)
- #2954 Support in-memory GFF3 and GTF in JBrowse 1 connection (@garrettjstevens)
- #2947 Optimization for SNPCoverageAdapter and CRAM parsing (@cmdcolin)
- #2969 Fix link on yeast synteny demo and fix CIGAR rendering on dotplot (@cmdcolin)
- #2964 Fix crash displaying modifications called on softclipped regions of reads (@cmdcolin)
- #2965 Fix filter functionality on pileup tracks (@cmdcolin)
- #2953 Fix "Open" button on LGV ImportForm (@cmdcolin)
- #2952 Fix read vs ref not finding primary alignment on certain CRAM files (@cmdcolin)
- #2951 Fix viewing soft/hardclip indicator in some regions (@cmdcolin)
- #2955 Re-enable eslint autofix for prettier rules (@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- Colin Diesh (@cmdcolin)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/desktop |
- #2939 Fix loading CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse desktop (@cmdcolin)
- Colin Diesh (@cmdcolin)
Packages in this release
core- Other
core,text-indexing- #2684 Text-indexing in desktop (@teresam856)
- #2863 Render gene with CDS subfeatures properly (@cmdcolin)
- #2934 Bump @gmod/trix to fix prefix size calculation and searching first word in index (@cmdcolin)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
Packages in this release
- Other
core- #2923 Add babel/runtime to dependencies (@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
Packages in this release
core- Other
- Colin Diesh (@cmdcolin)
Packages in this release
- Other
- #2909 Add --prefixSize flag to @jbrowse/cli text-index (@cmdcolin)
- #2887 Optimize filtering on alignments tracks (@cmdcolin)
- #2879 Multi-level synteny rubberband (@cmdcolin)
- #2874 Optimizations for rendering long syntenic alignments e.g. CHM13 vs GRCh38 (@cmdcolin)
- #2872 Better connection between paired-end alignments in breakpoint split view and optimizations (@cmdcolin)
core
- Other
- #2908 Fix AboutDialog under vite for embedded components (@cmdcolin)
- #2900 Fix the 'Open assembly' menu item in jbrowse desktop (@cmdcolin)
- #2882 Add padding at the bottom of the configuration editor to help color editing popup being cutoff (@cmdcolin)
- #2877 Fix strand on arrows in horizontally flipped mode (@cmdcolin)
core
- #2894 Add create-react-app v5 embedded component demos (@cmdcolin)
- #2830 Documentation comparing main app with embedded components (@carolinebridge-oicr)
core__mocks__,core
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Robert Buels (@rbuels)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- Other
- #2847 Add option to color all the letters on all the reads to the pileup renderer (@cmdcolin)
- #2849 Avoid drawing intron subfeatures for gene glyphs (@cmdcolin)
- #2835 Hide add track and connection menu items when using embedded component (@carolinebridge-oicr)
- #2836 Display low-quality modifications in SNPCoverage renderer for MM tag (@cmdcolin)
core
- Other
- #2852 Fix misaligned features under breakpoint split view (@cmdcolin)
- #2844 Fix layout of small features without labels for SvgFeatureRenderer (@cmdcolin)
- #2839 Fix the drawing of SNP height when the SNPCoverage track is using log scale (@cmdcolin)
- #2825 Fix tracklabels positioning not updating in UI after user selection (@cmdcolin)
core- #2841 Fix alignments tracks loading excessive data on chromosomes where no features exist (@cmdcolin)
- #2829 Allow user to specify number of workers (@garrettjstevens)
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-authentication | |
| @jbrowse/plugin-comparative-adapters | |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- #2821 Fixup scroll on wiggle tracks with trackLabels->offset (@cmdcolin)
- #2819 Fix bug in desktop where first track gets stuck loading (@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
core- #2796 Add collapsible accordion sections in configuration editor (@cmdcolin)
- #2791 Add new coloring options for dotplot and ability to "rectangularize" dotplot view (@cmdcolin)
- #2741 Allow ability to enter a space-separated locstring to open a list of regions (@cmdcolin)
- #2725 Refactor InternetAccounts, add standard getFetcher (@garrettjstevens)
- #2787 Display the total bp viewed in the header of the dotplot view (@cmdcolin)
- #2767 Wiggle and SNPCoverage look and feel improvements (@cmdcolin)
- #2746 Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view (@cmdcolin)
- Other
- #2799 Exit process after rendering to speed up jb2export (@cmdcolin)
- #2793 Add abortcontroller polyfill to jbrowse-img to allow it to run under node 14 (@cmdcolin)
- #2761 Add a --clean
argument to
jbrowse upgradeto clean up old files (@cmdcolin) - #2760 Make a configurable refNameColumn in RefNameAliasAdapter (@cmdcolin)
core- #2798 Fix bug where web worker would sometimes be called before it was ready (@garrettjstevens)
- Other
- #2797 Fix crash plotting methylation in sparse regions (@cmdcolin)
- #2782 Fix display of cytobands when horizontally flipped (@cmdcolin)
- #2678 Preserve double border line when using trackLabel offset and use smaller gap between snpcoverage and reads (@cmdcolin)
- #2774 Fix overwriting broken symlink with --force in add-track CLI (@cmdcolin)
- #2773 Fix using global stats autoscale on wiggle tracks (@cmdcolin)
- #2766 Add a check for empty content blocks to fix rare empty stats estimation (@cmdcolin)
