Genome Browser Software Features

This page contains a list of major new software features found in the UCSC Genome Browser. The most recent features are always at the top of the page. A more detailed list can be found at https://genecats.gi.ucsc.edu/builds/versions-all/v<versionNumber>.html

2024

17 December 2024, v475

• Improved hgsql error message when hg.conf is missing. It has been simplified to remove internal and incorrect details
• Have bedPartition generate a unique name for record. Remove -partSize, which just groups by number of partations, and was not useful. It is replaced by -partMergeSize, to allow for merging partations within a certain distance
• Fixes for openssl3
• CGI version now shows up on the configuration page

26 November 2024, v474

• Added setColorWith to allow wiggles to be colored by a bigBed
• Allow people to select Exit Mult-region on the pop-up box
• Better error messages if an assembly hub db isn't found for some reason
• Added a cart rewrite to support moving decipher tracks into a supertrack
• More work on adding support for non-ASCII characters in hgTracks and PDF
• Fixed a subtle drawing bug in zoomed-in bigWigs
• More fixes for hideOthers, make sure that tracks that are on by default are really hidden
• Hide legend if all gnomad pli tracks are hidden
• Suppressed unnecessary error log messages due to loading a hic file with an invalid normalization type
• Add in GENCODE hgc gene and transcript name display in table, as check for HGCN is missing miRNAs not in HGNC but in mirBASE
• Fixed an issue in loading expRatio data when the number of experiments exceeded the number of exons; such files should now be able to be loaded and processed (e.g. for conversion to bigBed)

5 November 2024, v473

• Fix density mode for vcfTabix
• Fix problem with hubUrl being trashed if Genark hub was specified as db
• Ongoing work on behaving rationally when certain limits are exceeded in hgTracks
• Primer3 outlink from hgGene now gets +-200bp flanking seq around the first and last exon to design primers around the exons
• Fix freeType and Postscript handling to deal with UTF-8 encoded strings
• Adapting the tutorial reminder to say where users can find the tutorial if they click it away now
• Right click - move to top respects the ruler track
• Click OK when "enter" key is pressed on trackUi dialog box
• Now we just filter all the types, like BLATs guess, which makes them consistent and correct, the same as the default behavior it always had
• The configuration page for some track types can include a selector to change the track color, but the selectors for subtracks of a composite were all being placed in the configuration block of the first subtrack. They are now distributed among the subtracks
• Don't show download link to big* files on the table browser for non-distribution tracks
• Fixed jQuery upgrade bugs: group drag and drop of tracks, drop-down checklist position, checkboxes marked as change during a form submit
• Disable the "download track data in window" option on GBiBs since they don't have an API available

15 October 2024, v472

• Added new options to the right-click menu: hide all others, move to top, move to bottom
• Upgraded jQuery and jQuery-ui to the latest versions
• Force all tracks into coverage mode if 32K image size would otherwise be exceeded
• Users can now specify their parallel load timeout value
• Added (i) icons to table browser to better indicate you can mouseover for help text
• The hgLiftOver CGI and the command-line liftOver tool now include an option to keep a copy of the positions from the input file in the lifted output (for formats like BED, genePred, and others that include an item name field or something similar). This should help keep track of which items get mapped where for some users
• Various improvements to both the hgGateway search and new GenArk search
• Amino acid display now only shows up at base level
• Made the two reset genome browser links in the menu the same
• Performance improvements for Hi-C tracks (and anything else that uses fakeCurl) - we now do a better job of re-using an existing udc handle for a series of requests on the same file. This should also fix some issues associated with having "too many file handles" open when viewing multiple Hi-C files at once
• The option to change some track draw colors is now available on their hgTrackUi page as well as the pop-up configure box in the main browser, and that option remembers what color was previously chosen for that track

24 September 2024, v471

• Changed track control labels so they word-wrap
• For assembly hubs, strip hub_ prefix in table browser fasta output
• Made hgTrackUi schema links visible in the window, even when a subtrack config is open. Limit the subtrack config to the size of the window, but make it scrollable
• Improved genbank search by reducing number of MySQL commands
• Allow configuration of bigBed filters on bigGenePred tracks
• Fixed a few instances of '.' in table names not being allowed/anticipated

9 September 2024, v470

• Basic support for multiple decorators on one track is in place; documentation (and UI review) pending
• Added checkbox to hgTrackUi of ruler track to make amino acid display more on by default
• If a track hub has a track specified with a group that is not defined, put the track in the generic group for that hub, not in "other"
• Allow bigInteract tracks' endsVisible to be set via trackDb in addition to hgTrackUi
• Decorator UI should now respect trackDb settings for blockMode and glyphMode
• Fixed up mouseOver wiggle track when a track in wiggle mode switches to not wiggle mode, do not display the mouseOver
• Fixed a bug where an automatic switch to density mode was not setting the track type to wig
• Fixed a problem in the bigBed library with summary levels failing on very large chromosomes
• Fixed an issue where the newly-introduced fakeCurl library had a namespace collision with libcurl, which broke remote halSnake tracks
• Support added for multiple filterBy sets on the same page of HTML

13 August 2024, v469

• Added a configure page option for controlling whether hgc clicks open in pop-ups or not
• Made knownGene handle like regular tracks by hgSearch, moved HGNC and MANE search results ahead of knownGene in priority
• Hi-C tracks now have support for version 9 of the hic file format (the current latest). Basic support for other normalization modes is also included, but we recommend you add any normalization to all resolutions in the file instead of only selected ones
• Standardized the font size of our dialog windows (rec. track sets, multi-region, etc)
• Changed chroms to chromAuthority names in hgBlat and hgPcr
• Track heights now capped at 31,000px
• Print BLAT version on hgPcr form since ask for it
• Made priority optional in groups.txt. for the hub groups feature. Also actually sort by priority if specified
• Fixed defaultIsClosed flag on the hub groups feature and changed it to sort groups by name without regard to case
• hgSession will now only load sessions from URLs that are actually URLs, and no longer reports the content of bad settings (it was a security flaw)

23 July 2024, v468

• Pop-up hgc pages can now be exited by clicking outside the box
• Extended DNA case/color output now works for track hubs
• Increased the font size for jquery dialogs
• Force underlines under lowercase g in modern web browsers that are too smart for biology
• PSL custom track default settings now shows mismatches
• Removed the requirement for defaultIsClosed and Priority from the hub groups setting
• In some situations, the browser mouseover text was reporting the same exon number for multiple different exons in a track. This is now fixed, and the mouseover text for each exon should accurately reflect its index

2 July 2024, v467

• Removed some of the text below the hgTracks image
• Made some tooltips have longer delays than others and removed some of the less helpful tooltips
• hgc page for BAM: removed the "English" CIGAR text and added a new legend for normal cigar string
• Added endpoint to the API: genarkGenomes - to list the GenArk genome assemblies or test if one exists, remains to be documented
• Added support in the API for bigChain, bigMaf and bigDbSnp track types, remains to be documented
• Added new API function -revComp to the get sequence complement (reverse)
• bigBedInfo now outputs the no. of defined fields
• Added hg.conf option to load a mirror-specific .js file (for china mirror)
• Made the hgTracks basic tutorial on by default and document the hg.conf parameter
• hg.conf option to switch on itemRgb by default
• hg.conf option to remove the dink left/right buttons under the image

11 June 2024, v466

• Added the number of start/end hard and soft clipped bases to BAM hgc page
• Plug trackDbCache into hgc and hgTrackUi
• Skip BAM details if the read is very long
• Added a new baseView track type that will draw something like the base position track given a set of coordinates from a bigBed file
• Removed the click & drag to scroll tooltip from hgTracks image
• Fixed native assemblies not being selectable in hgGateway autocomplete
• Search results in hgTables now bold properly
• Unify the different color pickers (drag select highlights, track item highlights and track item colors) into hui.js. Ensure the text box and palette selector work
• Merged blatHuge implementation. This adds a gfServer and blat that search genomes greater than 4 gigbases

21 May 2024, v465

• Allow hubs to have their to declare their own track groups
• Added a new bigBed trackDb setting for highlighting items, specified the same way as trackDb filters
• Added a filter on filterBy (dropdown filters) to hgTrackUi
• Genark hubs can be selected by using db=GC* in trackDb
• Added 'in new tab' link to hgBlat output page and an info icon to the "make custom track" BLAT button
• Allow n. notation in HGVS parser
• Chevrons are no longer drawn in squish mode even if intronGap is set
• Fixed hgGateway autocomplete to not show nulls for assembly hub hits
• Made drag selects not open hgc pages
• Changed exon mouseover after user feedback
• Skip super long CIGARs on hgc page so the page doesn't crash anymore on long reads
• Strip off hub_#_ when sending Genark hub data to Galaxy

30 April 2024, v464

• Track hubs can now designate their own track groups
• Made clicks from hgTracks to hgc open in a dialog so the user stays on hgTracks
• Tooltip improvements: made the timeout for the next tooltip a little slower and fixed a positioning bug
• Fixed the arrow buttons, but this time hopefully without breaking the entire site
• Added back the link with hub info to track hub in blue bar
• Improved exon mouseover as per Ana and user ML

9 April 2024, v463

• hgSession now has a "view count" column in the session list and a new copy to clipboard button for every session link
• The > and >> buttons on hgTracks now move by at least on bp when zoomed in to a small window
• Added a reset buttons for hgTrackUi filterText text input boxes
• Made maxItemsPossible an hg.conf variable. This variable limits maxItems to be no more than maxItemsPossible.
• Added a link "chrom sizes" to the menu bar, and pushed up the chrom.sizes download instructions on that page

19 March 2024, v462

• bigBed coverage graphs now always include zero
• Track hubs: added a "more info" link to their description.txt in their group blue bar on the right
• Increased maxItemsPossible to 100,000 in response to user MLQ
• Fixed CRAM custom tracks on hs1

27 February 2024, v461

• Fixed exon numbering mouseovers in squish mode
• Auto-resize hgTracks if user comes in not from hgGateway
• Added a way to limit RAM used by the browser
• Hub subtrack shortlabels now show up in the "table" dropdown of the table browser
• Mouseover speed optimization: wait for the actual element to be moused over before creating all the related mouseover node elements

6 February 2024, v460

• Save the last 5 searched terms into the autocomplete dropdown
• Big based tracks now go straight into density coverage instead of lowering visibility on item overflow or exceeding height
• Fixed mouseover event not re-raising after the mouseover timer completes
• Fixed bug with tracks not updating when zooming out
• Added a note to longLabel if a VCF track is in coverage mode
• Added hg.conf variable to trust trackDb and not check for data presence at startup
• Exons now show the phase of the first and last codon on mouseover
• Added a menu entry "find short exact DNA match" to the "genome browser" menu
• Added a new button "highlight" and a menu entry to the UI, the same as the "h+m" keyboard shortcut
• The hgBlat "sequence too short" error message now points to our help docs, Hiram's findMotifs tools, and oligoMatch track
• Summary modes now used in bigBeds for coverage mode
• Decoupled item limits for bigBeds from item limits in the display
• Limit VCF fetch to 10,000 items instead of unlimited
• Make the tutorial warning go away if it has been viewed more than 5 times without being explicitly closed
• When submitting the track search form, don't send an empty hubUrl setting as it confuses the cart code
• Fixed up seg fault when doing mrna singlePos searching
• Fixed bug where csv output on Table Browser header was still tsv
• If you add '&verbose=x' to any URL, the CGI will now output the verbose() messages. This means that you can see what UDC is doing. Does not stay in the cart. Feedback by engineers is appreciated
• Modified gff3ToGenePred to try hard to find meaningful names for records that don't have a Name attribute

