yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.5.1
3.5.1 (2025-06-05)
:rocket: Enhancement
- Other
- #5064 Optimize
fetching many small sequences from IndexedFasta (e.g. MSA datasets)
(@cmdcolin)
- #5059 Canonicalize
refNames in search results (@cmdcolin)
- #5056 Use assembly
displayName on synteny header and ruler
(@garrettjstevens)
- #5050 Use standard
sessionId for linear synteny view to reduce data re-fetching
(@cmdcolin)
app-core
, core
, embedded-core
- #5063 Improve
usability of dropdown menus by making submenus not disappear immediately
onMouseLeave (@cmdcolin)
core
app-core
, core
- #5044 Allow plugins
to register entries onto the root configuration
(@cmdcolin)
:bug: Bug Fix
- Other
core
- #5058 Improve speed
of navigation for fragmented assemblies
(@cmdcolin)
:memo: Documentation
:house: Internal
- Other
core
- #5061 Modularize
some integration tests for launching views
(@cmdcolin)
Committers: 2
yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.5.0
3.5.0 (2025-05-27)
:rocket: Enhancement
- #5042 Avoid inferring
CDS subfeatures from non-coding gene pred features
(@cmdcolin)
- #5035 Use trash icon
for uninstall in plugin store, and add version number string
(@cmdcolin)
- #4735 Remove
jbrowse-web start screen (@cmdcolin)
- #5025 Allow hiding
insertion and deletion in synteny view to help chain file visualization
(@cmdcolin)
:bug: Bug Fix
- Other
- #5037 Check that
breakpoint split view is ready before fetching to avoid crash/large data
fetching (@cmdcolin)
- #5033 Bump @gmod/bbi
to fix loading bigwig files from bigtools
(@cmdcolin)
- #5024 Fix lines
crossing over view headers in breakpoint split view by only setting sticky
view headers on top-level views (@cmdcolin)
core
:house: Internal
core
- Other
- #5036 Remove the
async keyword from BaseLinearDisplayModel
(@cmdcolin)
Committers: 2
yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.4.0
3.4.0 (2025-05-13)
:rocket: Enhancement
core
- #5018 Avoid
serializing large features to sessions to fix quota exceeded errors in
localstorage (@cmdcolin)
- #5010 Add mouseover
metadata for fields in the base feature widget
(@cmdcolin)
- #4998 Add padding to
the genomic window of search result hits
(@cmdcolin)
- #4995 Add uFuzzy to
improve gene name search (@cmdcolin)
- #4983 Update some
data parser packages for ESM compat
(@cmdcolin)
- #4980 Synthesize
displayId if none provided in display config
(@cmdcolin)
- #4972 Support
cytoband bed files starting with "#"
(@cmdcolin)
- Other
- #5008 Allow parsing
non-indexed BED files larger than 512MB
(@cmdcolin)
- #4997 Better message
for "quota exceeded" message from localstorage
(@cmdcolin)
- #4974 Minor
optimizations in multi-sample variant rendering
(@cmdcolin)
- #4973 Add basic
cytoband for Drosophila (@cmdcolin)
- #4970 Dynamically
toggle wheel-scroll normalization to improve touchpad pinch-to-zoom usage
(@cmdcolin)
:bug: Bug Fix
core
- #5013 Fix UCSC chain
parsing which have header lines (@cmdcolin)
- #4993 Fix re-export
of @mui/material/styles, and re-export theme
(@cmdcolin)
- #4968 Fix theme
augmentation for primary/secondary colors in v3.3.0
(@cmdcolin)
- Other
- #5004 Fix
modifications rendering broken in v3.2.0
(@cmdcolin)
- #4992 Fix mouseover
for some variable width bigwig features
(@cmdcolin)
- #4984 Avoid
rendering 'yellow' for low scores in wiggle density renderings with
'log-scale' enabled (@cmdcolin)
- #4969 Avoid
aggregating bigbed features with geneName === 'none'
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 2
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.3.0
3.3.0 (2025-04-18)
:rocket: Enhancement
core
- #4956 Add simplified
display of REF/ALT to help with long strings produced by e.g. Cactus VCF
(@cmdcolin)
- #4954 Add genotype
frequency table to variant feature details
(@cmdcolin)
- #4952 Add 'genotype'
column to the Variant sample grid (@cmdcolin)
- #4944 Show ALT
allele description on multi-variant mouseover
(@cmdcolin)
- #4922 Add
Multi-variant SV display (@cmdcolin)
- Other
app-core
, core
, embedded-core
, product-core
, sv-core
, web-core
:bug: Bug Fix
- Other
- #4929 Fix broken
bigbed features when there is gene level aggregation
(@cmdcolin)
core
:memo: Documentation
core
- #4949 Controlling
navigation of embedded component - storybook examples
(@cmdcolin)
- #4924 Add config
docs for pre-processors with simplified config snapshots
(@cmdcolin)
- Other
:house: Internal
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.2.0
3.2.0 (2025-03-22)
:rocket: Enhancement
core
- #4919 Add in-app
clustering method for multi-wiggle tracks
(@cmdcolin)
- #4909 Add ability to
load refNameAliases from chromAliases.bb file
(@cmdcolin)
- #4906 Add in-app
clustering method for genotype matrix
(@cmdcolin)
- Other
- #4914 Allow looking
up header column by name for RefNameAliases
(@cmdcolin)
- #4910 Allow
refNameColumn in RefNameAliasAdapter to override the default displayed
refnames (@cmdcolin)
- #4907 Simplified
snapshot API for initial navigation of LGV
(@cmdcolin)
app-core
, core
, product-core
, web-core
- #4899 Add aborting
to multi-variant rendering, multi-wiggle rendering
(@cmdcolin)
:bug: Bug Fix
- #4920 Fix issue where
multi-level linear synteny view would show a blank tracklist
(@cmdcolin)
- #4913 Fix parent
aggregation in BigBed files using larger request window
(@cmdcolin)
- #4905 Fix bug where
applying genotype clustering twice produces randomness
(@cmdcolin)
- #4897 Fix clustering
for certain sets of bigwig files (@cmdcolin)
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.1.0
3.1.0 (2025-03-14)
:rocket: Enhancement
- Other
- #4876 Allow
inferring default values of adapter urls to simplify config.json
(@cmdcolin)
- #4875 Add sample
data from HGSVCv3 to 1000 genomes demo and config_demo
(@cmdcolin)
- #4880 Allow
selecting track error messages with click and drag
(@cmdcolin)
- #4882 Allow
clustering multi-wiggle tracks on the fly
(@cmdcolin)
- #4874 Use a '012'
matrix to improve clustering of genotypes
(@cmdcolin)
core
- #4871 Add deletion,
insertion, skip, softclip, hardclip to theme
(@cmdcolin)
app-core
, core
, product-core
:bug: Bug Fix
Committers: 2
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.5
3.0.5 (2025-03-04)
:bug: Bug Fix
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.4
3.0.4 (2025-03-01)
:rocket: Enhancement
- Other
core
- #4854 Add status
callback for parsing PAF, BLAST tabular, MashMap files
(@cmdcolin)
:bug: Bug Fix
core
- #4862 Fix name
indexing failure on jbrowse desktop
(@cmdcolin)
- #4851 Fix NCBI
sequence aliases refNameAliases adapter for some sequence_report.tsv files
(@cmdcolin)
- Other
- #4849 Fix height of
Hi-C track, and add adjust-to-height
(@cmdcolin)
- #4845 Fix retrieval
of VCF metadata for tooltips in VCF feature details
(@cmdcolin)
- #4842 Fix occasional
1px gap in sequence track (@cmdcolin)
:house: Internal
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.3
Done in 0.44s.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.2
3.0.2 (2025-02-13)
:rocket: Enhancement
core
- Other
- #4829 Less gappyness
at SVG features block boundaries (@cmdcolin)
- #4828 Additional
?hubURL compat (@cmdcolin)
- #4827 Improve status
updating for BedTabixAdapter, Gff3TabixAdapter, VcfTabixAdapter,
BigBedAdapter (@cmdcolin)
- #4825 Handle
multiple jobs with the same name
(@garrettjstevens)
- #4826 Calculate most
frequent non-ref allele for multi-variant renderer
(@cmdcolin)
- #4824 Aggregate
transcript level features in GTF based on "gene_name" field
(@cmdcolin)
- #4810 Ensure
embedded users get the latest semver @gmod/vcf for multi-variant fixes
(@cmdcolin)
app-core
, core
:bug: Bug Fix
sv-core
- #4837 Update
@gmod/cram for fixed decoding of some CRAM files
(@cmdcolin)
- Other
- #4808 Fix random
palette color generation for multi-variant colors
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 2
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.1
Done in 0.69s.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.0
3.0.0 (2025-01-29)
:boom: Breaking Change
core
__mocks__
, app-core
, core
, embedded-core
, product-core
, sv-core
:rocket: Enhancement
- Other
core
, web-core
core
, product-core
- #4798 Add more track
metadata to UCSC assembly hub loading
(@cmdcolin)
core
- #4795 Improved
rendering of phased VCF and polyploid VCF in multi-variant view
(@cmdcolin)
- #4792 Allow
uploading a sampleTsv file with per-sample metadata for VCF files
(@cmdcolin)
- #4786 Allow opening
"synteny tracks" from the default Add track workflow
(@cmdcolin)
- #4785 Allow opening
BedGraph et al in the default Add track workflow
(@cmdcolin)
- #4784 Improve UI for
choosing query and target assemblies in the "New track" workflow for synteny
tracks (@cmdcolin)
- #4767 Improve load
time when multiple tracks use same data file