- #2804 Add note about additional pre-requisites to README (@cmdcolin)
- #2762 Add bookmark widget docs to user guide (@cmdcolin)
- #2813 Create codeVerifierPKCE only when needed (@garrettjstevens)
- #2808 Polyfill window.crypto.getRandomValues in tests (@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
- #2736 Add better display of error state in dotplot view and load gzipped PAF files (@cmdcolin)
- #2705 Increase admin-server payload limit (@garrettjstevens)
- Other
- #2758 Use VariantTrack for plaintext VCF type (@cmdcolin)
- #2738 Add better catch for XS and TS tag detection from CRAM (@cmdcolin)
- #2733 Use sparse array for alignments coverage to fix bug viewing large sparse regions (@cmdcolin)
- #2734 Use node fetch instead of follow-redirects in cli (@cmdcolin)
- #2726 Handle .bgz file extension for text-index (@cmdcolin)
- #2727 Add engines 16 to @jbrowse/img (@cmdcolin)
- #2723 Make jbrowse desktop more robust to errors when reading recent sessions file (@cmdcolin)
- #2715 Change --target to --root for jbrowse CLI admin-server (@cmdcolin)
core- #2757 Fix type confusion with stats estimation causing BAM files to fail byte size calculation (@cmdcolin)
- #2750 Add bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in alignments track in webkit and firefox (@cmdcolin)
- #2719 Avoid uninitialized state during stats estimation (@cmdcolin)
- #2707 Fix ability to use authenticated assembly files (@garrettjstevens)
- #2695 Fix disabled state on the linear genome view track labels dropdown menu (@cmdcolin)
- #2716 Update to node12 requirement for @jbrowse/cli (@cmdcolin)
- #2605 Developer guide reorganization and create new API document (@cmdcolin)
core- #2664 Use babel config from core in root (@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Sebastian Benjamin (@hextraza)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
core- #2679 Optimizations and usability improvements to synteny view (@cmdcolin)
- #2677 Save user settings from LGV (@cmdcolin)
- #2571 Add stats estimation to JB2 (@cmdcolin)
- #2666 Add option to display curved lines and to square the dotplot and synteny views (@cmdcolin)
- #2672 Optimize dot plot rendering (@cmdcolin)
- Other
__mocks__,core
core- Other
- #2663 Add documentation for URL params and session spec (@cmdcolin)
- #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)
core- #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
- #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
- Other
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- @bbimber
Packages in this release
core- #2679 Optimizations and usability improvements to synteny view (@cmdcolin)
- #2677 Save user settings from LGV (@cmdcolin)
- #2571 Add stats estimation to JB2 (@cmdcolin)
- #2666 Add option to display curved lines and to square the dotplot and synteny views (@cmdcolin)
- #2672 Optimize dot plot rendering (@cmdcolin)
- Other
__mocks__,core
core- Other
- #2663 Add documentation for URL params and session spec (@cmdcolin)
- #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)
core- #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
- #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
- Other
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- @bbimber
Packages in this release
core- #2679 Optimizations and usability improvements to synteny view (@cmdcolin)
- #2677 Save user settings from LGV (@cmdcolin)
- #2571 Add stats estimation to JB2 (@cmdcolin)
- #2666 Add option to display curved lines and to square the dotplot and synteny views (@cmdcolin)
- #2672 Optimize dot plot rendering (@cmdcolin)
- Other
__mocks__,core
core- Other
- #2663 Add documentation for URL params and session spec (@cmdcolin)
- #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)
core- #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
- #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
- Other
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- @bbimber
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- #2645 Fix core by not using absolute runtime in babel (@garrettjstevens)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/desktop | |
| @jbrowse/web |
- Colin Diesh (@cmdcolin)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
core
- Colin Diesh (@cmdcolin)
- Teresa Martinez (@teresam856)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/desktop | |
| @jbrowse/img | https://www.npmjs.com/package/@jbrowse/img |
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
Packages in this release
- Other
core- #2623 Adjust label width on base feature detail to enforce better alignment (@carolinebridge-oicr)
- Other
core
core- #2595 Use some newly available TypeScript types (@garrettjstevens)
- #2576 Use TypeScript parameter properties (@garrettjstevens)
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |
development-tools- #2600 Fix broken published build of jbrowse/development-tools (@garrettjstevens)
- Garrett Stevens (@garrettjstevens)
Packages in this release
- Other
- #2579 Add help text and help dialog for the RefNameAutocomplete (@cmdcolin)
- #2553 Add sashimi-style arcs for RNA-seq type skips on SNPCoverage display (@cmdcolin)
- #2552 Change border on non-cytoband OverviewScaleBar visible region back to blue and cytoband OverviewScaleBar to a little lighter fill (@cmdcolin)
