@jbrowse/plugin-bed

JBrowse 2 bed adapters, tracks, etc.

1.0.4
Source
npm

Version published: 4 years ago

Weekly downloads: 442; decreased by-33.83%

Maintainers: 6

Weekly downloads

Created: 4 years ago

The README file is missing

1.0.4 (2021-03-08)

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

| Package | --------------------------------------- | @jbrowse/core | @jbrowse/plugin-alignments | @jbrowse/plugin-bed | @jbrowse/plugin-breakpoint-split-view | @jbrowse/plugin-circular-view | @jbrowse/plugin-config | @jbrowse/plugin-data-management | @jbrowse/plugin-dotplot-view | @jbrowse/plugin-filtering | @jbrowse/plugin-gff3 | @jbrowse/plugin-legacy-jbrowse | @jbrowse/plugin-linear-comparative-view | @jbrowse/plugin-linear-genome-view | @jbrowse/plugin-lollipop | @jbrowse/plugin-menus | @jbrowse/plugin-sequence | @jbrowse/plugin-spreadsheet-view | @jbrowse/plugin-sv-inspector | @jbrowse/plugin-svg | @jbrowse/plugin-variants | @jbrowse/plugin-wiggle | @jbrowse/cli | @jbrowse/desktop | @jbrowse/protein-widget | @jbrowse/react-linear-genome-view | @jbrowse/web | Download | | ---------------------------------------------------------------- | | https://www.npmjs.com/package/@jbrowse/core | | https://www.npmjs.com/package/@jbrowse/plugin-alignments | | https://www.npmjs.com/package/@jbrowse/plugin-bed | | | | https://www.npmjs.com/package/@jbrowse/plugin-circular-view | | https://www.npmjs.com/package/@jbrowse/plugin-config | | https://www.npmjs.com/package/@jbrowse/plugin-data-management | | | | | | https://www.npmjs.com/package/@jbrowse/plugin-gff3 | | | | | | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view | | | | | | https://www.npmjs.com/package/@jbrowse/plugin-sequence | | | | | | https://www.npmjs.com/package/@jbrowse/plugin-svg | | https://www.npmjs.com/package/@jbrowse/plugin-variants | | https://www.npmjs.com/package/@jbrowse/plugin-wiggle | | https://www.npmjs.com/package/@jbrowse/cli | | | | | | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view | | |

</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)

Keywords

FAQs

What is @jbrowse/plugin-bed?

Is @jbrowse/plugin-bed popular?

Is @jbrowse/plugin-bed well maintained?

Package last updated on 08 Mar 2021

Did you know?

Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.

Install