(@cmdcolin)
- #4750 Add some more
lazy loading for smaller bundle size
(@cmdcolin)
sv-core
- #4753 Allow
launching a single level breakpoint split view focused on the breakends
(@cmdcolin)
web-core
app-core
, core
- #4729 Update cram-js
to avoid requesting file size for more CORS compatibility
(@cmdcolin)
:bug: Bug Fix
- Other
- #4778 Fix GC content
calculation consistency across blocks
(@cmdcolin)
- #4773 Fix "Color by
CDS" for BED12 features (@cmdcolin)
- #4771 Fix generating
categories for composite tracks in UCSC hubs
(@cmdcolin)
- #4769 Fix facet
filter crash (@cmdcolin)
- #4765 Fix repeat
masker track BED interpretation (@cmdcolin)
- #4764 Fix
modifications coverage calculations
(@cmdcolin)
- #4731 Fix naming of
subtracks produced by "group by tag" operation
(@cmdcolin)
- #4732 Fix persisting
alignments "color by" and "filter by" settings in snapshots/session
shares/page reloads (@cmdcolin)
core
- #4776 Fix maximum
recursion error in linear synteny view import form
(@cmdcolin)
- #4768 Fix navigation
via CIGAR string alignment in synteny view
(@cmdcolin)
- #4766 Fix some bed12
transcripts displaying as bedMethyl features
(@cmdcolin)
- #4727 Fix type
confusion where sequence feature details crashes for empty subfeatures
(@cmdcolin)
- #4725 Avoid error on
closing draggable dialog and a couple more refactors
(@cmdcolin)
:house: Internal
Committers: 2
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.18.0
2.18.0 (2024-12-10)
:rocket: Enhancement
core
, product-core
, sv-core
- Other
app-core
, core
, product-core
, web-core
- #4074 Autosave
sessions in jbrowse-web IndexedDB database to make it easier to access old
sessions (@cmdcolin)
app-core
, core
, embedded-core
, product-core
, sv-core
,
text-indexing
, web-core
- #4682 SV inspector
improvements (x-data-grid, opening track data, re-navigate breakpoint split
view, support INV/DEL/more) (@cmdcolin)
core
, product-core
- #4178 Add ability to
use colorBy and filterBy for alignments track configs, and group by strand
(@cmdcolin)
core
, product-core
, text-indexing
- #4663 Replace
AbortSignal with "stop token" to rescue some aborting behavior
(@cmdcolin)
:bug: Bug Fix
- #4708 Avoid full
length sequence fetch on SNP coverage calculation
(@cmdcolin)
- #4676 Fix
MCScanAnchorsAdapter rendering in linear genome view
(@cmdcolin)
- #4670 Fix GC-content
track regression in v2.17.0 (@cmdcolin)
- #4667 Reduce
self-pairing for some paired-end read data in breakpoint split view
(@cmdcolin)
:house: Internal
__mocks__
, app-core
, core
, embedded-core
, product-core
, sv-core
,
text-indexing
, web-core
- Other
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.17.0
2.17.0 (2024-11-18)
:rocket: Enhancement
core
- #4662 Add better
handling for bedMethyl files (@cmdcolin)
- #4652 Reduce
re-rendering on quantitative and snpcoverage track height adjustments
(@cmdcolin)
- #4651 Add mismatches
cache to improve performance on ultra-long reads
(@cmdcolin)
- Other
:bug: Bug Fix
- Other
core
- #4639 Fix RNA-seq
stranded arc coloring, change the color of RNA-seq introns, and improve
compact rendering (@cmdcolin)
- #4638 Fix rendering
of UCSC repeatmasker BigBed and BED files
(@cmdcolin)
:house: Internal
Committers: 2
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.16.1
2.16.1 (2024-11-03)
:rocket: Enhancement
app-core
, core
, product-core
, text-indexing
- #4624 Add utility
links to synteny feature details to allow centering a view on a feature
(@cmdcolin)
- Other
- #4628 Allow
configuring Hi-C normalization and default resolution multiplier
(@cmdcolin)
- #4619 Add
resolutionMultiplier config slot to BigWigAdapter
(@cmdcolin)
:bug: Bug Fix
- #4634 Fix opening
local files in the multi-wiggle add track selector
(@cmdcolin)
- #4633 Fix "Add track"
select box not going away after selecting element
(@cmdcolin)
- #4632 Standardize
modification colors between alignments track coverage and pileup subtracks
(@cmdcolin)
- #4631 Fix config
description of assembly name ordering for synteny data adapters
(@cmdcolin)
- #4630 Fix MM tag
modifications from particular BAM file failing to render on the negative
strand (@cmdcolin)
- #4626 Fix dark redraw
on selected features after vertical resize of the synteny canvas
(@cmdcolin)
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.16.0
2.16.0 (2024-10-23)
:rocket: Enhancement
- Other
- #4615 Add
configuration of transcriptTypes and containerTypes to the svg feature
rendering (@cmdcolin)
app-core
, core
:bug: Bug Fix
- Other
- #4593 Fix navigating
to a refname result that is also indexed in search track index
(@cmdcolin)
- #4612 Fix error with
tooltips in embedded components in vite dev mode
(@cmdcolin)
- #4602 Fix decoding
of CRAM ML tag (@cmdcolin)
- #4594 Fix highlight
button causing issues clicking underlying track features
(@cmdcolin)
- #4586 Update
electron-builder to fix broken desktop builds
(@cmdcolin)
core
:memo: Documentation
- #4607 Add tiberius
sample dataset and updated gencode and ncbi GFF gene sets
(@cmdcolin)
:house: Internal
- Other
- #4607 Add tiberius
sample dataset and updated gencode and ncbi GFF gene sets
(@cmdcolin)
app-core
, core
, embedded-core
, product-core
, web-core
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.4
2.15.4 (2024-09-20)
:bug: Bug Fix
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3
Done in 0.57s.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2
2.15.2 (2024-09-18)
:rocket: Enhancement
:bug: Bug Fix
:house: Internal
- #4569 Refactor GFF3
parser to avoid returning internal _linehash variable
(@cmdcolin)
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.1
2.15.1 (2024-09-12)
:rocket: Enhancement
core
, sv-core
- #4561 Create notion
of launching a single-row breakpoint split view
(@cmdcolin)
- Other
core
- #4554 Fix the
ability to sort menu items by priority for CascadingMenu
(@cmdcolin)
:bug: Bug Fix
- Other
core
- #4553 Fix
performance regression since v2.14.0 in assembly loading
(@cmdcolin)
:house: Internal
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.0
Done in 1.26s.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.14.0
2.14.0 (2024-08-28)
:rocket: Enhancement
core
- #4532 De-duplicate
snackbar messages (@cmdcolin)
- #4516 Add NCBI
sequence_report.tsv alias adapter, with ability to recode NCBI fasta files
to use UCSC style names (@cmdcolin)
- Other
- #4533 Allow setting
sequenceType='pep' in ReferenceSequenceTrack configuration
(@cmdcolin)
- #4531 Add
UnindexedFastaAdapter for fetching small plaintext FASTA files
(@cmdcolin)
- #4528 Add
description config slot to reference sequence track
(@cmdcolin)
app-core
, core
- #4523 Allow
plaintext GTF and VCF files greater than 512Mb
(@cmdcolin)
core
, product-core
:bug: Bug Fix
:house: Internal
- Other
- #4530 Consolidate
gff3 adapter featureData routine, avoid Number-ifying null phase
(@cmdcolin)
core
- #4518 Don't send
displayModel to "rendering" components on server side
(@cmdcolin)
__mocks__
, app-core
, core
, embedded-core
, product-core
,
text-indexing
, web-core
- #4513 Add new eslint
rules (no-unnecessary-condition, no-unused-expressions, etc) and tsconfig
noUncheckedIndexedAccess (@cmdcolin)
app-core
, core
, embedded-core
, product-core
, text-indexing
,
web-core
core
, product-core
, text-indexing
Committers: 2
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.13.1
2.13.1 (2024-07-31)
:rocket: Enhancement
:bug: Bug Fix
- #4501 Fix opening
track selector in linear synteny view causing crash in v2.13.0
(@cmdcolin)
- #4495 Fix log scale
for some types of signal tracks (@cmdcolin)
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.13.0
2.13.0 (2024-07-25)
:rocket: Enhancement
- #4494 Add assembly
name to scalebar in synteny views (@cmdcolin)
- #4480 Changes default
height for SVG rendering to maxHeight to fix blank track effect on slow CPU
(@carolinebridge)
- #4478 Add ability to
use CSI indexes in @jbrowse/img (@cmdcolin)
:bug: Bug Fix
core
- #4483 Fix
configuration settings for track sorting in the track selector
(@cmdcolin)
- Other
- #4476 Fix config
editor crash in vite usage of embedded components in dev mode
(@cmdcolin)
- #4473 Fix 'Show no
tracks active button' checkbox not working
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 3
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.3
2.12.3 (2024-06-27)
:rocket: Enhancement
- #4465 Add
contig
to
the default dontRedispatch list for Gff3TabixAdapter
(@cmdcolin)
- #4464 Bump
generic-filehandle to put URL in error messages
(@cmdcolin)
:bug: Bug Fix
:memo: Documentation
- #4466 Add demo of
using farm-fe bundler for embedded components
(@cmdcolin)
Committers: 1
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.2
Done in 0.74s.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.1
Done in 0.81s.