- #2509 Implement prop interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer (@hextraza)
- #2485 Only use one button, "Go", in text search ambiguous results dialog (@cmdcolin)
- #2501 Add a tooltip to desktop session path so you can see the full path if it's cut off (@garrettjstevens)
core- #2580 Make core snackbar notifications module with auto-dismissing info/success level notifications (@cmdcolin)
- #2534 New display type for drawing arcs (@carolinebridge-oicr)
- #2590 Add more exports that can be used by plugins (@garrettjstevens)
- #2578 Add layouts code to core re-exports (@garrettjstevens)
- #2523 Performance optimizations for alignments tracks, particularly those with many short reads (@cmdcolin)
- #2500 Add RenderProps to core/pluggableElementTypes export (@garrettjstevens)
core,development-tools- #2487 Add support for additional types of plugin formats (commonjs, esm) to allow access to node modules on jbrowse desktop (@garrettjstevens)
- Other
- #2594 Fix infinite loop bug while searching certain strings and handle multi-word searches better (@cmdcolin)
- #2589 Fix occasional failures observed from running text-index command (@cmdcolin)
- #2583 Fix for alignments track base modifications display regarding skipped bases on Mm tag (@cmdcolin)
- #2556 Fix ability to access BigWig tracks on http basic auth for some cases (@cmdcolin)
- #2577 Fix ability to use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, GTF support to add-track CLI (@cmdcolin)
- #2521 Fix ability to search for tracks with parentheses in tracklist (@cmdcolin)
- #2512 Fix [object Window] issue in alignment read vs reference dialog (@cmdcolin)
- #2499 Add missing dependency to CLI (@garrettjstevens)
core- #2585 Fix ability to use "Color by methylation" on files that require refname renaming (@cmdcolin)
- #2517 Remove aborting on adapter loading process to fix some tracks getting stuck in infinite loading state (@cmdcolin)
- #2564 Start looking for parents with parent, not self in findParentThat (@garrettjstevens)
- #2563 Restore ability to load plugins from relative URL (@garrettjstevens)
- #2533 Fix drawer widget minimized button being unclickable when overlapping with a view (@cmdcolin)
- #2522 Add circular genome view storybook (@cmdcolin)
- #2508 Update docs for embedded components (@teresam856)
- #2495 Improve organization on docs landing page (@cmdcolin)
core
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Peter Xie (@peterkxie)
- Sebastian Benjamin (@hextraza)
- Teresa Martinez (@teresam856)
Packages in this release
core- #2488 Improve usability of the search result autocomplete when typing in via keyboard (@cmdcolin)
- #2267 Add cytoband to overview scale bar in LGV (@cmdcolin)
- #2447 Drawer widget tooltips and use position: fixed on fab (@cmdcolin)
- #2299 Add new pluggable element type and properties to adapter type for registering adapter association with 'add track' workflow (@carolinebridge-oicr)
- Other
- #2484 "Add custom plugin" dialog improvements (@cmdcolin)
- #2389 Create plaintext GtfAdapter in plugins/gtf (@teresam856)
- #2443 Support plaintext fasta on desktop by dynamically creating a FAI file on the fly (@cmdcolin)
- #2479 Allow gzipped Gff3Adapter input and use 512MB limit (@cmdcolin)
- #2467 Set default session dialog redesign (@cmdcolin)
- #2461 Add assembly manager back into tools menu on jbrowse-desktop (@cmdcolin)
- #2442 Add simple loading screen for LGV (@cmdcolin)
- Other
- #2494 Add polyfill for text-index compatibility with node 10 (@cmdcolin)
- #2492 Fix ability to open breakpoint split view from a BEDPE row in SV inspector (@cmdcolin)
- #2480 Fix refName renaming on VcfAdapter for files that don't have ##contig lines (@cmdcolin)
- #2469 Fix embedded crash when opening dialogs (@garrettjstevens)
- #2451 Fix issue with intermittent text-index failures and improve speed (@cmdcolin)
- #2439 Fix adding plugins on desktop (@cmdcolin)
- #2426 Fix CLI create/upgrade failing to find the latest release (@cmdcolin)
core
- #2446 Improve some CLI --help messages (@cmdcolin)
- #2437 Add example of defining and using a plugin with the embedded component (@cmdcolin)
- #2430 Website optimize for less layout shift (@cmdcolin)
core- #2445 Create core snapshot error message component (@cmdcolin)
- #2288 Add extra re-exports for default modules (@garrettjstevens)
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
Packages in this release
core- #2413 Bundle size savings (@cmdcolin)
- #2390 Support plain text (non-tabix'ed) GFF files with new Gff3Adapter (@teresam856)
- #2384 Allow docking the drawer on the left side of the screen (@cmdcolin)
- #2387 Add bulk delete of sessions on jbrowse-desktop (@cmdcolin)
- #2279 Add ability to access authenticated resources using pluggable internet accounts framework (@peterkxie)
- Other
- #2388 Create "quickstart list" on jbrowse-desktop which users can add to (@cmdcolin)
- #2385 Ensure all dependencies are properly specified in package.json files using eslint-plugin-import (@cmdcolin)
- #2373 Add auto update functionality for jbrowse-desktop (@cmdcolin)
- #2369 Add tooltip with track description to track selector (@garrettjstevens)
- #2258 Update admin-server to accept value from ?config= so that multiple configs could be edited (@cmdcolin)