16 January 2024, v459

• Added a search bar to the home page
• longLabel is now updated when maxWindowCoverage is active and format is BED4-8
• When CGIs running on RR or euro/asia-node cannot connect to hgcentral they now output a long email message with contact email address
• Last mouseover now re-triggers event that fired while we were blocking when a tootlip was already visible (#32697)
• Small bug fix to bigBed extra fields display after a user complaint
• Added hg.conf variable (trustTrackDb) to force the CGI's to validate trackDb instead of just trusting it
• Ongoing work on hgGeneGraph against bots (#32714)

2023

19 December 2023, v458

• Custom track parsing: don't remove custom track files when there is an error
• Add the ability to simulate a custom track load error using ctTest=1 on the URL
• Additional tooltip improvements: make the tooltips go away when mouse leaves the web browser window or enters an input box or right-click. Improved the tooltip Y position to go lower or higher depending on where the mouse enters from. Made the font size of the tooltips be a configurable option
• Added right-click option to enter exon position for genePred tracks
• Made enter key submit forms in dialog boxes
• Made ref seq historical track open when HGVS term hit an outdated transcript
• Hide children of superTracks when loading RTSs
• YPs (chrM genes) got dropped from Refseq curated track, changing doNcbiRefSeq to put them back
• Added utility (fixTrackDb) to update trackDb to what files are actually on the system
• Fixed problem in tdbQuery with overrides not being addressed properly, this came up with the RefSeq composite edits by Lou
• Fixed problem in hgNear building bad links into hgGene on the description field
• hgTables: sped up bigBed identifier search by using name index so it doesn't time out on huge files like dbSnp155
• Improved the ability to restore symlinked files back into their wrangle or submit directories so they are not lost in cdwReallyRemoveDataset
• Added -tsv option to bigBedToBed to create a TSV-style header that can be used with tools that work with TSVs, such as python CVS/TSV reader and Pandas
• Optionally replacing links to Youtube with links to videos hosted on our website using SSI
• Better adherence to W3C html coding standards in static html pages
• hgPhyloPlace: improvements for RSV, better config support for new species, support for reference not from db or hub

28 November 2023, v457

• Added (i) icons to hgLiftOver, to explain the various obscure options without so much text on the page. Note that this uses the new printInfoIcon(text) function, which we can use on many CGIs
• Try again: users can now query old NCBI transcripts, both by name and in hgvs coordinates, for hg38 only
• Fixed problems with RTS load where composite and supertrack children were stuck in positions set by previous RTS loads
• hgSearch now allows clicking the text to show/hide results instead of just the small button
• Made more improvements to tooltips: left click or contextmenu click closes tooltip, fix tooltip y positioning when it would normally be above the viewport, left justify the tooltip text
• Snp hgc pages now use mitochondrial codon table
• Fixed never-used multi-term searches that each resolves to a singlePos structure to show a range with each item highlighted
• Fixed problems with forcing bigBed filtering to pass items found with hgFind
• Parse of bigGenePred record now generates a somewhat useful error message rather than abort when bigGenePred is incorrectly specified as track type. This prevents a blank-screen failure and gives the user some hint as to what might be wrong
• Now using forceTwoBit by default, no more .nib files are needed, (the RR has .2bit now for all assemblies)

7 November 2023, v456

• Both exonNumber on and "mouseOver ${fieldName}" are now allowed in trackDb, this means that gene tracks now can have mouseovers
• hgFind items now always pass the bigBed filters and always are in pack when we're doing squishyPack. This fixed a bug where squishyPack search results are not highlighted and stay squished
• Track short labels that are displayed on the main page now correctly encode special characters like < and >
• Stopped checking for data accessibility on the assumption that the trackDb build already did that. Add a little side-effect up higher in the call chain. This should probably be somewhere else, but in fear of breaking something new, I'm just popping it up one link in the call chain
• Added chainDupFilter which addresses a problem in axtChain where duplicated blocks are not chained

17 October 2023, v455

• Initial commit of track decorators feature, which permits drawing blocks and glyphs over bed-like tracks
• Added link from child trackUi page back to parent track
• Table browser "data format" (="schema") page now points to bigBed file for knownGene track
• Modified HGVS searching code to query an additional table of old alignments, if available bedToBigBed now allows the input to be compressed
• Turned off and fixed logo calculations which were slowing down the browser
• Made a change to not seek on the input levels when calculating zoom if it's already at the beginning of the file
• hgTables - Made links work better to support http or https
• Increased timeout in https.c from 10 seconds to 90 seconds. Needed for C-language htmlPage Robots on https like hgNearTest and others
• Made a change to no longer check to see if a track's bigDataUrl files or tables are available at hgTracks run time, just trust trackDb
• Now avoiding a million stat() calls in hReplaceGbdb
• Existing tooltip function hui.c:printInfoIcon() now uses new mouseover code
• Additional fixups to multiple PCR results code
• Relaxed the constraint on sorting for bedToBigBed and bedGraphToBigWig

26 September 2023, v454

• Added the assembly name to hgc page titles
• Fixed ancient word break bug on bigBed extra fields with super long strings
• There is now a more descriptive error message when no regions are in the output of the Table Browser
• Download track data in window improvements, disabled multi/math wig tracks because those are not supported in the api yet. Chris
• Made java utils configurable between http and https, and https is the default in preparation for turning on redirect to https everywhere
• Tweaked the scripts that run robots written in C that should use https, since htmlPage code can use https but does not support redirects at this time
• Fixed notification box setup code to account for udcTimeout messages being set up server-side instead of client-side
• Made track hub search indexes otto update
• Added trix snippet index updates to knownGene build process
• hgPhyloPlace: added linkouts to MicrobeTrace (for subtrees up to 500 sequences)

5 September 2023, v453

• Allow hgTracks tutorial to automatically start when a special variable is on the URL
• First version of liftOver-on-the-fly to liftOver annotations between assemblies in 'real' time
• Added VCV outlink to clinvar page
• Warnings now show up properly in hgSearch
• More fixes to multiple PCR results code
• Fixed pgSnp items not scaling correctly when item is off the left side of the window
• Fixed bug in length spec search, if the user entered a length search, like chrA:X+Y, we first need to add Y to X before checking if the start and were a mistakenly swapped position
• Fixed a problem reported by user security scan in which the too-liberal CSP Content Security Policy needed to be tightened up, and only whitelist specific libraries, not entire domains. Updated the CSP policy in python hgLib and hgLib3 too
• Fixed dead url to primer3 in hgPcr
• Small bugfix to kent-core github repo, a copy of the kent repo with just the MIT licenses code

25 July 2023, v451

• Changed track list to 90% of screen width on hgTracks
• Fixed addition bugs on hgGeneGraph for Python3 now that Python2 has been stopped
• Fixed trash icon bug that happens when one clicks a lot of trash icons very quickly and a race condition on ctfile changes occurs
• Added -bed option to bigBedToBed, for cases where people have thousands of regions to export, not just one
• Changed the default maxItems from 250 to 10,000
• Fixed javascript bug that was preventing the warnSeconds and interactive tutorial popups
• Fixed old bug where html tags could show up in hgGatway
• Removed a spurious warning in Apache logs due to my careless coding in last release
• Tweaked sendLogEmail.pl and makeKentCore scripts for build meister role
• Continuous GenArk process improvements

5 July 2023, v450

• Added code to show an interactive tutorial to new users on hgTracks
• Added little trash icons next to custom tracks for quicker custom trash disposal
• 8 columns are now allowed instead of 6 in the tracks table under the track image on hgTracks, and also restricting the shortLabel width to 16 em (=characters)
• Added a new -bed option to bigBedToBed, also removing the -maxItems option as it never worked and is not used anywhere in our code
• cartReset now resets the entire localStorage. For now, this only resets the status of the "don't show this again buttons"
• Added a note about _alt _fix and _hap to hgTracks
• Fixed up notification box to show multiple different notifications, make notifications hideable/showeable via localStorage
• Added silent Google reCAPTCHA v3 to the user suggestion form
• Fixed a few places where we did not encode user inputs
• Enhanced initial geoIpToCountry command from Galt to allow processing all IP addresses in all apache logs archived here. Hiram
• Made a utility that uses our existing geoIp infrastructure to lookup the country code from an IP address (IPv4 or IPv6). We are using it to identify the UCSC Genome Browser usage even when Google Analytics is being blocked in some regions of the world
• Ongoing painful work to port hgGeneGraph to python3
• Ongoing work on summary tracks and blat displays for Human Pangenome Reference Consortium alignments to hg38
• Added mechanism to pslMap to fix problems with mapping prot-prot via prot-na alignment by explicitly specifying the type of alignments. Specifying types of input PSLs adds new checking for unsupported combinations

13 June 2023, v449

• Added short sequence blat search to hgGateway search bar, which was already available on hgTracks
• Cart is now dumped to trash if the browser took too long to draw in order to review long-loading sessions
• Increased maxItemsInFullTrack to 10,000 from 1,000
• Updated the https whitelist after doing a full re-scan of data
• Updated hgTrackHubHelp to add -trusted_first option to the command-line
• Added a flag to tell openssl to verify the host name which is not done by default

23 May 2023, v448

• The API 'list' function is now available and documented
• Continued work on squishy-pack display
• Fixed html problems with hgHubConnect where the alignment of columns to headers was wrong. Also improved the alignment of the search details section
• Fixed search bugs: encode hub track names with non [a-z] names, allow psuedo HGVS searches that resolve to a rough position (while eliciting a warn) to still resolve, don't show unencoded search strings when a search fails
• Minor changes to wording of duplicate track feature to now say "duplicate #N" instead of "copy #N"
• Fixed bug where hub URLs were getting truncated
• bigMaf is now supported for sequence logos, also added logoMaf to bigWig tag types in support of adding the setting to all popular hg* and mm* conservation tracks
• Longer descriptions now allowed in autoSql column names, separated by a pipe character. (Crossing fingers that no one has pipe characters already in their labels)
• pslMap now trims overlapping blocks that can happen when mapping protein to DNA alignments from BLAT translated alignments

2 May 2023, v447

• Users can now keep multiple isPCR results in one track rather than overwriting the custom track with each new hit
• Changed recommended track sets to merge into the current session instead of overwriting it
• Longer descriptions are now allowed in .as field labels, separated by | character
• hgTracks searches that go to only one place now correctly set their parent track visibilities on the url
• Added a new endpoint to API: /list/files?genome=someGenome to provide a list of download files for the specified genome. TBD: document this feature and add error catching
• Added format=text argument to the API /list/files endpoint to return plain text list of files rather than the standard API JSON
• Added a new "downloadUrl" trackDb statement which adds a download link to the trackUi page
• Improved code around browser "themes" (=user-selected CSS files) which are now more resilient to crashing if there are missing files
• Ongoing work on incorporating snake display in the chain and psl support (including big versions)
• Cleaned up logoMaf display so it scales to the existing window instead of by the viewing region
• The DNA retrieval tool would sometimes fail to color bases in exons appropriately if the transcript began outside the window of retrieved DNA. This is now fixed
• Details pages for Interact tracks could fail to load if the track was set to generate multi-region view links and the file for the track was using chromosome aliases instead of native names. Chromosome aliases are now handled properly in that situation
• All CGIs now support a secret argument for logging to the Apache error log. utils.js contains an asynchronous function to call the CGI that included it with this argument. Used currently for reporting our javascript run time back to the server. Chris
• Errors were not being caught when trying to load a hic track with a missing file. Those errors are now caught and reported appropriately
• Small improvements to bigGuessDb
• GBiC patch to fix mysql tables that are in a broken state on hgdownload, like GBIB
• Fixed a dump bug in the pipeline library module that could cause second pipeline calls in a process to fail under some circumstances