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.0
2.12.0 (2024-06-20)
:rocket: Enhancement
- Other
- #4459 Allow using
keyboard shortcut for devtools in production desktop builds
(@cmdcolin)
- #4455 Add slot.type
to configuration editor elements (@cmdcolin)
- #4427 Add ctrl+wheel
scroll to zoom both top and bottom of synteny view
(@cmdcolin)
- #4425 Add ability to
dismiss dotplot warnings (@cmdcolin)
- #4422 Make initial
linear synteny view import form submit show all regions by default
(@cmdcolin)
core
- #4456 Add
aggregation to BigBedAdapter to group bigGenePred transcripts
(@cmdcolin)
- #4448 Adds genomic
coordinates back into the sequence panel accounting for strand direction
(@carolinebridge)
- #4423 Speed up large
displayedRegions sets by converting MST array of Region[] into a
types.frozen<IRegion[]> (@cmdcolin)
- #4399 Allow viewing
coordinates in sequence feature display panel
(@cmdcolin)
app-core
- #4443 Allow drawer
widget to be "popped out" into a dialog box
(@cmdcolin)
core
, product-core
- #3992 Add ability to
get refNames for a track in the "About track" panel
(@cmdcolin)
:bug: Bug Fix
- Other
- #4458 Fix sandbox
error on AppImage startup on certain linux systems
(@cmdcolin)
- #4441 Fix sorting
data grid on multi-wiggle 'Edit colors/arrangement' dialog
(@cmdcolin)
- #4439 Fix blank
lines in multi-wiggle add track workflow causing crash
(@cmdcolin)
- #4438 Fix
cursor:pointer style on an alignments feature detail clickable link
(@cmdcolin)
- #4436 Fix "Open
synteny view at this position" when file contains CIGAR X/= operators
(@cmdcolin)
- #4426 Fix side
scroll in linear synteny view causing the browser "back" action
(@cmdcolin)
- #4417 Fix error
message shown on chromosomes with missing data for plaintext GFF3
(@cmdcolin)
core
- #4442 Fix unstable
dialog width in "About track" dialog for multi-quantitative tracks
(@cmdcolin)
:house: Internal
Committers: 2
yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.11.2
2.11.2 (2024-06-03)
:rocket: Enhancement
:bug: Bug Fix
Committers: 3
yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.11.1
2.11.1 (2024-05-11)
:rocket: Enhancement
core
- #4354 Allow
capitalizing CDS sequences and lowercasing introns in sequence feature panel
(@cmdcolin)
- Other
- #4351 Store and
retrieve user track selector settings in local storage
(@cmdcolin)
:bug: Bug Fix
core
- #4381 Replace all
rgba(...) color strings with rgb(...) in SVG exports to fix usage in
illustrator/inkscape (@cmdcolin)
- #4364 Fix tooltips
creating a scrollbar when overflowing off the screen in Chrome
(@cmdcolin)
- Other
app-core
Committers: 1
yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.11.0
2.11.0 (2024-04-16)
:rocket: Enhancement
core
- Other
app-core
, product-core
- #4337 Allow moving
tracks and views up/down/to top/to bottom, and better click and drag track
re-ordering (@cmdcolin)
core
, product-core
core
, web-core
- #4284 Allow getting
stack trace error dialog from session.notify errors
(@cmdcolin)
:bug: Bug Fix
- Other
- #4318 Use
node-fetch-native to fix warning from JBrowse CLI on node 21+
(@cmdcolin)
- #4319 Fix Hi-C
rendering for some high resolution files
(@cmdcolin)
- #4314 Fix loading of
BED12 data from a plaintext BED with column headers
(@cmdcolin)
- #4293 Fix alignment
curves showing up in inkscape for breakpoint svg
(@cmdcolin)
- #4287 Fix snap
package and also add deb package (@cmdcolin)
- #4277 Fix usage of
--assemblyNames in
jbrowse add-connection
(@cmdcolin)
- #4275 Fixes bug on
URL highlight param in which refName aliases were not working
(@carolinebridge-oicr)
text-indexing
Committers: 3
yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.3
2.10.3 (2024-03-06)
:rocket: Enhancement
:bug: Bug Fix
- #4254 Throw if no
sequenceAdapter supplied to CramAdapter
(@cmdcolin)
- #4250 Fix the viewport
calculations for when URL params includes &tracklist=true
(@cmdcolin)
- #4232 Fix for missing
INFO.STRANDS tag for TRA features in breakpoint split view
(@cmdcolin)
- #4224 Fix parsing of
BAM and CRAM refNames that contain a colon
(@cmdcolin)
:memo: Documentation
Committers: 5
yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.2
2.10.2 (2024-02-19)
:rocket: Enhancement
- Other
- #4219 Add ability to
render only snpcoverage in jbrowse-img
(@cmdcolin)
- #4196 Allow adding
&tracklist=true to URL bar to open the track selector, &nav=false to hide
linear genome view header (@cmdcolin)
core
- #4215 Launch
breakpoint split view directly from alignments feature details
(@cmdcolin)
- #4184 Add ability to
get stack trace for error messages in the UI
(@cmdcolin)
:bug: Bug Fix
- Other
- #4220 Fix hydration
error from translocation features in plaintext VCF adapter
(@cmdcolin)
- #4217 Fix breakpoint
split view SVG export occasionally having wrong clipping
(@cmdcolin)
- #4213 Fix issue with
tagFilter * in alignments track (@cmdcolin)
- #4208 Fix
@jbrowse/img under node environment
(@cmdcolin)
- #4146 Remove
--tracks and --view options from set-default-session CLI
(@cmdcolin)
core
- #4190 Remove text
selection on sequence track with user-select: none
(@cmdcolin)
core
, product-core
- #4177 Fix session
tracks being displayed in the tracklist on @jbrowse/react-linear-genome-view
(@cmdcolin)
:memo: Documentation
Committers: 1
yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.1
2.10.1 (2024-01-09)
:rocket: Enhancement
:bug: Bug Fix
- Other
core
- #4147 Fix bad svg
output in v2.10.0 in cases where feature names have angle brackets
(@cmdcolin)
:memo: Documentation
Committers: 2
yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.0
2.10.0 (2023-12-15)
:rocket: Enhancement
core
- #4138 Speed up large
FromConfigAdapter usages with alternative adapter id calculation
(@cmdcolin)
- #4114 Improve
pluginManager.jexl typescript definition
(@cmdcolin)
- Other
- #4135 Split
"recently used tracks" local storage keys by view assemblies
(@cmdcolin)
- #4003 Adds the
ability to highlight regions using the bookmarks widget
(@carolinebridge-oicr)
- #4123 Remove
session.notify after using the Add track workflow
(@cmdcolin)
- #3859 Add new
pairwise indexed PAF adapter format with CLI creation workflow
(@cmdcolin)
- #4109 Allow right
clicking synteny features (@cmdcolin)
- #4110 Scroll both
panels of the linear synteny view when side scrolling the middle panel
(@cmdcolin)
- #4108 Convert to
floating-ui for tooltips for small speedup
(@cmdcolin)
- #4107 Refactors and
bundle size improvements (@cmdcolin)
app-core
, core
- #4134 Add ability to
click and drag synteny area of synteny view to side scroll
(@cmdcolin)
:bug: Bug Fix
- Other
core
- #4136 Fix "Export
SVG" feature in next 14 (@cmdcolin)
- #4125 Fix internet
accounts not being shown in file selector after page refresh and hide HTTP
basic internet accounts (@cmdcolin)
app-core
, embedded-core
- #4121 Fix view menu
checkboxes not responding in some cases
(@cmdcolin)
:memo: Documentation
app-core
, product-core
, web-core
:house: Internal
Committers: 2
yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.9.0
2.9.0 (2023-11-30)
:rocket: Enhancement
- Other
- #4070 Add support
for single file hubs (@cmdcolin)
- #4096 Allow
searching by gene name using linear synteny view
(@cmdcolin)
- #4068 Allow
searching the text-index by gene name from the URL bar
(@cmdcolin)
- #3948 Make the
default setting for the dotplot/synteny views use 'Existing tracks' by
default (@cmdcolin)
- #4039 Adds
"Favorites" and "Recently used" track categories to the track selector
(@carolinebridge-oicr)
- #4067 Add arc plugin
to @jbrowse/react-linear-genome-view core plugins
(@cmdcolin)
core
, product-core
- #4091 Allow hiding
subfeatures in the feature details panel
(@cmdcolin)
:bug: Bug Fix
core
- Other
- #4095 Fix faceted
metadata header names colliding with non-metadata header names
(@cmdcolin)
- #4071 Fix Mac
auto-updates fetching non-existent zip
(@cmdcolin)
- #4062 Fix duplicate
key error in hierarchical track selector from using connections
(@cmdcolin)
Committers: 2
yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.8.0
2.8.0 (2023-11-09)
:rocket: Enhancement
- Other
product-core
core
- #4035 Prompt to
horizontally flip view when launching linear synteny view on inverted
feature (@cmdcolin)
app-core
:bug: Bug Fix
- #4052 Fix browser back
button behavior in jbrowse-web (@cmdcolin)
- #4043 Fix crash in
"Open session" widget for sessions that have 'track-less views'
(@cmdcolin)
:memo: Documentation
Committers: 2
yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.7.2
2.7.2 (2023-10-27)
:rocket: Enhancement
core
- Other
- #4020 Allow
configuring LGV trackLabels setting via config
(@cmdcolin)
- #3999 Example of
using customElement + ShadowDOM for @jbrowse/react-linear-genome-view
(@AcaDemIQ)
- #4015 Create MacOS
universal build of jbrowse-desktop to help M1 macs
(@cmdcolin)
core
, product-core
:bug: Bug Fix
:house: Internal
core
- #4005 Refactors and
typescript improvements for jbrowse-web loader
(@cmdcolin)
