@jbrowse/plugin-bed - npm Package Versions

1.5.3 (2021-12-21)

| Package | Download | | -------------------------- | -------------------------------------------------------- | | @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |

:bug: Bug Fix

• development-tools
  • #2600 Fix broken published build of jbrowse/development-tools (@garrettjstevens)

Committers: 1

• Garrett Stevens (@garrettjstevens)

1.5.2 (2021-12-20)

| 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-arc | | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-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-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @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-menus | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @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/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 | |

:rocket: Enhancement

• 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)

:bug: Bug Fix

• 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)

:memo: Documentation

• #2522 Add circular genome view storybook (@cmdcolin)
• #2508 Update docs for embedded components (@teresam856)
• #2495 Improve organization on docs landing page (@cmdcolin)

:house: Internal

• core
  • #2597 Fix flaky tests related to auth and canvas image snapshots (@cmdcolin)
  • #2504 Spreadsheet change jbrequire to es6 imports (@cmdcolin)

Committers: 6

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Peter Xie (@peterkxie)
• Sebastian Benjamin (@hextraza)
• Teresa Martinez (@teresam856)

1.5.1 (2021-11-04)

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @jbrowse/plugin-authentication | | | @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed | | @jbrowse/plugin-breakpoint-split-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-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @jbrowse/plugin-gtf | https://www.npmjs.com/package/@jbrowse/plugin-gtf | | @jbrowse/plugin-hic | | | @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-rdf | | | @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-sv-inspector | | | @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 | |

:rocket: Enhancement

• 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)

:bug: Bug Fix

• 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
  • #2457 Fix linear synteny view import form failure (@cmdcolin)
  • #2444 Fix crash when chromSizesLocation not specified when loading TwoBitAdapter in GUI (@cmdcolin)

:memo: Documentation

• #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)

:house: Internal

• core
  • #2445 Create core snapshot error message component (@cmdcolin)
  • #2288 Add extra re-exports for default modules (@garrettjstevens)

Committers: 4

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Teresa Martinez (@teresam856)

1.5.0 (2021-10-18)

| Package | Download | | --------------------------------------- | ----------------------------------------------------------------- | | @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core | | @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | @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-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-hic | | | @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-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-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 | |

:rocket: Enhancement

• 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)

:bug: Bug Fix

• 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
  • #2352 Better keyboard navigations on text search autocomplete component (@cmdcolin)
  • #2332 Fix ability to use LocalFile on nodejs-based apps e.g. @jbrowse/img (@cmdcolin)

:memo: Documentation

• #2407 Update website for jbrowse-desktop release (@carolinebridge-oicr)
• #2328 Use ../ for all doc links and use trailing slash to fix links (@cmdcolin)

:house: Internal

• Other
  • #2382 Export RefNameAutocomplete and ViewModel from LinearGenomeView for downstream usage (@hextraza)
  • #2336 Add jbrowse-img to monorepo (@cmdcolin)
  • #2324 Remove unused wrapForRpc functionality (@cmdcolin)
• 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)

Committers: 6

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Peter Xie (@peterkxie)
• Sebastian Benjamin (@hextraza)
• Teresa Martinez (@teresam856)

1.4.4 (2021-09-14)

| 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-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-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @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-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | @jbrowse/plugin-spreadsheet-view | | | @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg | | @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/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 | |

:rocket: Enhancement

• 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
  • #2247 New jbrowse-desktop start screen design (@cmdcolin)
  • #2254 Better error reporting from web worker and chrom sizes adapter errors (@cmdcolin)
  • #1881 Add new text searching functionality to core, with jbrowse text-index CLI command to generate trix index (@teresam856)

:bug: Bug Fix

• core
  • #2320 Fix issue where add track widget doesn't infer adapters on second usage (@cmdcolin)
  • #2250 Prevent the ToggleButton for the FileSelector toggling to local file when only URL should be available (@cmdcolin)
• Other
  • #2309 Fix mouseover selection appearing across unrelated blocks (@cmdcolin)
  • #2283 Fix ability for the variant detail panel to create breakpoint split view for <TRA> elements (@cmdcolin)
  • #2268 Fix autocomplete height on small displays (@cmdcolin)

:memo: Documentation

• #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)

:house: Internal

• #2263 Force publish all packages on release (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Teresa Martinez (@teresam856)
• @Akusem

1.4.3

Failed NPM upload, partial release

1.4.2

Failed NPM upload, partial release

1.4.1

Broken releases missing some packages

1.4.0

Broken releases missing some packages

1.3.4 (2021-08-23)

| 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-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | @jbrowse/plugin-dotplot-view | | | @jbrowse/plugin-grid-bookmark | https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark | | @jbrowse/plugin-hic | | | @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-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/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli | | @jbrowse/desktop | | | @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 | |

:rocket: Enhancement

• 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)

:bug: Bug Fix

• 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
  • #2208 Fix issue where collapsed categories were not remembered after toggling a track (@cmdcolin)

:memo: Documentation

• #2192 Update Linear Genome View embedding docs (@garrettjstevens)

:house: Internal

• 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
  • #2232 Remove filtering display type from core (@cmdcolin)
  • #2234 Add rootModel setError on jbrowse-desktop (@cmdcolin)

Committers: 4

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)