11 April 2023, v446

• Moved the download current track data button to blue bar menu under "Downloads" (#30865). Chris
• Added a little help box with link to new FAQ if hgTracks takes longer than x seconds (-> hg.conf) to load (#30591). Max
• Changed the way we load recommended track sets. We now overlay their contents, no longer obliterating the current session (#28525). Brian
• Added downloadUrl trackDb statement, to show link to GFF files for gene tracks above the docs page, so it cannot be missed anymore (#30904). Max
• Added support for chromAlias to the hubApi (#30544). Hiram
• Fixed up broken support for curated assemblies in the API (#30544). Hiram
• Fixed non-knownCanonical results not showing up in a knownGene search (#25078). Chris
• Turned on phyloP logo for 100 way on hgwdev, phyloP scores are shown as a sequence logo if zoomed in to near base mode. Brian
• Single position search coming from hgGateway now goes directly to hgTracks before drawing any html. Chris
• Fixed dbSnp pipeline for handling clinvar records that had multiple significances (#30617). Galt
• Restored color to the Short Match track, which was being drawn with an alpha of 0 (invisible) after the transparency changes (#30866). Jonathan
• Restored standard color parsing for 3-value colors in BED files, as 255,255,255 (white) was causing an error with full alpha added (the color 0xffffffff has the value -1, which is interpreted as an error instead of a valid color) (#30569). Jonathan
• Highlights should now appear in multi-region mode; they were being ignored due to an error in chromosome name handling (#30833). Jonathan
• In image and PDF output, highlights would be broken by vertical bars from the blue ruler lines in the background. The combination of the two is now handled in the same way as the web display, which looks better (#30833). Jonathan
• Made hubId's portable in newly created sessions by saving away the hubUrl's of attached hubs in the cart (#28525). Brian
• Fixed a bug in trackDb caching that I introduced when saving trackDb parsing errors in each tdb rather than crashing the whole browser (#30881). Brian
• Added download links for gene track GTF files in GenArk assemblies in description pages for tracks, soon to be obsolete by downloadUrl trackDb statement. Hiram

bigMafToMaf program has been updated to use significantly less memory, allowing large bigMaf files to be converted back to MAF (#28491). Mark

• Made kent-core repo with all MIT-licensed kent-code only see https://github.com/ucscGenomeBrowser/kent-core. Max
• Added a change list to trackDb, see https://genome-test.gi.ucsc.edu/goldenPath/help/trackDb/changes.html. Max
• Continuous GenArk process improvements (#29545). Hiram

21 March 2023, v445

• Transparency settings added with the new ghostscript (version >= 9.52). Internal effects gain the ability to use alpha-valued colors in both images and PDF output. This supports highlight effects in things like vcfPhasedTrio tracks. This may be a breaking change for some mirrors with custom code modifications - any hard-coded rgbColor structures will need to be updated to include an alpha specification. (#30569)
• Changed the multiwig solution for logos to use the specified track color rather than hardcoded value (#30828). Brian
• Fixed bug where liftover was interpreting colons in bed names as position format (#30705). Chris
• Added support for Genark genomes to the minuscule tool chromToUcsc (#30454). Max
• Fishing up snakes on bigPsl and chains (added some developer only dotplots). Brian
• Ongoing work on making Recommended Track Sets not trash custom tracks or highlights (#26404). Brian
• Added logos built on-the-fly using a wiggle and an associated MAF track. Brian
• Added support for Google Analytics 4. I am unable to use their new UI though, the new version is very hard to use (#30725). Max
• Added a 'vm' option to gbib's update script that can update the underlying operating system to the next version (#24254). Chris
• Tiny GBIC fix for the brand new Fedora 37 linux which we would have run into with all other linux distros soon (#30578). Max
• Various uniprot track updates (#30701). Max
• More work on the trackDb tableBrowser setting in the hubApi, including added tests. Chris
• Fixed table browser schema page when a non-assembly database table. Chris
• Added a few more domains to the https domain whitelist. Galt
• Fixed crash in chromAlias resolution in hgTracks (#30578). Max

28 February 2023, v444

• Added two new right click options when clicking on a genePred track, zoom to codon and zoom to exon (#2724). Chris
• Added query strand and position as color and mouseover to BLAT results tracks (both bigPsl custom track and special BLAT output track), (#30578). Max
• Added a "track snapshot" button to hgTracks. Under hg.conf control (#30024). Chris
• Added "download file" links directly to the table browser "schema / data format" button for bigDataUrl tracks (#30491). Max
• We no longer provide links to EPS versions of the hgTracks and hgGenome images. This is in preparation for creating non-compliant EPS files to facilitate transparency effects in Browser images and PDF output (#30606). Jonathan
• Redraw barChart svgs on the client so the column widths can be wide enough for labels (#28439). Chris
• Prevent faceted barChart configuration when doing right-click config (#30102). Chris
• hubApi "track" argument can now be a comma sep list to return data from multiple tracks at once (#30024). Chris
• Fixed bug in logo display that caused a crash if it was the child of a composite (#30626). Brian
• Added a note in TB helping users who do not know the full wiggle data format (#30585). Max
• tableBrowser trackDb setting now works correctly in the hubApi (#30024). Chris
• Fixed hgc crash on new hgGene link when protocol is not https (#30545). Max
• Work with the asmEquivalent hgFixed table to get an assembly name for the GDV browser. Hiram
• Fixed a bug in the calculation of knownCanonical that let some totally weird transcripts slip in. Brian
• Ongoing work to optionally show snakes in chain and psl display (#30280). Brian
• Made track duplication to be on by default without hg.conf variable (#30586). Brian
• gff3ToGenePred updated to handle Ensembl feature types. Mark
• Fixed minor problems found with newer gcc compiler on Ubuntu 20, compiled on a vm. Galt
• Disabled parallel loading in hgCustom on hic and bigMaf tracks which are not thread safe (#26445). Brian
• Added support for clould URLS for mirrors. A URL resolver plugin functionality allows an external program to convert cloud URLs (s3:, gs: drs:) to http/https URLs (#30445). Mark

7 February 2023, v443

• Added support for curated hubs to hubApi
• Users can now get exon-exon-straddling primers from primer3 by following an outlink on hgGene
• Fixed negative strand intron numbering in table browser bed output
• Fixed the enter key picking first search result on hgGateway
• Added support for s3:// and other cloud protocols to ud
• Added CSS 'themes' to hgConfigure

17 January 2023, v442

• Improved handling of track hub error messages
• Added assembly aliasing via table asmAlias

2022

20 December 2022, v441

• New "return to current position" button on hgCustom
• Added option to invert Hi-C plots
• New utility, bigGuessDb, to guess the db given a big* file

29 November 2022, v440

• Track duplication feature merged and released
• Links to AlphaFold for predicted protein structure are now displayed in hgGene when a UniProt ID is available
• Fixed negative strand exon number output in Table Browser
• Fixed up kent source build to work OK on Mac OSX on arm64 architecture

8 November 2022, v439

• New search feature release that matches on tracks, hubs and docs
• hgGateway genome search has been expanded to match on dbDb description field
• Various teaks to wiggle display, such as mean default on density coverage setting and adding sum mode to the windowing methods

18 October 2022, v438

• Added 'copy link' function to gateway description page on GenArk hubs

27 September 2022, v437

• Adapted Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. Now users can see variant effects with version 153 or later
• Added a loading icon on hgGateway when a species or a position is searched
• Updated OMiM build process to use ncbiRefSeq on hg19 and hg38 instead of refGene

6 September 2022, v436

• Added support for monkeypox/hMPXV to hgPhyloPlace

16 August 2022, v435

• Gene search on hgGateway now automatically goes to hgTracks position

26 July 2022, v434

• Expanded support for psl and chain display
• Added message to track long label if either doWiggle or maxWindowCoverage is active

7 July 2022, v433

• Expanded chromAuthority support to more track hubs and now available as an option in the Table Browser.
• Copy link icon added to freshly made sessions as well as connected hubs. Likewise "My hubs" renamed to "Connected hubs".

14 June 2022, v432

• Fixed bug where track hubs attached to assembly hubs were not being searched
• Changed trackDb html search to not require files end in ".html"
• New style RepeatMasker track display now added to GenArk hubs

24 May 2022, v431

• SQL INJECTION Prevention Version 2 protects subclauses with new %-s behavior that enforces correctness
• Hashtag '#' character now allowed in chrom names
• Made a bedGraphToWig utility for people who have made bedGraphs that could be more densely represented as wigs
• Added first draft code to support specifying a chromosome naming authority

3 May 2022, v430

• Released new Genark request page
• Added support for chromAlias.bb to bedGraphToBigWig
• Genark hubs now supported in hgConvert and hgLiftOver if they are in hgcentral
• Hi-C tracks now have pack and squish display modes to help limit how much screen space they consume. Pack behaves like the old dense display (1/2 height), squish is 1/4 height, and dense is now 1/8 height
• Hi-C tracks can now filter on interaction distance
• Added chromAlias support to snake display

12 April 2022, v429

• Sessions must now have a description before they can be added to the Public Sessions listing
• Added chromAlias support to BAM display
• Enabled density coverage mode for PSL tracks
• Allow big* tracks with only a bigDataUrl to be used in Extended DNA

22 March 2022, v428

• Added barChartBarMinWidth and barChartBarMinPadding trackDb statements for barChart tracks in hubs to specify the minimum pixel width and padding of bars in hgTracks
• Made change to allow trackDb.txt files to be 256K, up from 64K
• Added support for using a bigBed as a chromAlias file in order to take advantage of bPlus tree indices on native chroms as well as aliases
• Added support to bedToBigBed to pass in bigBed as chrom sizes so bigBeds can be built with any sequence names in the chromAlias file

1 March 2022, v427

• Reduced size of title font on hgTracks
• Added support for chromAlias table in big* files
• Added comma separated output option to table browser when doing primary table or selected fields output for easy opening in excel
• Committed work on GenArk request form
• Fixed multi-threading issues caused by setenv
• Fixed the last instance of back-quoting needed for the new keyword `offset` for MariaDb upgrade
• Made cart rewrites on by default via hg.conf, previously the cartVersion var

8 February 2022, v426

• Expanded support for chromAlias, now works with big* files and IGV-style format+chromToUcsc
• Fixed compatibility for MariaDb 10.6 which has a new keyword 'offset'
• Smaller hgTracks assembly titles