app-core
, core
Committers: 3
yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.7.1
2.7.1 (2023-10-18)
:rocket: Enhancement
- Other
- #3986 Allow editing
step size and window size of GC content adapter
(@cmdcolin)
core
- #3982 Allow
rendering semi-circles in the arc renderer + SVG rendering of arcs
(@cmdcolin)
__mocks__
, core
- #3981 Auto-create
HTML links for URLs, and strip HTML tags where they can't be rendered
(@cmdcolin)
:bug: Bug Fix
- Other
- #3991 Remove some
non-functioning options from top level menu in @jbrowse/react-app
(@cmdcolin)
- #3980 Downgrade
electron 26->25 to fix screen blanking
(@cmdcolin)
core
- #3971 Fix rendering
multi-quantitative tracks when blank data is present
(@cmdcolin)
Committers: 1
yarn run v1.22.18 $ lerna-changelog --next-version 2.7.0
2.7.0 (2023-10-04)
:rocket: Enhancement
- Other
core
app-core
, core
, embedded-core
app-core
- #3916 Use
theme.secondary.main instead of theme.secondary.light on focusedView
(@cmdcolin)
app-core
, core
, embedded-core
, product-core
, text-indexing
,
web-core
app-core
, core
, web-core
:bug: Bug Fix
app-core
, core
- #3959 Remove type
any
from return value of getContainingView, getSession
(@cmdcolin)
- Other
- #3946 Fix setting
multiple hierarchical defaultCollapsed config options at initialization
(@cmdcolin)
- #3937 Fix dev mode
error from LGV overview scalebar (@cmdcolin)
- #3925 Reduce amount
of canvas commands issued to the dotplot renderer
(@cmdcolin)
- #3924 Fix incorrect
tick mark label on dotplot axes happening in some cases
(@cmdcolin)
- #3921 Fix hydration
warning by only rendering the SvgFeature "selected feature" and "mouseover"
client side (@cmdcolin)
- #3910 Fix feature
label offsets in SVG exports with main thread RPC
(@cmdcolin)
- #3905 Fix alignments
track infinite loading when applying same "Color by" or "Sort by" setting
twice (@cmdcolin)
- #3904 Fix "Color
by"->"Mapping quality" for CRAM files
(@cmdcolin)
- #3902 Fix ability to
use plaintext bed in add-track CLI
(@cmdcolin)
core
- #3929 Fix mouse
getting out of sync while dragging resize handle
(@cmdcolin)
- #3912 Avoid
undefined getConf on assembly.configuration safeReference
(@cmdcolin)
- #3887 Add forwardRef
to wrapped re-exported lazy components
(@garrettjstevens)
- #3866 Fix
calculation of width of "view container title"
(@cmdcolin)
- #3865 Strip alpha
from colors for improved SVG export compatibility
(@cmdcolin)
:memo: Documentation
- #3957 Add error
handler example for embedded components
(@cmdcolin)
- #3913 Add color scheme
for pathogenicity for ClinVar config_demo track
(@scottcain)
- #3881 Improve some of
the extension point documentation (@cmdcolin)
:house: Internal
app-core
, core
, embedded-core
core
- #3920 Remove some
unused "renameReference" code in static/dynamic blocks
(@cmdcolin)
- Other
app-core
, core
, embedded-core
, product-core
, web-core
Committers: 4
yarn run v1.22.18 $ lerna-changelog 2.6.3
:rocket: Enhancement
- Other
app-core
- #3810 Add sorting
and collapsing options to the hierarchical track selector
(@cmdcolin)
- #3827 Add check for
document.activeElement == INPUT before undo/redo
(@cmdcolin)
:bug: Bug Fix
- #3839 Fix bug where
multi-quantitative tracks plotted incorrectly for some bigwigs with empty
regions (@cmdcolin)
- #3837 Fix text layout
in dotplots with long coordinate strings
(@cmdcolin)
- #3825 Fix SVG export
compatibility by removing rgba strings
(@cmdcolin)
- #3814 Fix suspense
fallback to track container for lazy loaded display components
(@cmdcolin)
- #3808 Fix track
ordering of hierarchical track selector to more closely match the config.json
(@cmdcolin)
- #3806 Fix a bug on the
BookmarkWidget mui data grid where labels were not saving
(@carolinebridge-oicr)
- #3804 Fix version
missing from about menu in @jbrowse/react-app
(@cmdcolin)
:house: Internal
Committers: 3
yarn run v1.22.18 $ lerna-changelog 2.6.2
:rocket: Enhancement
:bug: Bug Fix
- Other
- #3798 Fix VCF
feature starting at 1-based 1 (@cmdcolin)
- #3775 Fix stranded
RNA-seq rendering and rename option Color by -> "First-of-pair strand"
(@cmdcolin)
- #3758 Adds safety
checks on AlignmentsDisplay properties to avoid undefined rendering
(@carolinebridge-oicr)
- #3770 Fix potential
issue with display searchFeatureByID being undefined
(@cmdcolin)
core
app-core
, core
, embedded-core
, product-core
, text-indexing
,
web-core
- #3771 Use
inlineSourceMaps for tsc builds and other misc changes
(@cmdcolin)
:house: Internal
Committers: 3
yarn run v1.22.18 $ lerna-changelog 2.6.1
:rocket: Enhancement
- Other
- #3743 Create mixin
for shared code between LinearWiggleDisplay and MultiWiggleLinearDisplay
(@cmdcolin)
- #3711 Allow synteny
data adapters to open files larger than 512Mb
(@cmdcolin)
- #3639 Add button to
bookmark in jbrowse-web share dialog
(@cmdcolin)
- #3631 Add BEDPE add
track workflow, avoid showing "Add track" when disabled
(@carolinebridge-oicr)
- #3700 Render
alignment track arcs instantly after bpPerPx change
(@cmdcolin)
- #3695 Reduce
re-drawing on alignments track paired read arcs/cloud display types
(@cmdcolin)
core
- #3725 Filter tracks
that match all view.assemblyNames in multi-assembly track selector modes
(@cmdcolin)
- #3531 Add
@jbrowse/react-app embedded component
(@cmdcolin)
- #3653 Evaluate
extension point on track config pre-process snapshot
(@cmdcolin)
- #3706 Miscellaneous
alignments arc/cloud fixes (@cmdcolin)
- #3698 Add column
resizers to the variant ANN/CSQ panels
(@cmdcolin)
app-core
, product-core
, web-core
__mocks__
- #3707 Improved read
cloud display for long reads with inversions
(@cmdcolin)
:bug: Bug Fix
core
- #3749 Avoid
re-prompting a user login when refresh token is processed
(@cmdcolin)
- #3572 Add OAuth and
HTTP BasicAuth servers for local testing, fix some OAuth flows
(@garrettjstevens)
- #3708 Add
removable-media to jbrowse desktop snap
(@cmdcolin)
- #3687 Take into
account ML tag when showing MM tag on alignments, misc refactoring
(@cmdcolin)
- Other
- #3747 Fix blank
lines in GFF crashing text-index (@cmdcolin)
- #3739 Fix specifying
the assemblyNames config slot on add-connection CLI
(@cmdcolin)
- #3631 Add BEDPE add
track workflow, avoid showing "Add track" when disabled
(@carolinebridge-oicr)
- #3667 Fix horizontal
flip functionality for Hi-C display
(@studentshivang)
- #3703 Fix rendering
error in alignments tracks when filtering by tag in CRAM file
(@Lilas-w)
- #3694 Fix ability to
filter certain fields in BAM/CRAM files
(@cmdcolin)
- #3691 Fix breakpoint
split view alignment connections not pointing at right position in v2.5.0
(@cmdcolin)
- #3686 Fix jbrowse
create/jbrowse upgrade CLI intermittent failures
(@cmdcolin)
product-core
, web-core
- #3738 Don't throw on
UCSC connection containing assemblies not matching connection->assemblyNames
config (@cmdcolin)
app-core
, core
, embedded-core
app-core
:memo: Documentation
- Other
core
, embedded-core
, product-core
:house: Internal
app-core
, core
, product-core
, text-indexing
- #3740 Bump electron,
proxy-agent, fontsource-roboto, etc. and update SnackbarMessage from typed
array to object (@cmdcolin)
core
- #3741 Distinguish
between SessionWithConnections and SessionWithConnectionEditing
(@cmdcolin)
- Other
app-core
, core
, product-core
, web-core
product-core
app-core
, core
, embedded-core
, product-core
, text-indexing
core
, product-core
- #3661 Create
packages/product-core containing shared code between the various products
(@rbuels)
Committers: 6
2.5.0 (2023-05-04)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
core
- #3677 Adjust
RefNameAutocomplete width calculation to avoid ellipses
(@cmdcolin)
- #3660 Bump
x-data-grid dependency, refactors for BaseFeatureDetails, add GridToolbar
(@cmdcolin)
- #3626 Update to mui
x-data-grid 6 (@cmdcolin)
:bug: Bug Fix
core
- #3681 Guard against
undefined in CoreGetFeatureDetails
(@cmdcolin)
- #3662 Fix empty
feature sequence on top-level gene feature
(@cmdcolin)
- #3666 Fix text boxes
being too small in Dialog boxes (@cmdcolin)
- #3642 Fix error
handling of feature detail formatter jexl callbacks
(@cmdcolin)
- #3621 Update plugin
rollup polyfill package
(@garrettjstevens)
- #3620 Fix potential
crashes where alignment SEQ field may be empty, simplify some display model
code (@cmdcolin)
- Other
- #3670 Only
double-click zoom if not clicking on feature
(@cmdcolin)
- #3652 Fix text being
invisible on overview scalebar when cytobands shown
(@cmdcolin)
- #3632 Fix mouse
click-and-drag behavior in the alternative "cursor mode" for the dotplot
view (@cmdcolin)
- #3625 Fix UCSC
trackhub assembly aliases matching
(@andrzejgrzelak)
__mocks__
, core
:memo: Documentation
- Other
- #3676 Refactor
circular genome view storybook (@cmdcolin)
- #3671 Fix website
documentation sidebar on browsers with prefers-reduced-motion
(@cmdcolin)
- #3654 Add some docs
for configuring defaultSession (@cmdcolin)
core
:house: Internal
core
- #3647 Refactoring
navToMultiple, navToLocString, and related
