@jbrowse/plugin-bed - npm Package Versions

1.3.1 (2021-07-06)

<details><summary>Packages in this release</summary> <p>

| 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-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-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-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 | |

</p> </details>

:rocket: Enhancement

• 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)

:bug: Bug Fix

• 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)

:house: Internal

• 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
  • #2070 Remove service worker from jbrowse-web (@cmdcolin)
  • #1995 Pass initialDisplay snapshot via separate param to showTrack (@cmdcolin)

Committers: 5

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

1.2.0 (2021-05-03)

<details><summary>Packages in this release</summary> <p>

| 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 | |

</p> </details>

:rocket: Enhancement

• 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)

:bug: Bug Fix

• 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)

:memo: Documentation

• #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)

:house: Internal

• 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)

Committers: 4

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Peter Xie (@peterkxie)

1.1.0 (2021-03-29)

<details><summary>Packages in this release</summary> <p>

| 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-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-menus | | | @jbrowse/plugin-protein | | | @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-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 | |

</p> </details>

:rocket: Enhancement

• 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)

:bug: Bug Fix

• 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
  • #1815 Clear tracks when using "Return to import form" (@cmdcolin)
  • #1819 Standardized sentence casing on drawer widget titles (@cmdcolin)
  • #1796 Bump generic-filehandle for fixing CORS errors from Chrome cache pollution (@cmdcolin)

:memo: Documentation

• #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)

:house: Internal

• Other
  • #1820 Create v1.1.0.md, draft of release announcements (@garrettjstevens)
  • #1823 Add note about previewing changelog to CONTRIBUTING.md (@garrettjstevens)
• core
  • #1834 Change jbrowse-components monorepo default branch from 'master' to 'main' (@rbuels)

Committers: 6

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Peter Xie (@peterkxie)
• Robert Buels (@rbuels)
• Teresa Martinez (@teresam856)

1.0.4 (2021-03-08)

<details><summary>Packages in this release</summary> <p>

| 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-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-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-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 | |

</p> </details>

:rocket: Enhancement

• 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)

:bug: Bug Fix

• 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
  • #1714 Fix ability to add a PAF on initial dotplot view creation (@cmdcolin)
  • #1657 Fix for track using assembly alias not displaying (@garrettjstevens)
  • #1620 Add error reporting on a worker failure (@cmdcolin)

:memo: Documentation

• #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)

:house: Internal

• 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)

Committers: 7

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Liu ZH (@sqwwwok)
• Peter Xie (@peterkxie)
• Robert Buels (@rbuels)
• Teresa Martinez (@teresam856)

1.0.3 (2021-01-11)

<details><summary>Packages in this release</summary> <p>

| 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-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | @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-menus | | | @jbrowse/plugin-spreadsheet-view | | | @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 | |

</p> </details>

:rocket: Enhancement

• 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 create and jbrowse upgrade commands (@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)

:bug: Bug Fix

• 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
  • #1587 Fix positioning of scalebar tooltips, overview scalebar plotting, and refName label positioning when displaying many regions (@cmdcolin)
  • #1547 Fix analytics crashing when using plugins (@cmdcolin)

:memo: Documentation

• #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)

:house: Internal

• #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)

Committers: 6

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Peter Xie (@peterkxie)
• Teresa Martinez (@teresam856)
• @Akusem

v1.0.2 (2020-12-02)

<details><summary>Packages in this release</summary> <p>

| 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 | |

</p> </details>

:rocket: Enhancement

• core
  • #1513 Add a custom scrollbar that overrides the auto-hiding behavior of scrollbars on OSX (@elliothershberg)

:bug: Bug Fix

• 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
  • #1505 Fix loading of local files in jbrowse-desktop (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)

v1.0.1 (2020-11-25)

<details><summary>Packages in this release</summary> <p>

| 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 | |

</p> </details>

:rocket: Enhancement

• 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)

:bug: Bug Fix

• core
  • #1491 Fix ability to add a PAF synteny track with add-track (@cmdcolin)
  • #1470 Avoid rendering the literal string 'null' in the feature details (@cmdcolin)
• 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)

:memo: Documentation

• #1435 Updates to quickstart guides (@garrettjstevens)

:house: Internal

• 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)

Committers: 5

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Teresa Martinez (@teresam856)
• @peterkxie