18 January 2022, v425

• hg19 kgXref, kgAlias, and search index files to have modern gene symbols
• Removed incognito mode feature since it was proving confusing, and was not being used
• Fixed message in needMem when signed int has overflowed. Example from hgLiftOver when user submitted a 3GB file
• Fixed and updated GB dockerfile, icluding update to Ubuntu 20, fixing compatability with MaraDb, and sprucing up the docs
• Fixed message in needMem when signed int has overflowed. Example from hgLiftOver when user submitted a 3GB file

2021

14 December 2021, v424

• Checked in Robert Hubley's support for bigRmsk track type
• Moved the entire repo to a MIT-by-default license
• Added "incognito" mode to hgTracks which means the browser ignores cookies
• Major updates to the UniProt otto job, now running on 117 assemblies
• Added new features to https like cert verification, error messages that work right with warn and errAbort and our GUI in hgCustom and hgHubConnect and also logging especially for CGIs of problem certs. Also added callback so that we can support multiple levels like warn instead of abort. Cert verify options controlled by env vars and also hg.conf variables [abort|log|warn|none] for CGIs that use the cart. Default is log. Added basic info about the new httpsCertCheck setting to various documents. Added -httpsCertCheck=[abort|warn|none] command-line option to the hubCheck utility

16 November 2021, v423

• Added timeout option to pipeline functions to allow killing of long-running pipelines, especially ones run from CGIs
• Various UI and text changes to hgHubConnect to make it easier for newbie users
• Added google analytics key to hgdownload and static pages on hgdownload

26 October 2021, v422

• Added option to track search to also search tracks in unconnected hubs
• Added ssl certificate verification with LETSENCRYPT-compatible trust_first flag to https.c

5 October 2021, v421

• Changed the primary gene set on hg19 to Gencode V38lift37
• Removed botDelay sleep() until it reaches the warnMs threshold, then use the sleep() and begin issuing the warning message
• Highlight color now persists in the cart

14 September 2021, v420

• Review of custom track bottleneck penalty policy. Added variable in hg.conf, customTracks.botCheckMult which is an integer to set the penalty for custom track submissions
• Added small folder icons to composite and superTracks on hgTracks
• Added RedMine help widget

24 August 2021, v419

• Now allows matching on multiple transcripts instead of just the longest when a user enters a pseudo HGVS search term like Gene AminoAcidPos
• hgTrackUi pop-up control on hgTracks now scrollable. This prevents the pop-up window from extending past the bottom of the screen, in turn fixing the always the previously hidden submit buttons
• Finishing Kate's changes to the name of the virtual chrom from "virt" to "multi" in hgConvert, hgIntegrator, hgTables, hgVai
• Various fixes in support of bigMaf tracks

3 August 2021, v418

• Changed all calls to system() and popen() to use our pipeline library.
• Added Google Analytics button click tracking to hgTracks.
• Implemented mysql advisory locks to prevent duplications in hubStatus table.
• The local cache directory for remote files (udcCache, which is used for file types like bigBed, bigWig, VCF, and bam) now defaults to $TMPDIR/udcCache. The previous default of /tmp/udcCache will still be used if $TMPDIR is undefined in the local environment.
• Various updates to GBiC/GBiB - New push location, changes to GBiC install script to remove errors, no longer support Ubuntu 14, and support for local-only assemblies.

13 July 2021, v417

• Added the hogExit function to CGIs hgGene, hgTrackUi, hgBlat, hgc, hgPcr, cartDump.
• Changed udcTimeout warning text to a notification “bar” over the position box but under the menu bar.
• singeList bigBed filters fixed, and default filterValues set to filter by multiple.

22 June 2021, v416

• Added cart editing ability to address changing trackDb hierarchies.
• Allow variable size data tables on hgc.
• Moved warning box to be in the middle of the screen.

1 June 2021, v415

• Table Browser UI improvements: add section headers, improve layout and add help on mouseover.
• Enable dynamic blat service for all GenArk assembly hubs.
• Add mouseOverFunction option to trackDb to turn off mouse over value display when the numbers become averages.

11 May 2021, v414

• Auto-attach GenArk hubs if a track hub is attached that designates a non-native database found in GenArk.
• Add db argument to hgc and hgTrackUi URLs so they do not trigger error messages when shared.
• Escape dots in track names in hgTracks.js so track names support dots.

20 April 2021, v413

• Improvements to dynamic BLAT servers, better error reporting, blatServersCheck support, and activation.
• Make the use of FreeType fonts be the default.
• GBiC now updates its hgcentral.
• Make hgHubConnect use the pipeline library to run hubCheck instead of popen().

30 March 2021, v412

• Add support for dynamic BLAT servers. See http://genomewiki.ucsc.edu/index.php/Running_your_own_gfServer.
• Multi-region feature enhancements, using 'custom regions' mode for sparse tracks. Includes new trackDb setting "multiRegionsBedUrl".
• Implement maxWindowCoverage, a trackDb variable to force the browser to put a track into density coverage mode when the size of the window is bigger than N bases.

1 March 2021, v411

• New JSON output for hgBlat.
• Facet counts now added to Tracks with Dropdown SubGroups.
• Item and gene search refined to give fewer and better results.
• Work on new barChartFacets tag to allow faceted selection on bar charts.
• Add API support for tables with non-standard chrom names (e.g. tname).
• Fixes to better display Hubs using dimensions such as from ENCODE portal.
• Quality checks and improvements for liftOver.
• Ongoing improvements to hgPhyloPlace.

16 February 2021, v410

• Improvements to the Gateway page to help discover Public Assembly Hubs via the common name of the species for novel organisms.
• Final changes for the new wiggle mouse-over data display feature.
• Internal fixes and improvements on the process of data release to support data hosted from binary-indexed (/gbdb/) files and automatic track update procedures around formats like bigPsl.

26 January 2021, v409

• Enhancements to the site not limited to improving exon display, liftOver performance, multi-region display, and alignment functionality.
• Ongoing work to improve bigBarChart displays.
• Ongoing work for new wiggle mouseover pop-up with data values.
• Release of new font options.

2020

15 December 2020, v408

• New isPcr setting to allow PCR searches on assembly hubs.
• New barChart support settings barChartCategoryUrl to specify a tab-separated file containing category (bar) labels and colors.
• Ongoing work for new wiggle mouseover pop-up with data values.
• Ongoing work for new font options.

1 December 2020, v407

• New direct search results to Public Sessions, for example, http://genome.ucsc.edu/cgi-bin/hgPublicSessions?search=wuhCor1, where search=wuhCor1 will display all Public Sessions on the coronavirus wuhCor1 genome.
• Improvements to VCF data displays and mouseovers in clinical data, removing default exon display in bigBeds and adding strand and accession.
• Ongoing work for new features including new wiggle mouse over pop-up with data values.

3 November 2020, v406

• Work to support clinical users including adding a mouseOver for the OMIM Gene track, and reworking the Gene Reviews track format to support disease info in mouseOver and having default accession displays for refGene.
• Work to improve the speeds on the Track Setting page of large consortium hubs, so View, Facets, and Matrices display quickly.
• Work to improve Blat servers and the Blat All function to avoid timeouts from external mirror queries.
• Ongoing work for new features including new font options, new wiggle mouse over pop-up with data values.
• Work to support VCF data displays formats relating to the coronavirus genome.

13 October 2020, v405

• New display of chromosome alias names from the "view sequences" link on a genome's gateway page.
• Various UI improvements such as small grey boxes around the filters so one can see where a filter starts and where it ends when multiple ones are offered and a new trackDb setting sampleColorFile for coloring a tree in VCF+tree display.
• Enhancements to support clinical data tracks and the continuous updating of the data with automatic scripts.

22 September 2020, v404

• A new chromAlias function enabled for bed file custom track input to map to alternative names.
• Support for a new mouseOver trackDb setting, which allows constructing bigBed (and related) item mouseover's from a pattern using arbitrary text and fields in the data schema.
• Improvements to the VCF trio display to color by function when variants are in an intergenic region.
• Various fixes and improvements to highlights, shortcuts, hub support, and ongoing work on new features.

1 September 2020, v403

• Enhancements to meet Chrome Browser asynchronous requests changes.
• Enhancements to VCF functions, from details page to toleration of IUPAC ambiguous characters and handling of viewing monoploid data (such as SARS-CoV-2).
• Further steps toward a new feature of Recommended Track Sets and initial work on a new Related Tracks feature.

11 August 2020, v402

• New feature: Recommended Track Sets.
• Added new trackDb options to turn off VCF filters.
• Added two new color options for trio display - color by functional effect and de novo child variants.
• Updated geoIp data to ensure that users are directed to the nearest mirror site.

21 July 2020, v401

• Enhancements to new track and display type vcfPhasedTrio in development.
• Enabling VCF tracks to color haplotype display by variant's effect on gene.
• Speeding up VCF tree-parsing with tree files with thousands of nodes.
• Documentation to aid users desiring to obtain new dbSnp table data format from the Table Browser.
• Improvements to various tools such as genePredToGtf to correctly number exons on the negative strand.
• Work to merge the display of GENCODE data involving building a new database (for knownGene tables) and supporting software presenting details about genes (hgGene).

30 June 2020, v400

• New autocomplete in the position bar clicks the go button when selecting a gene search result.
• Improved the ability to allow the copying and pasting of genomic coordinates in the main browser page.
• Work to support new ENCODE Candidate cis-Regulatory Elements (cCRE) tracks for hg38 and mm10.
• Improvements and fixes to support Pubic Hubs, Assembly Hubs and BLAT.

9 June 2020, v399

• New super track display: to make hierarchy more apparent, the child member of supertracks now have a description and track list of all super track children on the configuration page.
• New track and display type vcfPhasedTrio in development.
• Support of smaller genomes and RNA genomes from BLAT searches to VCF configuration options.
• Improvements to Public Hub Search to avoid issues when remote hubs are non-functional.
• Improvements of links to GnomAD, ExAC VCF details.

19 May 2020, v398

• Increase in the default label character width from 17 characters to 20 characters.
• New feature mergeSpannedItems setting allows merging all track items that extend beyond both sides of the current viewing window into one bed item in the display.
• Interface enhancements to new hideEmptySubtracks setting.
• Improvements to support RNA viral genomes such as searching UUU in the shortMatch track and VCF improvements to display a phylogenetic tree of virus strains and improvements to BLAT for smaller genomes.

28 April 2020, v397

• Enhancements to the barChart format to take new barChartSizeWindows setting allowing customizability of display.
• Improvements to the ClinVar tracks for clinical use and enhancements to the VCF format for label display.
• Other work to improve the automatic update of data in the Browser and the building of new data tracks.

7 April 2020, v396

• New "Hub Development" tab enhanced with checkboxes to add "measureTiming" providing statistics about timing and "udcTimeout" allowing speedier checks of hub changes when developing.
• Enhancements to VCF file format handling, such as new option to cluster variants as ordered in the original file.
• Enhancements to new hideEmptySubtracks setting in regards to syntax and issues.
• Enhancements to support Hi-C file format, and to GBiC setup script to specify specific assemblies and other changes.

17 March 2020, v395

• Improvements across the site to better work with HiC data.
• Enhanced error control for unusual submitted custom data, such as invalid group assignments.
• Improvements to utilities to be more collaborative with external toolkits from better usage statements to the handling of chromosome name conversions.