- #2321 Add show descriptions toggle box to most feature tracks (@cmdcolin)
- Other
- #2355 Allow prefix and exact matches jb1 text search (@cmdcolin)
- #2348 Fix ability to use JB1 backcompat text search adapter (@teresam856)
- #2322 Fix install plugin workflow and error handling on desktop, update to electron 15 (@cmdcolin)
- #2329 Fix bugs preventing embedded circular genome view from rendering in some circumstances (@garrettjstevens)
core
- #2407 Update website for jbrowse-desktop release (@carolinebridge-oicr)
- #2328 Use ../ for all doc links and use trailing slash to fix links (@cmdcolin)
- Other
core- #2379 Bump typescript to 4.4.3 (@cmdcolin)
- #2363 Add some typescripting of some MST models and components (@cmdcolin)
- #2351 Use main "module" field instead of "browser" from dependency package json files electron builds (@cmdcolin)
- #2323 Remove session related menu items from jbrowse-desktop (@cmdcolin)
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Peter Xie (@peterkxie)
- Sebastian Benjamin (@hextraza)
- Teresa Martinez (@teresam856)
Packages in this release
- Other
- #2287 Use react-popper to reduce tooltip lag on pages with many elements (@cmdcolin)
- #2294 Don't rely on SVTYPE=BND for breakend split view options and thicker mouseover chords on circular views (@cmdcolin)
- #2272 Auto adjust box RefNameAutocomplete width based on refName length (@cmdcolin)
- #2243 Import bookmarks functionality for grid bookmark widget (@cmdcolin)
core
core- Other
- #2300 Release announcement draft v1.4.0 (@teresam856)
- #2310 Add cancer demos to the demos page on website (@cmdcolin)
- #2253 Add note about legacy-peer-deps to embedded component readme (@cmdcolin)
- #2262 Add more MDX documentation pages to @jbrowse/react-linear-genome-view storybooks (@cmdcolin)
- Colin Diesh (@cmdcolin)
- Teresa Martinez (@teresam856)
- @Akusem
Failed NPM upload, partial release
Failed NPM upload, partial release
Broken releases missing some packages
Broken releases missing some packages
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/react-circular-genome-view | https://www.npmjs.com/package/@jbrowse/react-circular-genome-view |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
Packages in this release
- Other
- #2163 Add new embeddable React Circular Genome View (@garrettjstevens)
- #2229 Use extendPluggableElement for context menu items (@garrettjstevens)
- #2233 Add optional chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files with many refseqs (@cmdcolin)
- #2199 Make the BED parser not interpret general tab delimited data as BED12 (@cmdcolin)
- #2241 Restore previous window location when re-opening on desktop (@garrettjstevens)
- #2203 Add a helpful message if there is a 404 on config.json error (@cmdcolin)
- #2204 Hide reads with unmapped flag by default in alignments tracks (@cmdcolin)
- #2198 Add better inversion visualization to read vs reference visualizations (@cmdcolin)
- #2154 Add UMD build of react-linear-genome-view for plain-js use (@garrettjstevens)
core- #2236 Detect assembly loading error and encapsulate error instead of failing at app level (@cmdcolin)
- #2029 Polish desktop builds (@elliothershberg)
- #2140 New core plugin that adds a "bookmarked regions" list widget, new extension points system (@elliothershberg)
core- #2245 Fix missing regenerator runtime dependency in core (@garrettjstevens)
- #2202 Fixed a crash when an incompatible adapter is selected for provided data in 'open track' (@carolinebridge-oicr)
- #2197 Fix handle leak for killed worker checker (@cmdcolin)
- Other
- #2192 Update Linear Genome View embedding docs (@garrettjstevens)
core- #2057 Use idMaker for dataAdapterCache key for faster FromConfigAdapter performance (@cmdcolin)
- #2231 Export offscreenCanvasUtils (@cmdcolin)
- #2226 Use superRenderProps and superTrackMenuItems for better simulated inheritance model (@cmdcolin)
- #1874 Add aborting to CoreGetFeatures rpcManager call (@cmdcolin)
- Other
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
Packages in this release
- Other
core- #2141 Update to @material-ui/[email protected] (@cmdcolin)
- #2126 Allow opening plaintext .vcf files from the "Add track" workflow (@cmdcolin)
- Other
- #2159 Stop local storage quota-exceeded errors preventing the app from starting (@cmdcolin)
- #2161 Remove outline from clicking on SVG chord tracks (@cmdcolin)
- #2157 Fix rendering of negative strand alignment modifications/methylation (@cmdcolin)
- #2131 Fix mouseovers/click handlers after "force load" button pressed (@cmdcolin)
- #2128 Fix using the "Color by modifications" setting on files that need ref renaming (@cmdcolin)
- #2115 Fix bug where sometimes plugin could not be removed from UI (@garrettjstevens)
- #2119 Fix loading indicator on the reference sequence selector getting stuck (@cmdcolin)
core- #2101 Fix behavior of the end-of-list indicator in refNameAutocomplete to always display as a disabled item (@teresam856)
- Other
- #2152 Remove storybook symlink workaround (@garrettjstevens)
core
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/desktop | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- Other
core
- #2109 Make sure to wait for assembly to load before downloading canonical refnames in SV inspector (@cmdcolin)
- #2111 Fix "Can't