(@cmdcolin)
- #3629 Typescript
checking for config slot names (@rbuels)
- #3618 Rename APIs
for feature density stats and quantitative stats
(@cmdcolin)
- #3615 Add check for
default export to plugin loader (@rbuels)
Committers: 4
2.4.2 (2023-03-27)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #3604 Alignments
tags description in feature details on mouseover
(@cmdcolin)
- Other
:bug: Bug Fix
- Other
- #3610 Avoid cutting
off import form of spreadsheet view, fix overflowed text in table header
(@cmdcolin)
- #3600 Fix using the
force load button after a stats timeout
(@cmdcolin)
- #3592 Fix shading on
synteny features after mouseout (@cmdcolin)
__mocks__
, core
- #3608 Fix
subfeatures formatter not being applied to feature detail panel
(@cmdcolin)
- #3607 Avoid
"ResizeObserver" loop warning during development
(@cmdcolin)
core
- #3593 Fix gene
without subfeatures not being displayed in sequence feature details
(@cmdcolin)
:house: Internal
- #3611 Use local data
instead of remote data for LGV component test
(@cmdcolin)
Committers: 2
2.4.1 (2023-03-14)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #3534 Improve
visibility of SNPs on alignments track
(@cmdcolin)
- #3561 Add scroll
zoom, d-pad, and more click+drag options to dotplot
(@cmdcolin)
- Other
- #3574 Add ability to
load all built-in synteny data sources from @jbrowse/cli
(@cmdcolin)
- #3564 Use
double-click to zoom in on particular offset in LGV, and make ctrl+scroll
also zoom in on particular offset (@cmdcolin)
:bug: Bug Fix
- #3578 Fix selected
synteny feature getting unselected after scroll
(@cmdcolin)
- #3566 Fix use of "show
all regions with data" feature in SV inspector with TRA entries (with CHR2
from INFO) (@cmdcolin)
- #3558 Fix visual
effect from using the overview scalebar click and dragging backwards
(@cmdcolin)
- #3556 Fix infinite
loading state when no synteny features are visible in synteny view
(@cmdcolin)
- #3551 Fix bad layout
on tabix tracks that have Unicode characters
(@cmdcolin)
- #3548 Fix upper case
querying of jbrowse 1 text search store
(@cmdcolin)
- #3545 Fix issue where
clearing search box on LGV import form turns search box into loading bar
(@cmdcolin)
:memo: Documentation
:house: Internal
- Other
__mocks__
, core
, text-indexing
- #3557 Add additional
lint rules from typescript-eslint and eslint-plugin-unicorn
(@cmdcolin)
Committers: 2
2.4.0 (2023-02-24)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
core
- #3513 Add ability to
open refNameAliases+cytobands in "Open sequence" start screen on desktop
(@cmdcolin)
- #3512 SVG export of
linear synteny view, dotplot, and circular views
(@cmdcolin)
- #3467 Create dark
theme and allow user to toggle different themes from preferences dialog
(@cmdcolin)
:bug: Bug Fix
:memo: Documentation
Committers: 2
2.3.4 (2023-02-01)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #3494 Use
transitionDuration 0 as defaultProp in theme for both popovers and menus
(@cmdcolin)
- #3488 Render HTML in
faceted track selector for track data/metadata
(@cmdcolin)
- #3483 Add
anchorOrigin/transformOrigin to default menu component
(@cmdcolin)
- #3470 Variant sample
grid auto-size columns and resizer
(@cmdcolin)
- Other
- #3304 Faceted/data
grid style track selector (@cmdcolin)
- #3477 Larger margins
to add track workflow to visually clarify next button behavior
(@cmdcolin)
- #3475 Bypass
plugins.json download if unneeded during app startup
(@cmdcolin)
- #3458 Improve
auto-update of sequence track height when toggling
forward/reverse/translation settings
(@cmdcolin)
:bug: Bug Fix
core
- #3482 Fix loading
external plugins in embedded linear-genome-view demo
(@cmdcolin)
- Other
- #3457 Fix synteny
view not drawing after horizontal flip in v2.3.3
(@cmdcolin)
- #3459 Booleanize
localstorage settings from older versions of LGV to avoid crash
(@cmdcolin)
:memo: Documentation
Committers: 1
2.3.3 (2023-01-11)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #3440 "Show all
regions" for dotplot and synteny views and refactor synteny rendering RPC to
optimize scrolling (@cmdcolin)
:bug: Bug Fix
- Other
- #3451 Fix
auto-updates on desktop not working since v2.2.2
(@cmdcolin)
core
- #3428 Add missing
dependencies to embedded component package.json's
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 1
2.3.2 (2022-12-20)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #3422 Auto-adjust
height of reference sequence track to current settings
(@cmdcolin)
- Other
- #3421 Add ability to
revcomp sequence in the "Get sequence" dialog
(@cmdcolin)
- #3413 Add a "base"
set of tracks and assemblies for the embedded demos
(@cmdcolin)
:bug: Bug Fix
- #3419 Fix rendering
base-level alignments on synteny visualizations, especially in inverted
regions (@cmdcolin)
- #3416 Fix rendering
alignment arcs on files that need refname renaming and add jitter setting
(@cmdcolin)
- #3415 Fix circular
view being rendered as a blank area if tab is opened in the background
(@cmdcolin)
Committers: 1
<summary>Packages in this release</summary>
2.3.0 (2022-12-15)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #3403 Reduce
overplotting on dotplot grid lines and other misc improvements
(@cmdcolin)
- #3381 Add method for
cache busting requests to the config file in jbrowse-web
(@cmdcolin)
- #3384 Add method to
more easily create compact view of alignments
(@cmdcolin)
core
- #3391 Allow arc
display to connect to "unpaired" positions using RNEXT/PNEXT or SA tag
(@cmdcolin)
- #3387 Small UI
tweaks for add track workflow (@cmdcolin)
- #3358 Create new
"arc" display type to show long range connections between paired-end and
split-reads (@cmdcolin)
text-indexing
- #3385 Optimize
prefix size for text indexing automatically
(@cmdcolin)
:bug: Bug Fix
- Other
- #3407 Remove
trackhub registry plugin from core plugins, moved to plugin store
(@cmdcolin)
- #3406 Fix loading
connection tracks from connections that don't specify assemblyNames in
config (@cmdcolin)
- #3390 Fix
positioning within large alignments for query->target LGV synteny navigation
(@cmdcolin)
- #3388 Fix search
result that matches synonyms that matches multiple locations
(@cmdcolin)
core
- #3404 Fix
double-render of some synteny features
(@cmdcolin)
- #3401 Remove
y-scalebar rendering placeholder values in blank and loading states
(@cmdcolin)
- #3389 Fix issue
where snackbar would not show up when same error message is triggered
multiple times (@cmdcolin)
:memo: Documentation
core
- Other
- #3383 Add note to
user guide about variant callers that can be used for SV inspector
(@cmdcolin)
:house: Internal
__mocks__
, core
, text-indexing
- #3400 Reduce
peerDependency warnings from installing dev environment
(@cmdcolin)
core
Committers: 1
2.2.2 (2022-12-06)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #3350 Retain feature
labels in compact display mode for SVG features, and allow turning off
keeping feature description without feature label
(@cmdcolin)
- #3357 Allow holding
shift key to create rubberband selection on LGV
(@cmdcolin)
- #3363 Create
remove-track CLI command (@cmdcolin)
- #3341 Add BEDPE
adapter type (@cmdcolin)
core
:bug: Bug Fix
- Other
- #3377 Fix rendering
and clicking synteny features when using MainThreadRpc
(@cmdcolin)
- #3375 Fix
jbrowse upgrade
CLI command overwriting config.json with --branch or
--nightly options (@cmdcolin)
- #3370 Fix error with
SNPCoverage not rendering MM tag modifications in some cases
(@cmdcolin)
- #3366 Fix ability to
use LGV synteny track on inverted alignments
(@cmdcolin)
- #3348 Fix for
breakpoint split view and circular view issues with
<TRA>
type entries in
v2.2.1 (@cmdcolin)
core
- #3369 Fix uncaught
promise errors and add lint rule for catching these
(@cmdcolin)
:memo: Documentation
:house: Internal
core
- #3368 Create base
"Dialog" component to standardize dialogs across codebase
(@cmdcolin)
text-indexing
Committers: 2
2.2.1 (2022-11-21)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #3277 Create new
"Add track workflow" that allows pasting JSON track configs
(@cmdcolin)
- #3328 Add GC content
display type to the reference sequence track
(@cmdcolin)
- #3316 Add LGV
typescripting to @jbrowse/react-linear-genome-view
(@cmdcolin)
core
- #3298 Add
authentication plugin to embedded components
(@garrettjstevens)
- #3329 Add ability to
minimize/collapse tracks and views and move views up/down in view stack
(@cmdcolin)
- #3308 Add ability to
display synteny track in a normal LGV showing regions of synteny as features
(@cmdcolin)
- #3317 Move
ErrorBoundary so that tracks/views that have crashed can be closed more
easily (@cmdcolin)
:bug: Bug Fix
- Other
- #3342 Fix CRAM
mismatches calculation regression in v2.2.0
(@cmdcolin)
- #3319 Fix pileup
"sort by" setting being lost on zoom level change
(@cmdcolin)
core
- #3340 Fix linear
genome view import form going into infinite loading state changing
assemblies with same refnames (@cmdcolin)
- #3339 Fix force flag