21 February 2020, v394

• Public sessions now sort by most recent addition.
• Fix of links to the GTEx portal from the details page of an item in the GTEx track.
• Improvements of the autoscale in Track Collections with add and subtract mode
• Improvements to the filtering function now provided for Track Hubs
• Improvements for using the Table Browser to extract data via identifiers for data in bigBeds such as Track Hubs
• Improvements to the hubClone tool allowing users to duplicate a hub's structural text files as well as simultaneously use a download option to acquire all of the remote data underlying the hub.
• Other fixes and enhancements, such as to automatic assembly hub building procedures and work to establish data archives.

4 February 2020, v393

• Increased in hubs the number of subGroups to support large external consortium projects, such as the ENCODE DAC hub.
• Various fixes to multiple levels of the code from VCF Filtering, enhancing recent new features and better supporting the GBiB mirroring operations.
• Various ongoing work to support quicker track display performance and work to allow IPv6 better for mixed IPv6/IPv4 systems (discovered by mirror site).

14 January 2020, v392

• Changes to the new lollipop display to use color field rather than automatically being colored.
• Changes to improve the new SNP data format.
• Improvements to the new API in regards to DNA extraction.
• Enhancements for future gnomAD track.
• Work to improve speeds with a trackDb caching mechanism.

2019

10 December 2019, v391

• Extensive enhancements to allow complex filtering options on bigBed files in Track Hubs.
• Improvements to hub connection performance and operation.
• Addition of tools to help convert between NCBI/EBI chromosome names (chromToUcsc) and various internal tools to add archiving tracks and test for hub configuration mistakes.
• Improvement to interact details display and ongoing work incorporating ENCODE data tracks and documenting new Hi-C track type.

12 November 2019, v390

• Release of a new bigDbSnp track type to support the pending release of dbSnp152.
• New "autoScale group" setting in trackDb for Track Hubs.
• New display of how many items are filtered out for tracks using filters.
• Improved performance for new Hi-C track data in using auto-scale mode.
• Improvements to speed of discovering public hub search results.
• Improvements for VCF filter operation and fixes for custom track interactions on the Data Integrator.

22 October 2019, v389

• New feature for barChart tracks a trackDb setting: barChartMaxHeight
• New feature for composite tracks a trackDb setting: hideEmptySubtracks.
• Further work toward the intial release of Hi-C track data.
• Improvements around the working of filters on tracks and a note displaying when a filter is activated.
• Improvements to API and various other tools.
• Work to display the plantinum genomes as assembly hubs.
• Continued work to import the latest SNP data in JSON format.

1 October 2019, v388

• Multiple Track Hubs can now be attached using the hubUrl= parameters by repeating it in the URL.
• Work to enable Track Hubs to have the ability to attach to other existing Assembly Track Hubs.
• New "group auto-scale" available for multiple tracks in a composite group enabling a group of signal tracks to scale in tandem to the highest auto-scaled track in the group.
• New feature for interact tracks to open a multi-region view of the two ends of the interact data with a custom track to annotate the ends.
• New code to attempt to thwart the abuse by bot-driven queries that could occasionally overwhelm the site.
• Enhancements to the new JSON API code to better output data on cases such as schema details.

10 September 2019, v387

• Added new highlighted indication of being in the multi-region or reverse browsing modes.
• Work to improve the checks of BLAT servers and work to improve the checking of Hubs.
• Fixes for various links to external sites such as to the Mutation Position Imaging Toolbox (MuPIT) from gene details pages.

20 August 2019, v386

• Improvements to new API to allow data fetching from gene models in bigGenePred format.
• Improvements to sorting BLAT results upon clicking into the details page when Browsing results.
• Enhancements to BLAT ability to better handle results with assemblies such as hg38 with many alt/fix patch sequences.
• Enhancements across the site to support IPv6 for different tools from BLAT, parasol, and IP Geolocation.
• Various fixes across the site to enhance tools, such as the Table Browser, or to further support ongoing work to handle Hi-C data.
• Development to expand Track Hub checking when a hub is first connected.

30 July 2019, v385

• A change to the code loading big* based custom tracks to append a "chr" if the data does not include it (1 becomes chr1).
• Work to make new Hi-C data output from Table Browser work.
• Ongoing work to handle sizeable snp152 involving new JSON downloads, new bigDbSnp track type.
• Continued improvements on new JSON data API Interface.
• Improvements to pipelines to handle changing input OMIM metadata.
• Work to bring in ENCODE3 mouse data.

9 July 2019, v384

• Zebrafish icon added in the popular species gateway menu.
• New trackDb setting interactMultiRegion allows interact track details' pages to activate multi-region link to view both ends simultaneously.
• Work to improve pennantIcons display in supertracks and composites.
• Further enhancements to the new JSON data API Interface.
• Initial commit of Hi-C draw support for custom tracks.
• Improvements across the site such as regarding custom tracks error_logs and handling of sessions data such as when multiRegionsBedUrl file is used.

18 June 2019, v383

• Improvements for BAM custom tracks so that the file.bam.bai data can be named file.bai as well.
• Continued work on new JSON data API Interface.
• Continued work on lollipop display mode for variation & frequency data,
• Further enhancements to storage preservation methods regarding sessions with custom data.

28 May 2019, v382

• Improvements to enable display of wide-ranging ENCODE3 TFBS data.
• Continued work on new JSON data API Interface.
• Initial commit of Hi-C draw support.
• Improvements to often used utilities such as htmlCheck and bedToBigBed
• Documentation enhancements to better explain the new BLAT All process.
• Enhancements to bigBeds ability to handle filtering of data.

7 May 2019, v381

• Improved the working of highlights and selecting regions while Browsing.
• Work to improve the ability to create Track Hubs and Tracks with a matrix of up to 1000 items for large data sets, such as for ENCODE3.
• Continued work on new JSON data API Interface.
• Continued work on lollipop display mode for variation & frequency data,
• Further enhancements to storage preservation methods regarding sessions with custom data.

16 April 2019, v380

• Improved support for VCF with automatic detection if data should be type vcfTabix or vcf and support for VCF UI in Track Hubs.
• Continued work on lollipop display mode for variation & frequency data,
• Continued work on new JSON data API Interface.
• Enhancements to storage preservation methods regarding sessions with custom data.

26 March 2019, v379

• Work on new JSON data API Interface
• Enhancements to findMotif utility to allow 32 character motifs and specified number of mis-matches.
• Improved error handling of Track Hubs when required type line missing and edge-case issue of custom tracks loaded onto disconnected assembly hubs.
• Improvement on right-click UI pop-up configurations in regards to updating nested composite tracks.
• Tools added to help build large track groups, tdbRename and tdbSort to sort and rename sections of large trackDb files.
• New hubClone tool to clone remote hub text files to a local copy, fixing up bigDataUrls to aid in debugging or providing a template for new hubs.
• Various fixes to browser performance with regards to memory, position and database information, display of individual items, links to external sites such as HGNC, and enhancements to new custom track backup feature.

5 March 2019, v378

• Fixed twoBitMask script to work with 64-bit twoBit files.
• Added <trackName>_hideKids=1 directive to URL parsing to turn off super track or composite children.
• Added default score filtering to Interact type.
• Added ability to backup Custom Tracks that have been saved in Sessions.
• Added hubClone utility to precompiled apps available for downloading.
• Added support for VCF 4.2 '*' ALT value.

12 February 2019, v377

• Added new Projects dropdown menu.
• Created hubClone utility for copying a remote hub to local and changing bigDataUrls to remote.
• Fixed Table Browser position radio button so that it remains selected after a search.
• Initial work on lollipop display mode.

22 January 2019, v376

• Added format checking of uploaded session files.
• Made hubCheck more resilient when trackDbHub spec file is mis-formatted.
• Cleaned up some code warnings found by gcc-7 version.
• ClinGen CNVs track items are now named '*_unk' instead of '*_not provided' when the variant origin is not provided.
• Fixed bug in hgSession where session thumbnails were not generated when short links were present.
• Fixed table schema for bigBed track tables to now show update time of the file, not the table.

2018

18 December 2018, v375

• Added feature to the Sessions tool to print short links to sessions.
• Allowed GBiBs to download from genome-euro if they are closer to the European server.
• Modified the GENCODE tracks on hg19 to link to the Ensembl GRCh37 browser.
• Handled corner cases in variantProjector caused by unnecessary gaps introduced by bug in RefSeq transcript alignments.
• Fixed a GBiC bug related to SELinux observed in Redhat Linux.
• Added support for labelFields statements at the view level.

27 November 2018, v374

• Added phylogenetic tree utility (binaryTree.pl) to convert NCBI Taxonomy polytomy trees to binary trees.
• Made enhancements to hgTracks & hgc for PSL alignments to alt/fix sequences.
• Fixed gff3ToPsl util: block-order bug when GFF3 strand is '+' and Target strand is '-'.
• GBiB link to shared data folder is now relative so menubar works when GBiB is accessed from a real server.

30 October 2018, v373

• Released new feature: BLAT ALL Genomes.
• Completed interact track type feature enhancements: pack/squish modes, cluster view, flipped (inverted) display.
• Fixed corner case: make multi-region config box ignore :start-end ranges after alt/fix sequence name.
• Fixed bug in hgvsToVcf: bug triggered by inconsistent tx version between ncbiRefSeq and genbank tables.
• Fixed bug in barChart track display when no items are in current range.
• Added ability to access UDC sparse file using virtual memory.

9 October 2018, v372

• Improvements to new interact track type.
• Work to expand track database arguments to work with new data visualizations.
• Improvements to barChart format and work on other tools used in generating data formats.

18 September 2018, v371

• Enhanced External Tools clicks to CRISPOR for larger regions.
• Made valid assembly links clickable on Public Hub page.
• Fixed a bug in VAI for deletion across exon/intron splice on - strand.
• Extract RefSeq Annotation Release from GFF header if present.
• Fixed bamToPsl to work on huge BAMs.
• On-going work on bigBed filtering.
• Extended trackDb setting for interact track, to support offset source/target endpoints.

28 August 2018, v370

• Enhancements to new Gene Interaction type to allow a filter to hide interactions missing at one or both endpoints in the window.
• Security improvements to prevent cross-site scripting.
• Fixes to allow the new interactions track type to work properly with track composites.

7 August 2018, v369

• New keyboard shortcut "v s" to jump to view sequences.
• An improvement to custom tracks error messages to check the assembly sequences when given invalid chromosome names.
• A fix to a bug in the Variation Annotation Integrator that caused duplicated lines of output and other similar fixes to scripts and tools.
• An improvement in the display color for ClinVar tracks.
• Ongoing work on introducing numeric and filterBy support to bigBeds and Hubs.

16 July 2018, v368

• Added support for url, urlLabel and extraFields trackDb settings for bigBarCharts format.
• Fixes to ensure the gnomAD track now correctly provides links out to that resource.
• Various work to support patch sequences and fixes to automated scripts to help improve site performance.

26 June 2018, v367

• New documentation for coming new interact and bigInteract track type.
• Enhancements to barChart and bigBarChart data to display barplot on hgc instead of boxplot when there are a small number of samples.
• Addition of links featuring GTEx body map page in various relevant code locations across the site.
• Various enhancements and fixes to the site to improve functionality across browser platforms, such as safari.

