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