Skip to content

Version.md

Latest commit

 

History

History
447 lines (315 loc) · 17.3 KB

Version.md

File metadata and controls

447 lines (315 loc) · 17.3 KB

Version History

54.0.4

  • add pixelsPadding option for modbed track while display in heatmap mode, used for padding the drawing tick pixel

54.0.3

  • fix an bug that screenshot UI doesn't show axis label
  • fix #319

54.0.2

  • Fix Chrome 112 Navbar nested css problem (by Shane)
  • small changes to modbed base pair level visualization

54.0.1

  • new genome for Parhyale hawaiensis version 5 is added
  • added an option to hide minimal annotations
  • removed some old version gene annotation tracks (files can be requested if still need)

54.0.0

  • added new track type modbed for display long read sequencing methylation data
  • added ensembl style for matplot and dynamic tracks
  • fixed a screenshot bug when svg imported to Adobe Illustrator
  • removed default highlight for gene/snp/region search
  • added highlightPosition url parameter, used with position, for example &position=chr3:181429711-181432223&highlightPosition=1 will jump to chr3:181429711-181432223 and highlight it at same time

53.8.0

  • added light/dark theme setting
  • added view sharing via email/embed/QR code

53.7.0

  • added MANE select 1.0 for hg38
  • updated gencode tracks for hg38, hg19, mm39 and mm10
  • add opitimization for dropbox shared hubs

53.6.3

  • 3D viewer can enable region set view from segments
  • fixed a bug that MIN/MAX aggregator in numeric track crash
  • added t2t-chm13-v2.0
  • fixed sceenshot issue with genome align track, reported by #252
  • added highlights in screenshot by #251

53.6.2

  • rn7 added
  • qBed add secondary color config and horizontal line option per Slack user request
  • imporved highlighting functions

53.6.1

  • changed circlet view UI slightly
  • added chord view
  • added Jaspar 2022 TF tracks to Annotation track sets

53.6.0

  • new genomes susScr3, calJac4, rheMac10 added.
  • UI, button styles changes from Shane Liu
  • added cookie consent notice

53.5.2

  • new genomes susScr11, oviAri4 and Brapa (#228) added.
  • image tracks/hubs update
  • add new feature to allow long range tracks with colors for each arc/heatmap diamond

53.5.1

  • add spin utility for 3d model viewer
  • add clampHeight option to chromatin interaction track for arc and heatmap style

53.5.0

  • removed unnecessary re-render of numerical track
  • adding push notification
  • allow HiC track bin size and normalization options linked to the hic file itself
  • add an option italicizeText to allow italic text/label on gene tracks
  • new genome xenTro10 added

53.4.1

  • added bigchain format support
  • bigchain and genomealign can be added from remote track UI with specify a query genome
  • layout header height bug fix
  • region jumping following UCSC Browser: position coordinates chr6:130129863-130129899 (1 based, 37bp), bed coordinate chr6 130129863 130129899 (0 based, 36bp)

53.4.0

  • new T2T genome assembly t2t-chm13-v1.1 added
  • improved 3D module
  • support Repeatmasker V2 format bigbed, track type rmskv2

53.3.2

  • for bigwig track, specify ensemblStyle option to true can enable data with chromosome names as 1, 2, 3...work in the browser
  • bedcolor track type
  • Roadmap (hg38) hub update
  • more genome alignment tracks
  • pdf output label alignment improvement

53.3.1

  • switched to @gmod/bbi library for bigwig data fetching
  • removed zoom level configuration for bigWig track

53.3.0

  • updated 4DN data hubs
  • fixed a screenshot bug while tracks are grouped

53.2.0

  • introduce boxplot track type show numerical data in small window as boxplots

53.1.0

  • vcf track bug fix for certain tooltip clicking
  • updated SARS-CoV-2 data hubs by Changxu Fan

53.0.0

  • 3D structure view module added, for more please check the 3D documentation
  • basic support for vcf format

52.5.2

  • add an option queryEndpoint to TrackModel allow customization of gene/feature annotaion query
  • added 2 new Trypanosome genomes TbruceiTREU927 and TbruceiLister427 per user's request

52.5.1

  • fixed a bug that dynseq track doesn't work correctly in Safari
  • fixed a bug that screenshot error on hic heatmap mode
  • fixed a bug that longrange track cannot change name/label
  • added a feature that sessions are sorted by date by dafault, can change to sorting by label
  • add a new track type rgbpeak to show the peaks in bigbed format supporting itemRgb attribute
  • added a new virus genome hpv16, ref sequence from https://www.ncbi.nlm.nih.gov/nuccore/NC_001526.4, gene annotation from https://www.ncbi.nlm.nih.gov/assembly/GCF_000863945.3/

52.5.0

  • Dynamic sequence track type dynseq added, the track type is proposed and initially developped by Surag Nair from Anshul Kundaje's lab at Stanford University

52.4.1

  • bug fix: numerical track y-scale threshold not working for negative values
  • bug fix: local data hub missed track's metadata attibute