5 June 2018, v366

• Improvement to enable bigBed searchIndex to work within composites.
• Changes to support DECIPHER CNVs new data format and work on the coming new track.
• Fix for the bedGraph format in assembly hubs and a fix for composite display in multi-exon mode and other browsing visualization improvements.
• A fix for links to mirbase in the related track and fixes for input from Martin Marcher from GitHub on GBiC operation.

15 May 2018, v365

• Increased tool support for Assembly Hubs using genomes that might include periods in names.
• Increases in speed and performance around custom tracks and default track displays.
• Improvements to error messages and data building scripts.
• Fixes and developments around newest Track Collection Builder tool and work on new interactions type track.

24 April 2018, v364

• Improvements to HGVS support for the Variant Annotation Integrator.
• Work on new interaction track type to allow displaying long distance genomic connections.
• Creation of pipelines to help users generate automated alignments, often requested in mailing list questions.

3 April 2018, v363

• Support for HGVS ENST* and ENSP* terms from latest GENCODE in position/search.
• Ongoing work for new interactions track type.
• Ongoing work on new Track Collection Builder tool.
• Further support for pipelines for NCBI RefSeq tracks and various fixes to tools and utilities.

13 March 2018, v362

• Searching Public Hubs now includes results from metadata tags on tracks.
• In GenBank mRNA tracks patent sequences are now off by default, and a new Track Setting enables turning them on.
• Track hubs can now be structured to exist entirely in the hub.txt file when a "useOneFile on" setting is included in the first hub stanza and the hub is limited to one genome.
• The file size limit of hub.txt file has been expanded from 256K to up to 16M.
• Improvements to the Variant Annotation Integrator for detection of ambiguous regions and HGVS term support.
• Various fixes across the site to improve security and on going work for a new collection tool.
• Work to allow Assembly Hubs to have additional Track Hubs attached to them.

20 February 2018, v361

• Improved Variant Annotation Integrator prediction results involving specific RefSeq annotations where reference genome and transcript sequence differ.
• Adding an additional recovery email address option when accounts first created for sessions, and improved sorting of existing sessions.
• Security improvements and url-encoding for parts of the site.
• Various fixes to tools, such as the Table Browser, and improvements to pipelines to generate new data tracks.

30 January 2018, v360

• Update of NCBI browser links from Map Viewer to new Genome Data Viewer.
• Fixed Variant Annotation Integrator bug with custom track type pgSNP with custom hub assembly.
• Fixed track details in assembly hubs around auto-generated tracks and for bigBarChart, pgSnp, VCF, bigMaf types.
• Improved gateway assembly search to find newer public hubs.

9 January 2018, v359

• Added Parasol binaries to list of downloadable apps
• Improved line limit exceed error messages from hgLoadBed.
• Enhanced new track type: longTabix.
• Fixed problem with saving session to file after cart dump.
• Fixed problem with loading assembly hubs with custom tracks.
• Fixed bug in hgTables for bigDataUrl-only tracks
• Fixed hgTablesTest blank line / no results corner case.

2017

5 December 2017, v358

• Work to enable new bigNarrowPeak format that can be used in Hubs, documentation pending release of code.
• Enhancements to trackDb pennantIcon setting that can be used in Hubs to support arbitrary text (e.g. for 'New' tag).
• Support for showing schema links for data hosted by bigDataUrls that can be used in Hubs.
• Various improvements to support hubs such as fixes to new disconnect button, ensuring assembly hubs can work in the Variant Annotation Integrator, and saving hub sessions with custom data.
• Addition of source code version printout to most utilities to help users track version number.
• Enhancement to site to help display current database and search with en-dashes or em-dashes in coordinate ranges.
• User session file support improvements around assembly hubs with custom track data and fixing files download code to enable backups.
• Improvements to the RefSeq tracks to better support links and versioning display of data.

7 November 2017, v357

• Enhancements to further improve HGVS search terms and search functionality and including HGVS output option in vai.pl script.
• Fixes to improve stability of user custom data connected with saved sessions.
• Enhancements to Genome Browser in the Cloud (GBiC) script to check response speeds and automatically select new genome-euro MySQL server on installation if faster.
• Ongoing work to introduce a new tool to allow novel collections of tracks.
• Various fixes and improvements across the Browser not limited to enhanced dataVersion to allow for better historical connection to track data revisions and updated display of version information on GENCODE gene track details pages, and updated links to external sites like the CDC HuGE database, MGI, and GAD on track data pages.

17 October 2017, v356

• Support for new big* formats such as bigMaf, bigPsl, and others for use in the Data Integrator tool.
• Ongoing work to introduce a new tool to allow novel collections of tracks and code enhancements for coming GTEx eQTL tracks.
• Various fixes and improvements across the Browser from highlighting functionality, HGVS search results, and infrequent empty cache issue for data in custom tracks and track hubs.

26 September 2017, v355

• Internal work to prepare for adding a MySQL server, genome-euro-mysql.soe.ucsc.edu, in Europe to improve GBiB performance.
• Improvements to processes for creating NCBI RefSeq Genes automation scripts and other track data under development.
• Ongoing work to introduce a new tool to allow novel collections of tracks.
• Various fixes and improvements across the Browser from highlighting functionality, clicks of detail description pages, and Table Browser output.

5 September 2017, v354

• HGVS variant nomenclature output now available with Variant Annotation Integrator when RefSeq Genes selected for gene prediction source, allowing turning custom tracks or variant identifiers like rs2021974 into NC_000020.10:g.15382919G>A or NM_001351661:c.541-29131G>A.
• New tool vcfToHgvs that produces HGVS using detailed alignments and sequence of RefSeq transcripts.
• Ongoing work for new tracks using new bigBarChart display and a new tools underdevelopment and other fixes and enhancements to source code.

15 August 2017, v353

• Improvements to new Public Hubs search page, search terms expanded ("H3K4ME" matches H3K4ME1, H3K4ME2, and H3K4ME3).
• Enhancements to halSnake format to allow display of the number of bases in inserts.
• Fixes for Table Browser selection options and support for "chr" sequence names in HGVS genomic (g.) terms.
• Fixes to the main Browser for right-click enabled track configuration option and the display of highlights displaying near the ends of chromosomes.
• Fixes to enhance GBiB and CRISPR data and recent Gene Interactions tool.

25 July 2017, v352

• Further support for HGVS position/search terms.
• Improvements for the Public Hubs page to load a bit faster.
• Enhancements to support the GBiB and GBiC products.
• Various fixes for tools and new software to support tagStorm format.

5 July 2017, v351

• Major enhancements to Public Hub searching feature, where search results can now be expanded, and right clicks provide direct links to matching tracks and assemblies.
• New CGI tool, hgLinkIn, which translates external identifiers to assembly positions for UniProt genes (http://genome.ucsc.edu/cgi-bin/hgLinkIn?id=O95477&resource=uniProt)
• Further support for HGVS position/search terms.
• Various fixes and new software to support metadata processing around the tagStorm format.

13 June 2017, v350

• New CGI tool: the gene interactions viewer, hgGeneGraph. Highlighted by new hg19 and hg38 Protein Interactions from Curated Databases and Text-Mining tracks.
• Final documentation of new barChart and bigBarChart track types that allow for GTEx like displays with custom data in custom tracks and track hubs.
• Added support for HGVS m. and n. terms in position/search.
• Added support to use optional Apache Basic Authentication instead of hgLogin.
• Various fixes and enhancements to code to support tracks, tools, and metadata storage.

22 May 2017, v349

• Enhanced multi-region feature now allows users to directly enter custom BED coordinates, instead of requiring a URL to remotely hosted BED coordinates.
• New barChart and bigBarChart track types that allow for GTEx like displays with custom data in custom tracks and track hubs.
• New tools added such as expMatrixToBarchartBed to support the new bigBarChart type available in Users Apps package.
• New CGI hgGeneGraph to allow for interactive protein interactions track viewer coming soon for hg19 and hg38.
• New hg.conf option, login.relativeLink for firewalled genome browsers.
• New hg.conf option, useBlatBigPsl=off, to turn off now default option to have custom track output from BLAT searches.
• Enhancements to density graph plot feature available for BAMs and other track types so that graph is more specific to alignment regions.
• Enhancements to HGVS search parameters such as to when they point to indel points or negative coordinates.
• Fix for colors on bigGenePred track type.
• Fix for VAI and background work for proper transcript HGVS VAI output.
• Various other enhancement and background improvements to improve Genome Browser in the Cloud (GBiC) sessions, track hubs, log-in user support and style across the site.

2 May 2017, v348

• New zoom dialog enhancements to allow multiple highlights including specification of custom colors, along with supporting shortcut keys.
• New Variant Annotation Integrator (VAI) script, vai.pl, added to our userApps.
• Enhancements for HGVS position search and highlight.
• Addition of ability to add metadata to track hubs using a tab separated file.
• Preliminary support for new barChart/bigBarchart track type to allow GTEx type display in hubs.
• Ongoing development for BLAT custom track output.
• Various improvements and fixes to improve user experience.

11 April 2017, v347

• Added Proxy support for HTTPS and FTP.
• Fixed udcCache to allow HIPAA-compliant Amazon Storage securely signed URL redirects.
• Added "filter activated" to labels for some tracks if filters are configured.
• Added HGVS terms as variant input option in Variant Annotation Integrator.
• After you change your password, you are now automatically logged in.

21 March 2017, v346

• New keyboard shortcuts h then m for highlight mark and h then c for highlight clear, and new ability to add more than a single highlight.
• Changes to the default width of the screen to 950px.
• Ongoing work to support custom track output from BLAT results.
• Fix to allow Public Sessions on mirror sites including genome-euro and genome-asia.
• Fixes and improvements to many tools after recent software changes in v345.

28 Feb 2017, v345

• Release of reestylized document pages to fit with the new homepage and genomes gateway page.
• Introduced feature to allow arbitrary fields within bigBeds to be used as labels in hgTracks. For example, using labelFields fieldName1, fieldName2 in trackDb.txt in a hub, the option to display those fields on the Browser will exist on that track's Track Settings page.
• Fixes and enhancements to various CGIs such as improving the Table Browser to tolerate characters like "/" in output file names.

7 Feb 2017, v344

• Changed restrictions on the maximum chromosome name length to 255 from 32 characters.
• Added support of cytoBand Ideogram on assembly hubs.
• Various bug fixes and ongoing work to fix bigMaf, bigPsl track types and bring tagStorm metadata support to hubs.

17 Jan 2017, v343

• Introduced limited support for pasting DNA sequence into the position box to trigger a BLAT search.
• Ongoing work to support custom track output from BLAT results.
• Feature to allow track hub track visibilities to be set via the URL without the track's "hub_1234_" decoration (&trackName=pack versus &hub_1234_trackName=pack).
• Improved documentation for the keyboard shortcuts, press "?" to see all shortcuts.

2016

13 Dec 2016, v342

• New CGI hgGtexTrackSettings that provides dynamic highlighting and selection of the 53 GTEx tissues on a human body illustration.
• New track database (trackDb) setting bigDataIndexfor vcfTabix and BAM files to allow indexed data file (bam.bai vcf.tbi) to exist at an alternate URL.
• New shortcut keys when browsing (1-6) that jump from 10 to 1,000,000 bp regions, press "?" to see all shortcuts.
• Implementation of default display of codon-numbering when zoomed into the base view. (Shortcut "e v" allows exon view; "d v" returns to default view).
• Features for Track Hubs: new tagStorm metadata format; ability to self-reference hub.txt, genomes.txt, trackDb.txt in one file.
• Fixes and enhancements for handling split tables, hal snake tracks, and developmental code to allow BLAT custom track output and a command-line variant annotator tool.