resolve '@jbrowse/plugin-legacy-jbrowse'" in
@jbrowse/react-linear-genome-view(@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Packages in this release
core- #2094 More usage of typography to improve consistent text styling (@cmdcolin)
- #2068 Add non-indexed and plaintext VCF Adapter to variants plugin (@carolinebridge-oicr)
- #2067 Better error message if a file location has an empty string (@garrettjstevens)
- #2064 Export offscreenCanvasPonyfil from core/util (@garrettjstevens)
- #2060 Improve performance with large numbers of reference sequences by using MST volatiles (@cmdcolin)
- #2050 Configurable app logo for web (@elliothershberg)
- Other
- #2104 Use ScopedCssBaseline to help style the embedded component (@cmdcolin)
- #2015 Deprecate
ThemeProvider in
@jbrowse/react-linear-genome-view(@garrettjstevens)
- Other
- #2097 Improve speed for laying out features for embedded/mainthreadrpc scenarios (@cmdcolin)
- #2096 Fix issue with page reload after editing session title (@cmdcolin)
- #2074 Fix support for opening local files in spreadsheet/SV inspector (@cmdcolin)
- #2061 Fix issue with using --force error when no track was previously loaded (@cmdcolin)
- #2024 Flip drawing of negative strand PAF features in linear synteny and dotplot views (@cmdcolin)
- #2023 Fix infinite loop in adding some plugins on desktop (@cmdcolin)
- #2019 Fix session import to use blob map for opening local files (@cmdcolin)
core- #2071 Add indicator to the end of ref name dropdown to suggest user to type the searchbox for more (@teresam856)
- #2056 Fix infinite recursion in FromConfigAdaptor by avoiding mutating the passed in data when using SimpleFeature (@cmdcolin)
- #2018 Fix 3'UTR in sequence detail panels when no UTRs are in gff (@cmdcolin)
core- #1967 Omit configurationSchema snapshot when it matches the default (@garrettjstevens)
- #2078 Restore eslint rule for no-unused-vars (@cmdcolin)
- #2051 Add missing named exports to shared core modules (@garrettjstevens)
- #2045 Add basic architecture for text searching (@teresam856)
- Other
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-filtering | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-legacy-jbrowse | |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- Other
core- #1982 Allow manually specifying adapter type if filename does not match expected pattern (@cmdcolin)
- #1975 Allow local files on the users computer to be opened as tracks in jbrowse-web (@cmdcolin)
- #1865 Show modified bases using MM and MP/ML tags in BAM/CRAM (@cmdcolin)
- #1984 Better feature details when there are short arrays of json supplied as feature data (@cmdcolin)
- #1931 Create in app graphical plugin store (@elliothershberg)
core- #1985 Avoid error calculating UTR on features that have no exon subfeatures (@cmdcolin)
- #1954 Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering (@cmdcolin)
- #1963 Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components (@cmdcolin)
- #1945 Fix hic not being able to render due to incorrect lazy loading (@cmdcolin)
- Other
- #2002 Add @jbrowse/img to homepage (@cmdcolin)
- #2007 Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details (@cmdcolin)
- #1976 reorganize the demo page to emphasize the cancer sv demo more (@rbuels)
- #1952 Add demo for 1000 genomes extended trio dataset to website (@cmdcolin)
- #1862 Add example for using a build-time included plugin to storybook (@cmdcolin)
- Other
core,development-tools
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Robert Buels (@rbuels)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-filtering | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-legacy-jbrowse | |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
core- #1125 Export SVG (@cmdcolin)
- #1867 Virtualized tree for tracklist to support having thousands of tracks (@cmdcolin)
- #1660 Allow connections to have multiple assemblies (@garrettjstevens)
- #1864 Add Material UI's DataGrid to re-exports (@garrettjstevens)
- #1875 Make drawer widget titles stay visible when scrolling inside the widget (@cmdcolin)
- #1877 Add ability to copy the text produced by the feature details sequence panel to MS Word/Google Docs and preserve styling (@cmdcolin)
- #1854 Make "About track" dialog available from tracklist and for non-LGV tracks (@cmdcolin)
- #1853 Add mouseovers in feature details that show field descriptions for VCF fields (@cmdcolin)
- Other
- #1892 Create new JB2 plugin store (@elliothershberg)
- #1901 Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink (@cmdcolin)
- #1850 Add true breakend ALT strings to the feature details panel (@cmdcolin)
- #1878 Add --delete to set-default-session, fix --session (@garrettjstevens)
- #1861 Change Alignments track "Fade mismatches by quality" setting to a separate config param and made it less strict (@cmdcolin)
core- #1924 Fix import of BED and navToLocString from spreadsheet views (@cmdcolin)
- #1918 Fix issue with some falsy values being hidden in feature details (@cmdcolin)
- #1911 Fix breakpoint split view visualizations for files that need ref renaming (e.g. chr1 vs 1) (@cmdcolin)
- #1904 Fix issue with synteny polygons displaying slightly offset (@cmdcolin)
- #1884 Fix rIC ponyfill for use on Safari (@cmdcolin)
- Other
- #1912 Fix reloading of local sessions when using React.StrictMode (@cmdcolin)