for drawing large regions and node-fetch polyfill for node 18 fix in
@jbrowse/img (@cmdcolin)
Committers: 2
2.2.0 (2022-11-04)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
core
- #3299 Add ability to
open a synteny track directly from the dotplot/linear synteny view import
forms (@cmdcolin)
- #3287 Lazy-load
assemblies on demand instead of all at app startup
(@cmdcolin)
- #3279 Remove
unnecessary expanded region query and small refactors
(@cmdcolin)
:bug: Bug Fix
core
- #3309 Fix animated
"Loading..." message keyframes (@cmdcolin)
- #3306 Fix the
RefNameAutocomplete displaying a stale value for chromosome names
(@cmdcolin)
- #3302 Improve
rubberband zooming across elided regions
(@cmdcolin)
- Other
- #3293 Fix CRAM
plotting for data files that encode insertions in uncommon way
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 3
2.1.7 (2022-10-20)
<summary>Packages in this release</summary>
:bug: Bug Fix
- #3282 Fix for embedded
build with webpack 4 failing with v2.1.6
(@cmdcolin)
Committers: 1
2.1.6 (2022-10-19)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #3272 Disable
resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff
(@cmdcolin)
- #3254 Use tick
labels that correspond to the overview's larger zoom level
(@cmdcolin)
core
- #3230 Add ability to
customize About dialog with callbacks and optionally hide links to data
(@cmdcolin)
- #3275 Add help
dialog for feature sequence panel (@cmdcolin)
- #3250 Handle
alternate line endings
(@garrettjstevens)
- #3252 Fix gene
sequence fetching in embedded, and allow fetching genomic sequence for other
feature types (@cmdcolin)
core
, text-indexing
:bug: Bug Fix
core
- Other
- #3274 Update bbi-js
for bugfix on webpack 4 (@cmdcolin)
- #3259 Fix issue with
breakpoint split view using view before initialized
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 3
2.1.5 (2022-10-03)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #3200 Use Alert
component for track messages
(@garrettjstevens)
- #3229 Allow user to
select local assembly to add tracks to for trackhub registry
(@cmdcolin)
- #3220 Improve error
reporting on SV inspector/spreadsheet view on import form
(@cmdcolin)
- #3198 Improve error
reporting on jbrowse-web start screen when user attempts to open a broken
recent session
(@carolinebridge-oicr)
core
- #3223 Allow adding
session tracks to embedded react component along with disableAddTracks
option if unwanted (@cmdcolin)
- #3227 Add
infrastructure for creating linear-genome-view sub-classes
(@carolinebridge-oicr)
- #3215 Add error
boundary on view, track, and drawer widget
(@cmdcolin)
- #3216 Add ability to
set number of bp to fetch up/down stream/inside intron in feature details
(@cmdcolin)
:bug: Bug Fix
- Other
- #3241 Fix local
session failing to load copying between tabs in some cases
(@cmdcolin)
- #3234 Fix circular
embedded view failing to load in v2.1.3 and v2.1.4
(@cmdcolin)
- #3233 Fix legend
being cutoff on multiwiggle tracks with wide window
(@cmdcolin)
- #3217 Fix loading
tracks from connection using assembly alias
(@cmdcolin)
- #3214 Fix trackhub
registry failing to load in 2.x.y versions of jbrowse
(@cmdcolin)
- #3204 Fix
authentication configuration on jbrowse-desktop
(@cmdcolin)
core
:memo: Documentation
:house: Internal
Committers: 3
2.1.4 (2022-09-16)
<summary>Packages in this release</summary>
:bug: Bug Fix
Committers: 1
2.1.3 (2022-09-15)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #3188 Add 'Open
saved session' button to start screen on desktop
(@cmdcolin)
- #3187 Add mouseover
tooltip descriptions to the header of the VariantFeatureDetails
sample/genotype table (@cmdcolin)
- #3179 Add
extendSession extension point to web and desktop
(@garrettjstevens)
- #3178 Allow X/Y
assemblies of dotplot or top/bottom selection of synteny views to be either
query or target (@cmdcolin)
- #3173 Add ability
for CLI to recognize plaintext BED files
(@cmdcolin)
- #3162 Add about
dialog with version number for embedded components
(@cmdcolin)
- #3163 Note for user
to wait before re-launching app on desktop update
(@cmdcolin)
- #3179 Add
extendSession extension point to web and desktop
(@garrettjstevens)
- #3178 Allow X/Y
assemblies of dotplot or top/bottom selection of synteny views to be either
query or target (@cmdcolin)
- #3173 Add ability
for CLI to recognize plaintext BED files
(@cmdcolin)
- #3162 Add about
dialog with version number for embedded components
(@cmdcolin)
- #3163 Note for user
to wait before re-launching app on desktop update
(@cmdcolin)
core
:bug: Bug Fix
core
- #3168 Fix search
behavior when there are multiple matches in LGV header and when feature
description matched in import form
(@cmdcolin)
- #3182 Fix "dead
state tree node" error by creating snapshots of parent region for block
calculations (@cmdcolin)
- #3182 Fix "dead
state tree node" error by creating snapshots of parent region for block
calculations (@cmdcolin)
- Other
:memo: Documentation
:house: Internal
Committers: 3
<summary>Packages in this release</summary>
2.1.1 (2022-08-25)
<summary>Packages in this release</summary>
:rocket: Enhancement
:bug: Bug Fix
- Other
- #3157 Support the
"name" field on multi-wiggle adapter subadapters instead of source
(@cmdcolin)
- #3154 Use the union
of all the subadapter refNames for the MultiWiggleAdapter getRefNames
(@cmdcolin)
- #3156 Fix for
mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode
(@cmdcolin)
- #3151 Fix ability to
click and drag overview scale bar dragging right to left
(@cmdcolin)
- #3133 Update the ref
name box when assembly is changed in LGV import form
(@garrettjstevens)
- #3131 Use "code"
instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo
(@garrettjstevens)
- #3119 Use es2015
setting for commonjs builds of packages to fix @jbrowse/img
(@cmdcolin)
- #3142 Fix unicode
arrow icon not rendering with some fonts in configuration editor
(@garrettjstevens)
core
- #3120 Fix menu items
for changing display type from track menu
(@cmdcolin)
Committers: 2
2.1.0 (2022-07-28)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #3111 Create undo
manager in jbrowse-web and jbrowse-desktop
(@cmdcolin)
- #3115 Add warning
when dotplot renders outside of it's boundaries, and create click-and-drag
panning of dotplot view (@cmdcolin)
- #3102 Allow creating
alternative "add track workflows" from within the "Add track" widget
(@cmdcolin)
- #3043 Create
MultiWiggle track type, adapter, and renderers
(@cmdcolin)
- Other
- #3113 Improve SVG
performance by avoiding re-render when feature is clicked
(@cmdcolin)
- #3110 Remove TSDX
from plugin development tools
(@garrettjstevens)
- #3106 Add "emphasis"
mode for no fill/scatterplot mode in XYPlot type renderings
(@cmdcolin)
:bug: Bug Fix
- Other
- #3109 Better support
for developing plugins from within yarn 2+ workspaces (include __virtual
folder in build) (@garrettjstevens)
core
:memo: Documentation
Committers: 2
2.0.1 (2022-07-13)
<summary>Packages in this release</summary>
:rocket: Enhancement
:bug: Bug Fix
- Other
- #3088 Fix labels
being cut-off in SVG features by rendering feature labels on main thread
(@cmdcolin)
- #3085 Fix zoom to
behavior being inaccurate with many displayed regions visible
(@cmdcolin)
- #3082 Fix negative
strand CIGAR renderings on linear synteny view
(@cmdcolin)
- #3077 Fix crash
opening multiple synteny track selectors launched from dotplot view
(@cmdcolin)
core
- #3086 Fix pxToBp and
bpToPx calculations when there are many displayed regions
(@cmdcolin)
Committers: 2
2.0.0 (2022-07-07)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #3001 Draw SNPs in
modifications/methylation views (@cmdcolin)
- #3068 Allow HTML in
feature tooltips, remove react-simple-code-editor
(@cmdcolin)
- #3065 Allow changing
between xyplot,line,density for linear wiggle tracks and other small fixes
(@cmdcolin)
text-indexing
- #3058 Improve bundle
size and code splitting on embedded builds (v2)
(@cmdcolin)
__mocks__
, core
, text-indexing
- #2949 Upgrade to MUI
v5, mobx-state-tree v5, mobx-react v6, mobx-react v7
(@cmdcolin)
:bug: Bug Fix
- Other
core
- #3064 Fix opening
link in new tab by default in feature details
(@cmdcolin)
- #3053 Avoid
displaying [object Object] on deeply nested data in base feature details
(@cmdcolin)
:house: Internal
Committers: 2
1.7.11 (2022-06-22)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #3044 Remove
node-canvas from @jbrowse/core dependencies
(@cmdcolin)
- #3041 Fix ability to
search and load data files using lower case refName aliases
(@cmdcolin)
- Other
:bug: Bug Fix
- #3049 Fix ability to
use callbacks for the linear arc renderer
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 1
1.7.10 (2022-06-13)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #3025 Add dotplot
session spec (@cmdcolin)
- #2975 Add simplified
URL format for loading synteny views
(@cmdcolin)
- #3023 Add error
handling in case of invalid OAuth2 configuration used.