15 Nov 2016, v341

• New track database (trackDb) setting darkerLabels allows left labels on a track to have a darker display, useful where the track color might be too light for readable labels.
• New link out to ExAC site for ExAC track detail pages like ExAC: 21:24451624 A/T.
• Enhancements for VCF tracks in the Browser and on a VCF details page.

For TUMOR/NORMAL VCF, show tumor allele counts in mouseover.

Infer genotypes from SGT tag for VCF from Strelka.

• Table Browser enhancement to support intersection feature when data supplied via bigDataUrl tracks.
• Error message improvement regarding track hubs created incorrectly with identical track names.

25 October 2016, v340

• New disconnect button for track hubs from the main browser.
• Improved HGVS position search.
• VCF parser support for VCFv4.2.
• Fix for urls using hideTracks=1 to recognize and adjust super track visibilities.
• Speed optimizations for MAF displays.

4 October 2016, v339

• A new method to display UCSC Genes knownGene tracks in the main Browser through the bigBed bigGenePred format to increase the speed of displays.
• Optimizations to increase the speed of codon drawing and other browser operations.
• Renaming of the CGI phyloGif renamed to phylPng.
• Fixes for fleeting network errors that displayed in Firefox and Safari, and fixes for new track data.
• Improvements to code and infrastructure for future tracks releases such as for CRISPR data.

13 September 2016, v338

• Introduce search support for Human Genome Variation Society (HGVS) simple substitutions such as "c." (Ex. hg38 search: NM_007294.3(BRCA1):c.2231C>A) and "p." (Ex. hg38 search: NP_002993.1:p.Asp92Glu), and pseudo-HGVS (gene symbol and protein change, ex. hg38 search: BRCA1 Ala744Cys) as position/search terms.
• Added GTEx gene expression to Gene Sorter in 3 columns: GTEx (expression), GTEX ID (ENS), and GTEX Delta (distance). The GTEx expression column is now the default expression column, GNF Atlas 2, is still available but not default.
• Various new command line tools, and enhancements to existing ones, around ongoing gene prediction work.
• Fixes to existing bugs on Gene Details pages and other browser pages and tools.

23 August 2016, v337

• Made hgSession/hgLogin use HTTPS for hgLogin, unless disabled with login.https=off in hg.conf file.
• Fix to remove limit on number of sessions listed in Public Sessions.
• Enhance track hub pennantIcon to take a URL.
• Enhance hgTracks to draw multiple highlights from the cart variable via URL (not UI).
• Fix for the ${ and $} variables to mean start and end location of clicked item.
• Fix track hub problem where tracks in composites were not sorted in initial display.
• Enhancements and fixes to bigBed, bigPsl, metadata display, and hubs.

2 August 2016, v336

• Added support for CRAM in GBiBs.
• Enhanced CRAM output choices to Table Browser.
• Fixes to various parts of software (hgTracks, hgc, hgVai, hgTables) to improve links to data.
• Improvements for new Public Sessions hub, including more configuration options for mirrors.
• Making density graphs automatic for mirrors by removing requirement of hg.conf setting to display.
• Introduced HTSlib library (open source code written, licensed and distributed by Genome Research Limited) to the kent source tree

12 July 2016, v335

• Improvements with new redesigned homepage.
• Improvements and further documentation to support new bigMaf, bigPsl, bigChain, bigGenePred and CRAM formats.
• Ongoing work related to the move of Genbank metadata to hgFixed, such as hgVai fix for refSeqStatus txStatus info.
• Genome Graphs fix to allow SNP queries again.
• Improvements to multi-region customUrl feature allowing user defined regions.
• Fix to maxIntron option in BLAT when non-default value is used in a protein query.
• Keyboard shortcut for new Public Sessions page.

21 June 2016, v334

• New CGI hgPublicSessions that allows users to submit their sessions to be viewed by all the public on a special gallery page.
• Initial release of Chromatin Interaction display (longTabix).
• Performance enhancement for ORegAnno tracks across wide regions.
• Improvements to bigMaf, bigChain, and bigPsl support.
• Table Browser noGenome support that can turn off genome-wide queries if needed for certain data types.
• Support changes for mirrors and GBiB regarding phylo tree drawn on hgGateway.
• Support changes for new genome-asia mirror.

31 May 2016, v333

• Added 'RNA-Seq Expression' section to hgGene, that displays GTEx tissue-specific gene expression in a box-plot graph. Support default collapsed sections of hgGene. Set microarray section to default off (and change label to 'Microarray Expression'.
• Add settings to improve display of large composite tracks with metadata (hoverMetadata) and many or fixed track colors (darkerLabels).
• Display metadata on details page directly (don't require click on metadata link).
• Restored cytoBand fuzzy search.
• Started implementing Chromatin interaction display mode; Libified ave program.
• Use autoscale and maximum mode as defaults for BAM density graphs.
• Support bigPsl, bigChain, and bigMaf as custom tracks.

10 May 2016, v332

• New Gateway display added.
• New keyboard shortcuts to the dropdown menu and the help menu added.
• Enhancements to support a BAM density display feature.
• Enhancements to improve support multi-region support for pgSnp, certain hgc clicks and certain custom region custom track displays.
• Fixes for GENCODE gene tracks regarding prefixes and ids when obtaining records.
• Library changes to improve fileModTime error message, and relaxing check of metadata in VCF files.

19 April 2016, v331

• Added calls to bottleneck sever for more of Table Browser; botting for BED files will be delayed appropriately.
• Changed Genbank procedures to allow pushing tables rather than updating them on each machine.
• Fixed bug in hgc for SNP effect prediction of liftUp'd genePredExt tracks with empty exonFrames column.
• Final changes to support GTEx Gene Tissue Expression track.
• Fixed two issues in GTEx display when in multi-region mode: better accounting for label width in pack mode; gtexGene for limitedVis full->pack->squish->dense.
• Fixed problem in pack mode with special exception for altGraphX spaceSavers.
• Fixed a bug where next/prev exon link did not stop at coding region start/end in both directions.
• Enhanced nextExon mouseover labels to more clearly explain what it does.

29 March 2016, v330

• Created automated script to fetch CRAM reference sequences in conjunction with hgTracks.
• Clarified mouse-over message on hgTracks image to more clearly explain that by pressing the double-headed arrow, you will move to the Next/Previous Exon Edge.
• Fixed crash in custom tracks of type big* when user pressed nextItem.
• Formatted bigBed extra fields as a table on hgc page.
• Fixed a problem with SIG_PIPE in our https connection handling.
• Fixed hgc position for multi-region modes with multiple different chromosomes on the screen, such as custom regions by url mode or alternate-haplotype mode.
• Fixed a problem with chain lines disappearing when zoomed way in.
• Fixed a bug in outputting sequence in the table browser for refSeq table.

8 March 2016, v329

• Added "Apply" button to popup dialog box for configuring tracks on Tracks page.
• Fixes and updates for OMIM data pipeline.
• Fixed error handling for bigDataUrl/network tracks to be consistent and work across all regions/windows.
• Fixed bug detected with clinGen track caused by missing chrom name in a structure.
• Fixed bug in query index order for ensGeneTrack for exon/Gene-Mostly.
• Added assembly hub fields organism, description and scientificName to index of hubCrawl.
• Fixed string-escaping bug that broke the "BRCA" autocomplete for hg38 in hgSuggest.
• Removed some human-specific tweaks so cytoBand search will support horse & other organisms.
• Fixed bug in hgGateway search-box autocomplete.js.
• Fixed problem where hub defaultPos is sometimes ignored when using using hubUrl= and genome=.
• Assume that the BAM index file is named fileName.bai.

16 Feb 2016, v328

• Multi-region display. This feature allows users to "slice" their track viewing experience into a variety of different modes that focus the display on certain features: exon-only, gene-only, or user-defined BED coordinates. Only the portions of track annotations that fall within these displayed regions are shown; extraneous intergenic, intronic and otherwise unwanted regions are hidden from view.
• Fixed VCF Custom Tracks loading problem over FTP: make lineFile code assume index is .tbi, and not check for .csi.
• Fixed bug that occurred when users supplied backwards coordinate range (start > end) which caused both the start and end to be off by 1.
• Ongoing work on GTEx gene expression track: track configuration page including popup version; added tissue selection via sortable table.
• Ongoing work on GBIB: allow R for GTEx tracks; security updates; local track loading.
• Ongoing work on supporting CRAM data type.

19 Jan 2016, v327

• Multi-region display. This feature allows users the ability to "slice" up their normal track viewing experience into a variety of different modes: exon, gene, or user defined BED coordinates, and visualize the track annotations only in those regions, effectively removing the intergenic, intron or otherwise unwanted regions from the viewing window.
• Added Server Name Indication (SNI) support for HTTPS with certificates for wild-card domains.
• Ongoing work to support CRAM, BAM, and tabix using htslib.

2015

15 Dec 2015, v326

• Folded in support for htslib to get CRAM support. Also supports tabix and BAM.
• Enlarged buffers to help prevent problems with long URLs.
• Ongoing work on GTEx gene expression track display.
• Added View DNA shortcut to View menu.
• Added hg.conf option to suppress "very early errors" that display on the browser.
• Added support to Data Integrator for adding in related tables and fields using all.joiner.

24 Nov 2015, v325

• Started work to support bigChain (remotely-hosted chain file) file type in the browser.
• Ongoing work to support bigMaf (use semi-colon instead of ^A as line separator).
• Fixed a problem with BAM files that have no alignment.
• Fixed bugs in Data Integrator: 'defined regions' was selected when there weren't regions anymore; autocomplete behavior didn't follow changes of db; added simple header (database, region, date) to hgIntegrator output.

3 Nov 2015, v324

• Added drop-down menus to the Genomes and Genome Browser menus.
• Initial work on supporting bigMaf (remotely-hosted multiple alignment file) data type in the browser.
• Initial support for GTEx gene expression and related tracks.
• Fixed loading bigWig files from local dir via hg.conf option.
• Changed some absolute links into relative links for the benefit of mirror sites.
• Fixed code so that relative links in CGIs are no longer confused by HTML base tags in included files.
• When returning to a previously-visited assembly, take the user back to their old position when position="lastDbRef".
• Provide a link back to the genome browser from BLAT results.
• Fixed bug in Data Integrator that broke output field selection for subtracks.

13 Oct 2015, v323

• Added "View -> In External Tool" menu which sends DNA in region to external tools.
• Added functionality to pslCheck program: it now verifies q/tNumInsert and q/tBaseInsert.
• Removed message and 2-second delay from cartReset.
• Added support (and cache) for UDC redirects.
• Ongoing additions and fixes to Data Integrator tool.