- #1900 Make clicking away from autocomplete popup on track container work (@cmdcolin)
- #1878 Add --delete to set-default-session, fix --session (@garrettjstevens)
- #1871 Fix crash on dotplot/linear synteny import form and when closing linear synteny track (@cmdcolin)
- #1860 Fix alignments read filter jexl syntax (@cmdcolin)
- #1914 Use MDX to add proper image captions in web and pdf documentation (@cmdcolin)
- #1855 Add download page in website header and new super-quick-start guide (@cmdcolin)
core- #1932 Update analytics and share API URLs to refer to more stable locations (@peterkxie)
- #1888 More lazy loading of react components to reduce bundle size (@cmdcolin)
- #1790 Allow MainThreadRpcDriver to skip serialization during RPC, improving main-thread rendering performance (@garrettjstevens)
- Other
- #1926 Update website to link to demos on cloudfront for better compression (@cmdcolin)
- #1868 Export XYPlotRenderer and configSchema (@elliothershberg)
- #1863 Update @gmod/indexedfasta (@cmdcolin)
- #1795 Make LinearAlignmentsDisplay fully configurable in the UI (@garrettjstevens)
- #1822 Let React LGV navigate without setting displayedRegion first (@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Peter Xie (@peterkxie)
Packages in this release
core- #1846 Improve copy+paste in the data grids for feature details (@cmdcolin)
- #1814 Add ability to get promoter sequence and intron sequence for genes from the feature details panel (@cmdcolin)
- #1816 Remove some animation effects (@cmdcolin)
- #1778 Adds dropdown to show drawer widget stack (@teresam856)
- #1685 Change callbacks language from JavaScript to Jexl (@peterkxie)
- Other
- #1831 Add dialog for launching breakpoint split view from variant feature details (@cmdcolin)
- #1803 Transcript and gene glyphs can now display implied UTRs, active by default (@cmdcolin)
- #1808 Add another heuristic for returning gene features from BigBed (@cmdcolin)
- #1774 Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view (@cmdcolin)
core- #1811 Check for existence of window more robustly to allow in SSR or node applications (@elliothershberg)
- #1793 Fix dotplot rendering outside it's allowed bounds (@cmdcolin)
- #1783 Add hic aborting and fix remoteAbort signal propagation (@cmdcolin)
- #1723 A few bugfixes (@garrettjstevens)
- Other
- #1824 Add storybook docs page for nextjs usage (@elliothershberg)
- #1770 1469 storybook deploy (@elliothershberg)
- #1807 Update developer guide to cover displays, and highlight working external plugins (@cmdcolin)
- #1779 Collaborative release announcement editing (@rbuels)
- #1791 Add a couple more demos for our live version with MDX (@cmdcolin)
- Other
- #1820 Create v1.1.0.md, draft of release announcements (@garrettjstevens)
- #1823 Add note about previewing changelog to CONTRIBUTING.md (@garrettjstevens)
core
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Peter Xie (@peterkxie)
- Robert Buels (@rbuels)
- Teresa Martinez (@teresam856)
Packages in this release
core- #1758 Add ability to get stitched together CDS, protein, and cDNA sequences in feature details (@cmdcolin)
- #1721 Manually adjust feature height and spacing on alignments track (@cmdcolin)
- #1728 Add list of loaded plugins to the "About widget" (@rbuels)
- #1711 Add plugin top-level configuration (@teresam856)
- #1699 Add sequence track for both read and reference genome in the "Linear read vs ref" comparison (@cmdcolin)
- #1701 Add clickable navigation links to supplementary alignments/paired ends locations and BND/TRA endpoints in detail widgets (@cmdcolin)
- #1601 Add ability to color by per-base quality in alignment tracks (@cmdcolin)
- #1640 Move stats calculation to BaseFeatureAdapter (@cmdcolin)
- #1588 Add "Get sequence" action to LGV rubber-band (@teresam856)
- Other
- #1743 Add color picker and choice of summary score style for wiggle track (@cmdcolin)
- #1763 Add a "CSS reset" to jbrowse-react-linear-genome-view to prevent parent styles from outside the component leaking in (@cmdcolin)
- #1756 Split alignments track menu items into "Pileup" and "SNPCoverage" submenus (@cmdcolin)
- #1742 Add ability to display crosshatches on the wiggle line/xyplot renderer (@cmdcolin)
- #1736 Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs (@cmdcolin)
- #1394 Add new menu items for show/hide feature labels, set max height, and set compact display mode (@cmdcolin)
- #1720 Standardize phred qual scaling between BAM and CRAM and add option to make mismatches render in a lighter color when quality is low (@cmdcolin)
- #1704 Add "Show all regions in assembly" to import form and make import form show entire region when refName selected (@cmdcolin)
- #1687 Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events (@cmdcolin)
- #1695 Improve zoomed-out display of quantitative displays tracks when bicolor pivot is active (@cmdcolin)
- #1680 Add on click functionality to quantitative track features (@teresam856)
- #1630 Get column names from BED tabix files and other utils for external jbrowse-plugin-gwas support (@cmdcolin)
- #1709 Improve sorting and filtering in variant detail widget (@cmdcolin)
- #1688 Bold insertion indicator for large insertions on pileup track (@cmdcolin)
- #1669 Allow plain json encoding of the session in the URL (@cmdcolin)
