@jbrowse/plugin-bed

JBrowse 2 bed adapters, tracks, etc.

1.0.3
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

1.0.3 (2021-01-11)

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

| Package | --------------------------------------- | @jbrowse/core | @jbrowse/development-tools | @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-gff3 | @jbrowse/plugin-hic | @jbrowse/plugin-linear-comparative-view | | @jbrowse/plugin-linear-genome-view | @jbrowse/plugin-menus | @jbrowse/plugin-spreadsheet-view | @jbrowse/plugin-trackhub-registry | @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/development-tools | | 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-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

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

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Package last updated on 11 Jan 2021

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