(@andrzejgrzelak)
- #3020 Allow choosing
trackId when using text-index with --file with --fileId
(@cmdcolin)
- #3016 Allow
whitespace separated refname,start,end type locstring
(@cmdcolin)
- #3006 Add string
array configuration slot UI improvements
(@cmdcolin)
- #2998 Avoid
rendering offscreen contents in pileup renderer
(@cmdcolin)
- #3000 Add reference
base and correct percentage calculations to tooltip on SNPCoverage display
(@cmdcolin)
core
- #2981 Add simplified
URL format for loading spreadsheet and SV inspector
(@cmdcolin)
- #2990 Use shortened
megabases (M) display when zoomed out, and option to hide the "open track
selector" button
(@carolinebridge-oicr)
- #3003 Add ability to
run field formatters on the feature details panel
(@cmdcolin)
- #3017 Add button to
copy track config in About track dialog
(@cmdcolin)
- #2999 Generate
clickable links to track data in about track dialog
(@cmdcolin)
__mocks__
, core
- #3005 Use cascading
menu helper library for track menu to avoid menu going offscreen
(@cmdcolin)
:bug: Bug Fix
Committers: 3
1.7.9 (2022-06-02)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #2991 Use canvas2svg
for SVG export, fixes non-rasterized usage of bezier, arcs, and more
(@cmdcolin)
- #2483 Add setting to
color by query score per alignment for dotplot, support HTML in config slot
descriptions (@cmdcolin)
- #2983 Set
target=_blank by default in user HTML links
(@cmdcolin)
- Other
:bug: Bug Fix
core
- Other
- #2977 Respect
--indexFile option when adding VCF and BED tracks
(@heavywatal)
- #2974 Fix track
indexing being ignored after first add track widget usage
(@teresam856)
:house: Internal
Committers: 4
1.7.8 (2022-05-20)
<summary>Packages in this release</summary>
:rocket: Enhancement
:bug: Bug Fix
- #2969 Fix link on
yeast synteny demo and fix CIGAR rendering on dotplot
(@cmdcolin)
- #2964 Fix crash
displaying modifications called on softclipped regions of reads
(@cmdcolin)
- #2965 Fix filter
functionality on pileup tracks (@cmdcolin)
- #2953 Fix "Open"
button on LGV ImportForm (@cmdcolin)
- #2952 Fix read vs ref
not finding primary alignment on certain CRAM files
(@cmdcolin)
- #2951 Fix viewing
soft/hardclip indicator in some regions
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 2
1.7.7 (2022-05-04)
<summary>Packages in this release</summary>
:bug: Bug Fix
:house: Internal
core
- #2944 Avoid stalling
on undefined assemblyName during ref name renaming
(@cmdcolin)
Committers: 1
1.7.6 (2022-04-26)
<summary>Packages in this release</summary>
Package |
Download |
@jbrowse/desktop |
|
:bug: Bug Fix
- #2939 Fix loading
CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse
desktop (@cmdcolin)
Committers: 1
1.7.5 (2022-04-26)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #2885 Reduce
serialization overhead on alignments tracks and access feature details
asynchronously (@cmdcolin)
- Other
core
, text-indexing
:bug: Bug Fix
- #2863 Render gene with
CDS subfeatures properly (@cmdcolin)
- #2934 Bump @gmod/trix
to fix prefix size calculation and searching first word in index
(@cmdcolin)
Committers: 3
1.7.4 (2022-04-19)
<summary>Packages in this release</summary>
:bug: Bug Fix
- Other
- #2925 Fix embedded
vanillaJS/script tag usage of embedded components
(@cmdcolin)
core
Committers: 2
<summary>Packages in this release</summary>
<summary>Packages in this release</summary>
1.7.1 (2022-04-15)
<summary>Packages in this release</summary>
:bug: Bug Fix
core
- #2917 Create
tsconfig.build.json to add types to plugins/embedded components
(@cmdcolin)
- Other
:memo: Documentation
Committers: 1
1.7.0 (2022-04-14)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #2909 Add
--prefixSize flag to @jbrowse/cli text-index
(@cmdcolin)
- #2887 Optimize
filtering on alignments tracks (@cmdcolin)
- #2879 Multi-level
synteny rubberband (@cmdcolin)
- #2874 Optimizations
for rendering long syntenic alignments e.g. CHM13 vs GRCh38
(@cmdcolin)
- #2872 Better
connection between paired-end alignments in breakpoint split view and
optimizations (@cmdcolin)
core
- #2902 Standardize
heights of widgets in LGV import form
(@cmdcolin)
- #2781 Add floating
labels to SVG features (@cmdcolin)
- #2875 Make assembly
selector remember your last selected assembly
(@cmdcolin)
- #2860 Avoid
performing many peekTransferables to optimize RPC serialization
(@rbuels)
:bug: Bug Fix
- Other
- #2908 Fix
AboutDialog under vite for embedded components
(@cmdcolin)
- #2900 Fix the 'Open
assembly' menu item in jbrowse desktop
(@cmdcolin)
- #2882 Add padding at
the bottom of the configuration editor to help color editing popup being
cutoff (@cmdcolin)
- #2877 Fix strand on
arrows in horizontally flipped mode
(@cmdcolin)
core
- #2891 Use a
user-supplied fetchESM callback to import ESM plugins to fix 'Critical
dependency...' errors from embedded components
(@cmdcolin)
:memo: Documentation
:house: Internal
core
- #2904 Use a
user-supplied fetchCJS callback to import CJS plugins
(@cmdcolin)
- #2891 Use a
user-supplied fetchESM callback to import ESM plugins to fix 'Critical
dependency...' errors from embedded components
(@cmdcolin)
- #2857 Refactor and
improve types of OffscreenCanvas shim and ponyfill
(@rbuels)
__mocks__
, core
Committers: 3
<summary>Packages in this release</summary>
<summary>Packages in this release</summary>
1.6.8 (2022-03-25)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #2847 Add option to
color all the letters on all the reads to the pileup renderer
(@cmdcolin)
- #2849 Avoid drawing
intron subfeatures for gene glyphs
(@cmdcolin)
- #2835 Hide add track
and connection menu items when using embedded component
(@carolinebridge-oicr)
- #2836 Display
low-quality modifications in SNPCoverage renderer for MM tag
(@cmdcolin)
core
:bug: Bug Fix
- Other
- #2852 Fix misaligned
features under breakpoint split view
(@cmdcolin)
- #2844 Fix layout of
small features without labels for SvgFeatureRenderer
(@cmdcolin)
- #2839 Fix the
drawing of SNP height when the SNPCoverage track is using log scale
(@cmdcolin)
- #2825 Fix
tracklabels positioning not updating in UI after user selection
(@cmdcolin)
core
Committers: 3
1.6.7 (2022-03-16)
<summary>Packages in this release</summary>
:rocket: Enhancement
:bug: Bug Fix
Committers: 2
1.6.6 (2022-03-15)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #2796 Add
collapsible accordion sections in configuration editor
(@cmdcolin)
- #2791 Add new
coloring options for dotplot and ability to "rectangularize" dotplot view
(@cmdcolin)
- #2741 Allow ability
to enter a space-separated locstring to open a list of regions
(@cmdcolin)
- #2725 Refactor
InternetAccounts, add standard getFetcher
(@garrettjstevens)
- #2787 Display the
total bp viewed in the header of the dotplot view
(@cmdcolin)
- #2767 Wiggle and
SNPCoverage look and feel improvements
(@cmdcolin)
- #2746 Add .delta and
.chain format adapters, fix ref name aliasing in synteny/dotplot views, and
optimize very long CIGAR string in synteny view
(@cmdcolin)
- Other
- #2799 Exit process
after rendering to speed up jb2export
(@cmdcolin)
- #2793 Add
abortcontroller polyfill to jbrowse-img to allow it to run under node 14
(@cmdcolin)
- #2761 Add a --clean
argument to
jbrowse upgrade
to clean up old files
(@cmdcolin)
- #2760 Make a
configurable refNameColumn in RefNameAliasAdapter
(@cmdcolin)
:bug: Bug Fix
core
- Other
- #2797 Fix crash
plotting methylation in sparse regions
(@cmdcolin)
- #2782 Fix display of
cytobands when horizontally flipped
(@cmdcolin)
- #2678 Preserve
double border line when using trackLabel offset and use smaller gap between
snpcoverage and reads (@cmdcolin)
- #2774 Fix
overwriting broken symlink with --force in add-track CLI
(@cmdcolin)
- #2773 Fix using
global stats autoscale on wiggle tracks
(@cmdcolin)
- #2766 Add a check
for empty content blocks to fix rare empty stats estimation
(@cmdcolin)
:memo: Documentation
:house: Internal
Committers: 2
1.6.5 (2022-02-18)
<summary>Packages in this release</summary>
:rocket: Enhancement
:bug: Bug Fix
- Other
- #2758 Use
VariantTrack for plaintext VCF type
(@cmdcolin)
- #2738 Add better
catch for XS and TS tag detection from CRAM
(@cmdcolin)
- #2733 Use sparse
array for alignments coverage to fix bug viewing large sparse regions
(@cmdcolin)
- #2734 Use node fetch
instead of follow-redirects in cli
(@cmdcolin)
- #2726 Handle .bgz
file extension for text-index (@cmdcolin)
- #2727 Add engines 16
to @jbrowse/img (@cmdcolin)
- #2723 Make jbrowse
desktop more robust to errors when reading recent sessions file
(@cmdcolin)
- #2715 Change
--target to --root for jbrowse CLI admin-server
(@cmdcolin)
core
- #2757 Fix type
confusion with stats estimation causing BAM files to fail byte size
calculation (@cmdcolin)
- #2750 Add
bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in
alignments track in webkit and firefox
(@cmdcolin)
- #2719 Avoid
uninitialized state during stats estimation
(@cmdcolin)
- #2707 Fix ability to
use authenticated assembly files
(@garrettjstevens)
- #2695 Fix disabled
state on the linear genome view track labels dropdown menu
(@cmdcolin)
:memo: Documentation
- #2716 Update to node12
requirement for @jbrowse/cli (@cmdcolin)
- #2605 Developer guide
reorganization and create new API document
(@cmdcolin)
:house: Internal
Committers: 3
<summary>Packages in this release</summary>
<summary>Packages in this release</summary>