52.4.0

  • added percentile scale for interaction tracks (hic, longrange) etc.
  • improved fixed scale config for numerical tracks
  • video output for dynamic track
  • added the highlight beams for interaction track at heatmap mode

52.3.0

  • fixed a bug that hic track fetches whole hic file when switch to other norm options with updated hic-straw package
  • fixed a bug that numerical track shows wrong threshold for negative data values
  • 6 new genomes added
  • new noDefaultTracks url parameter remove the default tracks while loading a remote hub
  • removed limitation that querygenome of genomealign track need be preconfigured
  • added default width and height for withAutoDimensions module
  • enhanced genomeailgn track by Silas Hsu

52.2.0

  • add the API key and secret for accessing 4DN tracks

52.1.0

  • added new genome Plasmodium falciparum (Pfal3D7)
  • fixed one bug that bam track at density mode not showing y scale config
  • fixed a bug when load g3d track from datahub caused browser track facet table lost
  • fixed issue #111 and #176 for long range track data filtering
  • add option to avoid use firebase database by remove session/live function (see doc for details)

52.0.0

  • upgrade dependent packages: react, react-dom -> 16.13.1
  • supports nodejs v12+
  • SARS-CoV-2 hubs updated by Fan
  • fixed a smooth option caused display issue (related to #163)
  • improved window/container resize listener using ResizeObserver API
  • improved responsive layout of navigation menu and tools bar
  • modified vendor bigwig.js to support chromosome names like chr1 or 1
  • introduced image track: image track example

51.0.6

  • track file information can be displayed with track data (like resolution and normalization for hic, g3d track etc)
  • new 'snv' track for display sequence variations from reference
  • update hubs of virus genomes

51.0.5

  • updated SARS-CoV-2 publib hubs and default tracks
  • enabled tracks can be loaded from both hub url and previous session storage with new URL parameter hubSessionStorage
  • fixed a qBed when mouseover outside of the track caused TypeError bug
  • fixed a bug that remote hub load button not working in Firefox

51.0.4

  • add dynamic arc view for dynamic hic tracks
  • fixed a bug arc with negative score not show up in screenshot
  • dynamic colors dynamicColors are supported for all dynamic tracks

51.0.3

  • add a new option greedyTooltip for arc display of chromatin interaction data, this option will show more than one interaction from same 2 loci if exists
  • track type callingcard renamed to 'qBed'
  • update hic-straw package

51.0.2

  • fixed a crash bug when reize window with a dynamic bedgraph track
  • added dynamic labels to dynamic tracks
  • fixed a bug when zooming in a dynamic bedgraph data not show

51.0.1

  • add tooltip for dynamic hic track
  • fixed one bug when bigwig files have just one zoomLevel causing data fetch error
  • a new option alwaysDrawLabel added to bed and categorical track for telling the browser always render the label
  • update nCoV2019 public hubs

51.0.0

  • added dynamic numerical track
  • added dynamic plot menu for >=2 numerical tracks
  • fixed a virusBrowserMode bug (redirected to main page) introduced in last few commits
  • fixed a bug long-range track data cannot have dot in chromosome names
  • added an option zoomLevel for bigwig track
  • changed custom track menu to remote track for better distinguish from local track
  • added dynamic hic plot track/menu
  • updated public hubs for nCoV2019

50.4.0

  • added 4 virus genomes for aiding virus research
  • global URL parameter virusBrowserMode added
  • VR freeze issue fixed
  • VR mode supports longrange track type now, thanks Silas for the help
  • certain public hubs added to 2019-nCoV by Changxu Fan

50.3.6

  • added sea hare genome (aplCal3) by Xiaoyu
  • added yeast sacCer3 genome
  • calling card track update by Arnav
  • multiple alignment track update by Xiaoyu

50.3.5

  • this version we implemented the PWA design
  • in case your device went offline, the local track and local text track function can still be used
  • whenever there is a new version, a notice will show if user still use the old version
  • fixed a bug for numerical track when there are negative values, set scale to fixed shifted values
  • fixed a bug metadata terms were loaded when hub was loaded from URL

50.3.1

  • fixed a small bug display view window in pixel
  • fixed numerical track y-axis scale while setting minimal y value

50.3.0

  • the square display for hic track is added
  • add all tracks button added for hub track table
  • text in refbed format supported

50.2.0

  • introducing the new support for text tracks, text files can be visualized directly in the browser, check the documentation for more details
  • text in bed format supported
  • text in bedGraph format supported
  • text in longrange format supported
  • please contact us for customized format

50.1.0

  • introduce a new track type g3d for genomic 3D structure display, see more at the docs
  • fixed link to slack invitation

50.0.4

  • fixed a sequence fetch bug
  • fixed a 'browser content empty' error for Go Live function

50.0.3

  • add sessionFile URL param for loading a session file/state from URL
  • add new genome fruit fly dm6 and C.elegans ce11

50.0.2

  • the browser can respond to window resize event now, thanks to Silas who stopped by and helped debug this function
  • add Zebrafish genome danRer11
  • from discussion with Arnav for callingcard track, plot a single circle (per track) at the midpoint of the interval