- #1642 Enable locstring navigation from LGV import form (@teresam856)
- #1655 Add GFF3Tabix and BEDTabix inference to JB1 connection (@garrettjstevens)
- #1643 Add an offset that allows all wiggle y-scalebar labels to be visible (@cmdcolin)
- #1632 Displays warnings when receiving a session with custom callbacks (@peterkxie)
- #1615 Increase pileup maxHeight (@cmdcolin)
- #1624 GCContent adapter (@cmdcolin)
- #1614 Add insertion and clip indicators to SNPCoverage views (part of Alignments tracks) (@cmdcolin)
- #1610 Display error message from dynamodb session sharing error (@cmdcolin)
- Other
- #1777 Quick fix for block error (@cmdcolin)
- #1748 External plugins load after confirming config warning (@peterkxie)
- #1750 Fix pileup sorting when using string tag (@cmdcolin)
- #1747 Fix the position of the popup menu after rubberband select when there is a margin on the component e.g. in embedded (@cmdcolin)
- #1736 Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs (@cmdcolin)
- #1731 Fix alignment track ability to remember the height of the SNPCoverage subtrack on refresh (@cmdcolin)
- #1719 Fix for navigation past end of chromosome (@cmdcolin)
- #1698 Fix rendering read vs ref comparisons with CIGAR strings that use = sign matches (@cmdcolin)
- #1697 Fix softclipping configuration setting causing bases to be missed (@cmdcolin)
- #1689 Disable copy/delete menu items for reference sequence track (@teresam856)
- #1682 Fix parsing of BED and BEDPE files with comment header for spreadsheet view (@cmdcolin)
- #1679 Fix issue with using launching the add track widget on views that are not displaying any regions (@teresam856)
- #1642 Enable locstring navigation from LGV import form (@teresam856)
- #1626 Bug Fix: specify assembly in locstring (@teresam856)
- #1619 Fix overview scale polygon not appearing properly in some cases (@cmdcolin)
core
- #1725 JBrowseR release (@elliothershberg)
- #1677 Config guide updates (@elliothershberg)
- #1665 Add Nextstrain COVID storybook (@elliothershberg)
- #1670 typo in developer guide docs (@teresam856)
- #1592 Website copy edits (@rbuels)
- #1646 Fix "See code" link in CLI docs (@garrettjstevens)
- #1618 Add whole-genome view and color/sort alignments tutorials to user guide (@cmdcolin)
- Other
- #1666 Move "mouseover" config from BaseLinearDisplay to LinearBasicDisplay display (@garrettjstevens)
- #1751 Make the variant display derive from the feature display (@cmdcolin)
- #1716 Stringify labels before adding to rendering to avoid undefineds on label.length (@cmdcolin)
- #1713 Add console.error log in block setError (@cmdcolin)
- #1663 Make LGV "initialized" not depend on displayedRegions (@garrettjstevens)
- #1672 Fix import forms crashing if there are no assemblies (@cmdcolin)
- #1644 Bump electron from 9.3.1 to 9.4.0 (@dependabot[bot])
- #1641 Remove codecov pr annotations (@cmdcolin)
- #1609 Add extra checks for release script (@peterkxie)
core- #1762 Add requestidlecallback ponyfill in @jbrowse/core/util (@cmdcolin)
- #1629 Add RegionsAdapter/SequenceAdapter, reorganize base adapters (@garrettjstevens)
- #1625 Make renderArgs consistent and don't duplicate data (@garrettjstevens)
- #1414 Typescriptify and MST'ify the add track workflow (@cmdcolin)
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Liu ZH (@sqwwwok)
- Peter Xie (@peterkxie)
- Robert Buels (@rbuels)
- Teresa Martinez (@teresam856)
Packages in this release
- Other
- #1560 Provide a dialog to add extra genomic context for linear read vs. ref visualization (@elliothershberg)
- #1604 Add ability to filter for read name to the alignments filter dialog (@cmdcolin)
- #1599 Replace 'show all regions' with 'show all regions in assembly' (@cmdcolin)
- #1595 Admin server GUI enhancements (@elliothershberg)
- #1584 Restructure demo page and release cancer demo (@elliothershberg)
- #1579 Create
--branch and --nightly flags for
jbrowse createandjbrowse upgradecommands (@cmdcolin) - #1575 Improve mobx-state-tree type validation errors (@cmdcolin)
- #1574 Make softclip indicator black if no seq available (@cmdcolin)
- #1554 Coloring options with simple color for tag (@peterkxie)
- #1565 Rename jbrowse cli add-track --type to --trackType (@cmdcolin)
- #1558 Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo (@cmdcolin)
- #1533 Display file headers in pre tag in about dialogs and bump @gmod/bam and @gmod/tabix package versions (@cmdcolin)
- #1541 Add more info about adding a PAF file to the synteny import form (@cmdcolin)
- #1509 Combine Search and Dropdown component on LGV (@teresam856)
- #1530 Add spreadsheet filter support for derived columns (@elliothershberg)
- #1483 Add session export to and import from file (@garrettjstevens)
- #1519 Add autoSql to the bigBed "About this track" dialog (@cmdcolin)
core- #1531 Add track menu options for autoscale, log scale, histogram fill, setting min/max score, and zoom level/resolution for wiggle/snpcoverage tracks (@cmdcolin)
- #1473 Color, filter, and sort options for the alignments (@cmdcolin)
- #1576 Add location string to tooltip for wiggle and SNPCoverage tracks (@cmdcolin)
- #1529 Display subfeatures in feature details widget (@cmdcolin)
core,development-tools- #1578 Update build system for external plugins (@garrettjstevens)
- Other