<summary>Packages in this release</summary>
<summary>Packages in this release</summary>
1.6.0 (2022-01-28)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- Other
__mocks__
, core
- #2165 Add ability to
create new sessions solely from a "session spec" in the URL
(@cmdcolin)
:bug: Bug Fix
core
- #2688 Fix
adapterType dropdown in add track widget
(@cmdcolin)
- #2654 Fix broken
@jbrowse/img by adding babel config back to core
(@cmdcolin)
- Other
:memo: Documentation
- #2663 Add
documentation for URL params and session spec
(@cmdcolin)
- #2655 Add link to PAG
2022 youtube tutorial on demos page and course archive
(@cmdcolin)
:house: Internal
core
- #2649 Add Cypress
test of package that uses embedded components
(@garrettjstevens)
- #2648 Avoid
console.warns in tests due to writing to MST nodes that are not alive
(@cmdcolin)
- Other
- #2657 Fix hot reload
using yarn resolution on react-error-overlay
(@cmdcolin)
Committers: 3
1.6.0 (2022-01-28)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- Other
__mocks__
, core
- #2165 Add ability to
create new sessions solely from a "session spec" in the URL
(@cmdcolin)
:bug: Bug Fix
core
- #2688 Fix
adapterType dropdown in add track widget
(@cmdcolin)
- #2654 Fix broken
@jbrowse/img by adding babel config back to core
(@cmdcolin)
- Other
:memo: Documentation
- #2663 Add
documentation for URL params and session spec
(@cmdcolin)
- #2655 Add link to PAG
2022 youtube tutorial on demos page and course archive
(@cmdcolin)
:house: Internal
core
- #2649 Add Cypress
test of package that uses embedded components
(@garrettjstevens)
- #2648 Avoid
console.warns in tests due to writing to MST nodes that are not alive
(@cmdcolin)
- Other
- #2657 Fix hot reload
using yarn resolution on react-error-overlay
(@cmdcolin)
Committers: 3
1.6.0 (2022-01-28)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- Other
__mocks__
, core
- #2165 Add ability to
create new sessions solely from a "session spec" in the URL
(@cmdcolin)
:bug: Bug Fix
core
- #2688 Fix
adapterType dropdown in add track widget
(@cmdcolin)
- #2654 Fix broken
@jbrowse/img by adding babel config back to core
(@cmdcolin)
- Other
:memo: Documentation
- #2663 Add
documentation for URL params and session spec
(@cmdcolin)
- #2655 Add link to PAG
2022 youtube tutorial on demos page and course archive
(@cmdcolin)
:house: Internal
core
- #2649 Add Cypress
test of package that uses embedded components
(@garrettjstevens)
- #2648 Avoid
console.warns in tests due to writing to MST nodes that are not alive
(@cmdcolin)
- Other
- #2657 Fix hot reload
using yarn resolution on react-error-overlay
(@cmdcolin)
Committers: 3
1.5.9 (2022-01-13)
<summary>Packages in this release</summary>
:bug: Bug Fix
Committers: 1
<summary>Packages in this release</summary>
1.5.7 (2022-01-13)
<summary>Packages in this release</summary>
Package |
Download |
@jbrowse/plugin-dotplot-view |
|
@jbrowse/desktop |
|
@jbrowse/web |
|
:rocket: Enhancement
Committers: 1
1.5.6 (2022-01-12)
<summary>Packages in this release</summary>
:rocket: Enhancement
core
- #2629 Add ability to
get parent feature in jexl syntax with either parent(feature) or
get(feature,'parent') (@cmdcolin)
Committers: 2
<summary>Packages in this release</summary>
1.5.4 (2022-01-07)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #2601 Allow opening
multiple sequences from the desktop start screen
(@cmdcolin)
core
:bug: Bug Fix
- Other
core
- #2626 Fix bad layout
resulting in features being unable to be clicked in embedded mode
(@cmdcolin)
:house: Internal
Committers: 3
1.5.3 (2021-12-21)
<summary>Packages in this release</summary>
:bug: Bug Fix
Committers: 1
1.5.2 (2021-12-20)
<summary>Packages in this release</summary>
: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
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
:house: Internal
Committers: 6
1.5.1 (2021-11-04)
<summary>Packages in this release</summary>
: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
: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
:house: Internal
Committers: 4
1.5.0 (2021-10-18)
<summary>Packages in this release</summary>
: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
:house: Internal
- Other
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
1.4.4 (2021-09-14)
<summary>Packages in this release</summary>
: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
Committers: 3
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
1.3.5 (2021-08-23)
<summary>Packages in this release</summary>
1.3.4 (2021-08-23)
<summary>Packages in this release</summary>
: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
:bug: Bug Fix
core
- Other
- #2208 Fix issue
where collapsed categories were not remembered after toggling a track
(@cmdcolin)
:memo: Documentation
: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
Committers: 4
1.3.3 (2021-08-02)
<summary>Packages in this release</summary>
:rocket: Enhancement
:bug: Bug Fix
- Other
- #2159 Stop local
storage quota-exceeded errors preventing the app from starting
(@cmdcolin)
- #2161 Remove outline
from clicking on SVG chord tracks (@cmdcolin)
- #2157 Fix rendering
of negative strand alignment modifications/methylation
(@cmdcolin)
- #2131 Fix
mouseovers/click handlers after "force load" button pressed
(@cmdcolin)
- #2128 Fix using the
"Color by modifications" setting on files that need ref renaming
(@cmdcolin)
- #2115 Fix bug where
sometimes plugin could not be removed from UI
(@garrettjstevens)
- #2119 Fix loading
indicator on the reference sequence selector getting stuck
(@cmdcolin)
core
- #2101 Fix behavior
of the end-of-list indicator in refNameAutocomplete to always display as a
disabled item (@teresam856)
:house: Internal
- Other
core
- #2099 Use rbush data
structure for layout of feature tracks
(@cmdcolin)
Committers: 3
1.3.2 (2021-07-07)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
core
- #2106 Use more
accurate estimator for feature label widths
(@cmdcolin)
:bug: Bug Fix
- #2109 Make sure to
wait for assembly to load before downloading canonical refnames in SV
inspector (@cmdcolin)
- #2111 Fix "Can't
resolve '@jbrowse/plugin-legacy-jbrowse'" in
@jbrowse/react-linear-genome-view
(@garrettjstevens)
Committers: 2
1.3.1 (2021-07-06)
<summary>Packages in this release</summary>
:rocket: Enhancement
: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
Committers: 5
1.3.0 (2021-05-24)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
- #2001 Make tracks
added using the add track widget a session track if not in adminMode
(@cmdcolin)
- #1980 Add popup
confirmation dialog for unknown session plugins, and use plugins.json as a
whitelist (@cmdcolin)
- #1977 Upgrade
@material-ui/data-grid (@cmdcolin)
core
- #1982 Allow manually
specifying adapter type if filename does not match expected pattern
(@cmdcolin)
- #1975 Allow local
files on the users computer to be opened as tracks in jbrowse-web
(@cmdcolin)
- #1865 Show modified
bases using MM and MP/ML tags in BAM/CRAM
(@cmdcolin)
- #1984 Better feature
details when there are short arrays of json supplied as feature data
(@cmdcolin)
- #1931 Create in app
graphical plugin store
(@elliothershberg)
:bug: Bug Fix
core
- #1985 Avoid error
calculating UTR on features that have no exon subfeatures
(@cmdcolin)
- #1954 Add more
environments to configSchema create calls to fix ability to use custom jexl
commands with main thread rendering
(@cmdcolin)
- #1963 Fix ability to
use DialogComponent (used for svg export, pileup sort, etc) on embedded
components (@cmdcolin)
- #1945 Fix hic not
being able to render due to incorrect lazy loading
(@cmdcolin)
- Other
:memo: Documentation
- #2002 Add @jbrowse/img
to homepage (@cmdcolin)
- #2007 Update docs for
modifications/methylation coloring, plugin store, and the sequence panel in
feature details (@cmdcolin)
- #1976 reorganize the
demo page to emphasize the cancer sv demo more
(@rbuels)
- #1952 Add demo for
1000 genomes extended trio dataset to website
(@cmdcolin)
- #1862 Add example for
using a build-time included plugin to storybook
(@cmdcolin)
:house: Internal
- Other
- #2003 Make
SNPCoverage independently generate the modifications tag-color mapping
(@cmdcolin)
core
, development-tools
Committers: 4
1.2.0 (2021-05-03)
<summary>Packages in this release</summary>
: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
Committers: 4
1.1.0 (2021-03-29)
<summary>Packages in this release</summary>
: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
- 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
:house: Internal
- Other
core
- #1834 Change
jbrowse-components monorepo default branch from 'master' to 'main'
(@rbuels)
Committers: 6
1.0.4 (2021-03-08)
<summary>Packages in this release</summary>
: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
:memo: Documentation
:house: Internal
Committers: 7
1.0.3 (2021-01-11)
<summary>Packages in this release</summary>
:rocket: Enhancement
- Other
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
: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
Committers: 6
v1.0.2 (2020-12-02)
<summary>Packages in this release</summary>
: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
Committers: 3
v1.0.1 (2020-11-25)
<summary>Packages in this release</summary>
:rocket: Enhancement
: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
:house: Internal
Committers: 5