50.0.1

  • fixed a facet table bug when metadata is undefined, cannot distinguish track type with substrings like bed and bedgraph
  • fixed a session saving bug due to updated firebase related packages
  • when user define height in string like "25" instead of 25, the browser won't complain
  • fixed a bug that genome align track shows data fetch error

50.0.0

  • this release is not an update for browser function but related to dependent package
  • updated to use webpack 4 and typescript 3.4
  • removed deprecated package react-scripts-ts, use typescript support from create-react-app
  • updated react-app-rewired to 2.1
  • motivated by an issue that ArcDisplay is not working on build version but development version

48.5.3

  • added chicken genome galGal6 and galGal5
  • a flatarc mode added for chromatin interacion track: flat arc mode
  • fixed a metadata bug when define customized color

48.5.2

  • fixed a bug that facet table shows error count of loaded tracks
  • Rhesus rheMac8 genome is added
  • fixed bug #117
  • enabled multiple rows for categorical track when categories overlap

48.5.1

  • a new option hiddenPixels is added to control an item should be hidden for annotation tracks
  • fixed a bug that screenshot missed chromosome label in Ruler track
  • user can input track options while submit a custom track or local track
  • url in track of a custom datahub can use relative path

48.5.0

  • track height and color configuration enabled for genome align track
  • tooltip on heatmap and heatmap style of interaction track
  • annotation tracks adding UI will be shown when corresponding genome align track is added
  • fixed a bug that intra-region arcs are not displayed
  • fixed an Unable to preventDefault inside passive event listener bug
  • fixed the bug highlight region error when genomealign track is added, related to #104
  • fixed an issue that tracks order in local hub doesn't follow order in hub.config.json file
  • local track supports BAM track now
  • fixed a bug that categorical track error when category not exists in hub file

48.4.6

  • tooltips on genome align track, both rough and fine mode (from Xiaoyu)
  • annotation tracks UI for genome align track
  • switched to latest bam-js from GMOD for bam file fetching

48.4.5

  • free text search for track in track table using fuse.js
  • pearson correlation value is added to scatter plot
  • add YouTube channel link
  • fix a bug for screenshot app missed background color for tracks
  • cleaning package.json file
  • screenshot can now generate pdf as well using svg2pdf.js, while the style may slight changed compared to SVG

48.4.4

  • hammock track type added with basic support
  • genome logo can now be clicked to change to another genome
  • mouse mm9 and cow bosTau8 added
  • arabidopsis araTha1 (same as TAIR10) added
  • session can either be downloaded as a session file or a datahub file
  • highlight box color could be configured now
  • color configurable for boxplot in geneplot
  • marker size and color configurable for scatter plot
  • heatmap type in geneplot switched back to using plotly.js as well

48.4.3

  • fixed a bug for long-range track has negative score
  • add line width config for interaction track when displayed as arcs
  • updated to hic-straw 0.9.0 as suggested by Jim Robinson
  • fixed a bug when reading local .hic file caused data fetch error
  • removed timeout mechanism for bigwig tracks

48.4.2

  • added the scatter plot app
  • enabled canvas renderer for arc and heatmap display of chromatin interaction tracks
  • enabled height config for chromatin interaction tracks

48.4.1

  • use CND hosted plotly scripts to reduce script bundle size
  • fix a bug that screenshot app shows left expanded region when there is interaction track
  • use nivo library for heatmap in geneplot app
  • fix a bug that values for geneplot missed strand information
  • fix a bug certain gene symbol cannot be found in geneplot
  • fix a bug strand for region sets by default sets to -

48.4.0

  • matplot function is added
  • configuration for matplot track is added with smooth, aggregate methods, line width etc.

48.3.1

  • retina screen display improved as track rendered in canvas
  • SNP search through Ensembl API
  • SNP track added as well, data comes from Ensembl API
  • Aggregate method is configurable for numerical tracks, MEAN, SUM, COUNT, MAX, MIN are supported, MEAN is default
  • smooth option added for numerical tracks

48.3.0

  • new function to re-order many tracks at one time by drap and drop
  • new hot key (Alt+G) to open the interface for re-order many function
  • new track type callingcard for displaying Calling card data
  • new function geneplot for plot overall signal from a numerical track over a gene/region set
  • function to download current session to local disk
  • accept session files uploaded from local disk

48.2.1

  • use hic-straw package for .hic data source, removed the dependency to igv.js and juicebox.js
  • added FetchSequence App to allow fetch sequence of current region or user specified regions
  • Fix a bug while upload file hub causing page freeze
  • Rough alignment enhanced by Xiaoyu

48.2.0

  • genome alignment track enhanced view, improved by Xiaoyu Zhuo
  • allow users to upload local file as tracks
  • allow users to upload entire folder or many files as a data hub by creating a hub.config.json file
  • HiC track normalization implemented by Silas Hsu

47.2.8

  • first stable version since we start coding the new version of the browser code
  • embedding browser function is available
  • browser code also uploaded to npm
  • (version number prior to 47 refers to the old browser codebase)