- #1608 Take into account offsetX of the rubberband on scalebar zooming (@cmdcolin)
- #1597 Fix crash when there are undefined references in the state tree e.g. when a track is deleted but still referred to by a session (@peterkxie)
- #1598 Disable 'copy to clipboard' while share url being generated (@peterkxie)
- #1589 Fix the display of trackhub registry results (@cmdcolin)
- #1573 Update hic-straw to fix error for hic files with many scaffolds (@cmdcolin)
- #1563 Remove softclip and hardclip from being counted as SNPs in the SNPCoverage (@cmdcolin)
- #1559 Avoid errors from breakpoint split view related to getBoundingClientRect on null track (@cmdcolin)
- #1540 Fix memory leak when side scrolling LGV blocks (@cmdcolin)
- #1534 Fix breakpoint split view showing too many connections for paired end ends (@cmdcolin)
- #1524 Move loading flag for spreadsheet import wizard to volatile to avoid it persisting across refresh (@cmdcolin)
- #1521 Add missing dep to react-linear-genome-view (@garrettjstevens)
core
- #1594 Add GFF3 example to quickstart (@cmdcolin)
- #1581 Add some features that are missing from jbrowse 2 to the feature comparison table (@cmdcolin)
- #1558 Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo (@cmdcolin)
- #1537 Add CONTRIBUTING.md with tips for getting started with codebase (@cmdcolin)
- #1606 Upgrade @testing-library/react and improve test reliability (@cmdcolin)
- #1555 Remove the TextDecoder/TextEncoder polyfill (@cmdcolin)
- #1522 Update oclif and remove now unnecessary file copy (@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Peter Xie (@peterkxie)
- Teresa Martinez (@teresam856)
- @Akusem
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | https://www.npmjs.com/package/@jbrowse/plugin-circular-view |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-filtering | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-legacy-jbrowse | |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/protein-widget | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
core- #1513 Add a custom scrollbar that overrides the auto-hiding behavior of scrollbars on OSX (@elliothershberg)
- Other
- #1514 react-linear-genome-view bug fixes (@garrettjstevens)
- #1517 Fix the use of filtering display on desktop (@cmdcolin)
- #1512 Fix setting maxDisplayedBpPerPx for pileup display, helps prevent too large an area from being rendered (@cmdcolin)
- #1442 Change track selector togglebutton to normal button (@cmdcolin)
- #1506 Fix horizontally flipped translation frames position (@cmdcolin)
- #1501 Fix CLI to allow jbrowse create to download newer monorepo tag format (@cmdcolin)
core
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-filtering | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-legacy-jbrowse | |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/protein-widget | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
- Other
- #1462 Allow importing gzip and bgzip files in the spreadsheet and SV inspector (@cmdcolin)
- #1460 Add support for more bigBed subtypes and fallback for unsupported types (@peterkxie)
- #1455 Add the ability to use connection across refreshes in jbrowse-web using session connections (@peterkxie)
- #1439 1381 improve assembly add form (@elliothershberg)
- #1433 Make add track warning a bit more lenient (@garrettjstevens)
- #1420 Add the assembly manager feature to jbrowse-desktop (@elliothershberg)
core- #1458 Add three frame translation to the sequence track (@cmdcolin)
- #1453 Change "Factory reset" to "Reset session" in jbrowse-web (@teresam856)
- #1441 New icon for the track selector (@cmdcolin)
- #1438 Improve assembly loading time by moving to main thread (@cmdcolin)
- #1434 Create separate config schema for ReferenceSequenceTrack (@elliothershberg)
core- Other
- #1489 Fix long read vs ref CIGAR rendering for horizontally flipped synteny view (@cmdcolin)
- #1460 Add support for more bigBed subtypes and fallback for unsupported types (@peterkxie)
- #1472 Wait on assemblies that are being tracked by the assemblyManager only (@cmdcolin)
- #1466 Avoid rendering the display and renderer settings in the about this track dialog (@cmdcolin)
- #1461 Fix usage of jbrowse-cli on node 10.9 related to fs.promises (@cmdcolin)
- #1452 Bug: search box disappears from LGV header on smaller widths (@teresam856)
- #1432 Make global variables window.JBrowseSession and window.JBrowseRootModel available in jbrowse-web (@teresam856)
- #1431 Fix connection tracks not showing up in track selector (@garrettjstevens)
- #1428 Fix the listVersions behavior of the jbrowse-cli returning duplicate entries (@cmdcolin)
- #1422 Fix crash from empty ALT field in VCF (@cmdcolin)
- #1413 Fix ability to add CRAM tracks using the web based add-track GUI (@cmdcolin)
- #1435 Updates to quickstart guides (@garrettjstevens)
- Other
- #1437 Use lerna-changelog for changelog generation (@cmdcolin)
- #1465 Establish minimum node version of 10.4 for using jbrowse-cli tools (@cmdcolin)
- #1454 Fix GH workflow build (@elliothershberg)
- #1448 Move building and testing from Travis to GitHub Workflow (@garrettjstevens)
- #1450 Fix website build (@garrettjstevens)
core- #1468 Have assembly manager get plugin manager from factory function args (@garrettjstevens)
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
- @peterkxie