22 Sept 2015, v322

• Flipped the switch to make GRCh38/hg38 the default human assembly browser.
• Activated keyboard shortcuts.
• Do not allow new default tracks to sneak into existing saved sessions; ensure that they maintain exact original track contents.
• Added chainToPslBasic utility which quickly converts chain files to PSL files without the overhead of computing match and mismatch counts.
• Added -max option to bigWigMerge.
• Added utilities to the user apps: hgLoadMaf, hgLoadMafSummary and hgLoadChain.
• Fixed phyloGif to accept spaces and special characters in tree node labels.
• Changes to Data Integrator: Fixed bug where wiggle db values were overhanging edges of search region; Fixed bug where it was using out-of-range large-bin items if query limit was hit (affects very large mysql tables like hg19.phastCons100Way); Added context-specific Help menu item.
• Fixed bug in hgTracks: lookupTrackHandler wasn't getting child tracks' trackHandler settings.
• Fixed bug in hgCustom: was using hardcoded default form action instead of cart value.
• Fixed bug in Table Browser: prevent mysql query for composite track with bigData type.
• Fixed bug in hubPublicCheck in the case of missing descriptionUrl.
• Fixed crash in snake track controls.
• Added the ability to specify genome within assembly hub on URL.

1 Sept 2015, v321

• Fixed the anno* libs to prevent region-average wiggle values from being split into multiple region averages.
• Exclude custom MAF tracks (not just wigMaf) from the Data Integrator.
• Added several tools to the Send To menu.
• Allow empty name fields in bigBed files.
• Turn on the Short Match track if anything is typed into the "motif" section of the hgTrackUi page.
• Added link on gene details page to GTEx (Genotype Tissue Expression) for all human assemblies.
• Added SSL Support to hg.conf, hg/lib/jksql.c and to the hgsql-and-family functions (#15751).
• Fixed bug with PSL to genePred frame correction when there is target deletion (#15803).
• Fixed bug converting GFF3 alignments to PSL when alignments start or end with indels.
• Added pslClone utility.
• Started work to support a new data type: bigPsl.

11 Aug 2015, v320

• Changed hgMenubar to work properly with Apache error pages.
• Final tweaks to the top menu bar color.
• Fixed the order of species in the hgMirror list.
• Added a returnTo option to the "sendto" menu to accommodate mirror sites.
• Fixed the postscript/PDF output so that all of the text is properly escaped.
• Added Data Integrator to hgCustom's 'manage custom tracks' page; changed UI from column of buttons to select + go button.
• Removed obsolete 8-bit color support.
• Fixed describe table schema and paste identifiers for assembly hubs.

21 July 2015, v319

• Released version 1 of trackDbDoc for Track Hubs.
• Upgraded hubCheck tool to verify versions.
• Added an hg.conf option to specify the Galaxy instance to connect to.
• Fixed searchs in VisiGene tool.
• Added new menus to static pages.
• Ongoing work on VAI.
• Added geneId to TransMap Genes tracks.

30 June 2015, v318

• Created new CGI, hgMenubar, in support of adding new menus to all static pages.
• Small tweaks GBiB: support remote data tracks without an associated table; fix species sort order in hgMirror.
• Added support for bigGenePred to hgVai and hgIntegrator.
• Ongoing work on the Data Integrator.
• Added support for v4.2 VCF files.
• Fixed bug in Table Browser: for join results, look for commas in the 2nd column not 1st.
• Fixed one-off bug in DAS for almost-BED tables (e.g. ctgPos).
• Added left label for snake tracks in pack and dense modes.

9 June 2015, v317

• Release of new CGI: Data Integrator (hgIntegrator).
• Tolerate absence of big genbank tables on mirrors.
• Fixed GBiB so that it does not overwrite local hg.conf file.
• Ensured that chromosomes are sorted by case in bedToBigBed.
• Fixed start/stop codon exon number in genePredToGtf.
• Started work on Track Hub spec versioning support. This includes new options to the hubCheck utility.

19 May 2015, v316

• Ongoing work on GBiB.
• Ongoing work on Data Integrator (previously referred to as Annotation Integrator), hgIntegrator.
• Fixed bug in BAM display to ignore mate-pairs that are on different chroms.
• Fixed Table Browser: fixed bug that broke MAF output; fixed filterFields for bigDataUrl-only tracks.
• Allowed hgloadBed to load zero-length BEDs at the beginning of a chromosome.

28 April 2015, v315

• Changed genome-euro redirect to be opt-in, rather than opt-out.
• Allow ORFeome and MGC synthetic mRNAs even when there is no Genbank entry.
• Added several new feature types to gff3ToGenePred (rRNA, ncRNA, primary_transcript).
• Allow mirrors to specify a different userDb and/or sessionDb table name.
• Changed UDC to allow: (1) load bigDataUrls from a specific local directory, configured in hg.conf. (2) deactivate the udc cache.
• Handle tags in VCF's INFO column that appear to have |-separated columns in both description and data by formatting the contents as HTML table for readability.
• Polished support for bigDataUrl-only tracks.
• Added extra column for gene symbol for UCSC Genes output from hgVai and hgIntegrator.

7 April 2015, v314

• Renamed hgAi CGI to hgIntegrator.
• Added assembly hub support for hgIntegrator.
• Added connections from Table Browser to the GREAT server for mm10.
• Updated details page to distinguish older ENCODE tracks from newer ones.
• Allow gff3ToPsl to work with query and target being different sets of sequences (e.g. to map between different genomes).
• Made the hgLogin email site-specific.
• In support of mirrors and GBiBs, made the dbDb, defaultDb, genomeClade, and clade table names configurable.

17 March 2015, v313

• Allow selection of coalescent ancestor to HAL snake tracks.
• Fixed menu duplication bug if there is a custom track on a track hub.
• Allow zero length blocks in browser and in bigBed's.
• Allow use of both itemRBG & the ability to used codon coloring in bigGenePred types.
• Initial implementation of schema and display code for Genotype-Tissue Expression (GTEX) tracks.
• Added link to chromInfo page to $db.chrom.sizes files on hgdownload.
• Added a more flexible display of options to hgAi.

24 Feb 2015, v312

• Implemented changes to hgAi suggested in review of JS for new UI framework.
• Fixed hgAi image-loading bug.
• Fixed checkTableCoords to exit error status on error.
• Added tolerance for hash table reaching its max size rather than exiting.
• Added support for bigBed custom tracks.
• Fixed a bug that caused split tables to crash in the browser.
• Extended mouseover to show exon and intron numbers for linkedFeatures tracks, added new trackDb setting "exonNumbers off" that allows track creators to suppress this new feature.
• Added command-line tools to inventory track settings in public hubs (hubTrackSettings) and check urls in a table (checkUrlsInTable).
• Fixed memory leak in pslPosTarget.
• Added genePredFilter program to discard invalid genePreds created by importing data from incorrect GFFs.
• Added ability to suppress auto-updates from outside GBiB.

3 Feb 2015, v311

• Created new UI framework based on ReactJS and ImmutableJS, with Annotation Integrator interface hgAi.
• Fixed the stacked bar chart display to stack in the order the wiggles appear in the order they are listed on the description page.
• Fixed disappearing bigBed items when zoomed way in.
• Added support for both '=' and 'X' in BAM cigar files.
• Fixed bug in subtrack table sort. It will now correctly sort in columns besides the primary sort column.
• Fixed menu link to hgTables so that it automatically selects the selected group track and table.
• Added a "data last updated" value to the schema page in hgTables.

13 Jan 2015, v310

• Added BLAT support to assembly hubs.
• Released first version of hgBeacon CGI (in support of GA4GH) for LOVD and HGMD tracks on hg19.
• Rearranged the way we compile in HAL libraries so testing can be done before installing the libraries. Upgraded to newest HAL library.
• Enabled pslCDnaGenomeMatch.c to take 2bit files as input instead of nib files since 2bit format is more common.
• Added hubPublicCheck to the list of utilities available to users.
• Turned off min/max in wiggle track configuration when autoscale is on.
• Added two new trackDb statements: labelOnFeature and linkIdInName.
• Fixed a bug so that the currently-selected table launches when the Table Browser starts.
• Fixed the instance where the chromosome position was displaying twice in the Web browser tab label.

2014

9 Dec 2014, v309

• Allowed for easier discovery of track hub track HTML.
• Allow for missing hg.conf file.
• Added support for bigGenePred in hubCheck and custom tracks.
• Added hubClear URL variable.
• Created beacon program for GA4GH.
• Fixed hgTables to show example missing identifiers.
• Added code for proteomics track support - PeptideAtlas.
• Bolded canonical gene in search results page.
• Fixed bug in hgVai that caused omission of many dbNSFP annotations.

12 Nov 2014, v308

• More perfection of GBiB product.
• Added support for GENCODE filter-by tag and highlight-by tag.
• Fixed custom wiggle tracks on assembly hubs.
• Started work on BAM density plots (turning BAMs into wiggles when they are too dense).

21 Oct 2014, v307

• Added new program (written in both C and in perl): pslScore program to calculate pslScore.
• Added MAF SNP view to MAF display.
• Created new utility, mafToSnpBed, used in construction of tables used in the new SNP-oriented MAF display.
• Fixed bug in chrom ideogram position-selection.
• Fixed a problem in MAF display resulting in empty displays when the start address was 1 or 2.
• Added an option to mafGene to output a unique character for every codon.
• Completed GBiB product for initial release.

30 Sept 2014, v306

• Created tool to lift UniProt annotations to a genome: uniprotLift.
• Created a tool to fix overlapping bed blocks, created by dnax blat and pslMap on protein psl files: bedFixBlockOverlaps.
• Corrected VCFs in hgTracks: detect haploid sequence properly instead of matching "chrY".
• Fixed missing NULL check in hacTree.c.
• Started work on program that makes a track hub for the hg38 DNAse data.
• Ongoing work on parallelized version of hacTree.
• Added "showSnp" mode to MAF display which shows red ticks for mismatches.
• Modified gff3 library to tolerate missing phase keyword.
• Modified hgHubConnect to not redirect to hgGateway if error on hub load.
• Added exon frames if missing in genePredToBigGenePred.
• Stripped tabs from custom track descriptions causing javascript crash.
• Fixed bedToBigBed crash when trying to create an index on a non-existant field.

9 Sept 2014, v305

• Added support for bigGenePred in track hubs.
• Fixed problem that resulted in trackDb include statements bypassing UDC cache.
• Added minMax option to bigWigAverageOverBed.
• Implemented ga4ghToBed to test out GA4GH APIs at Google.
• Created a multithreaded version of the hacTree code for clustering.
• Fixed missing null check in hgTables, also avoid null by looking up trackDb for second table in intersection.
• Fixed missing null check when loading user settings from URL.
• Improved hgBlat error messages for sizes of queries with ignored characters like N.
• Added option to pslCDnaFilter to save filtering statistics to file rather then writing to stderr.
• Started work on schema and loader for GTEx (Genotype Tissue Expression) data tables.

19 Aug 2014, v304

• Added code to distinguish IE-pre-version-11 from IE-post-11.
• Fixed problem for IE11 so users can properly set sub-track visibility.
• Added code to 'spectrum' (aka 'useScore') actually work on any pair of color/altColor settings.
• Added support to Table Browser: export to GenomeSpace.
• Added support for track hubs with "." in the name.
• Allow dash in GFF3 tags.
• Added functionality to bigWigCorrelate so that it can work on a whole list rather than just a pair of bigWigs.
• Added warning to hgTracks when udcTimeout variable is present, and provided link to remove from cart to enhance performance.
• Extended regulation cluster tools to incorporate metadata into DNase clusters.
• Added functionality to SNP display in hgTracks: option to show organism's alleles even when ortho alleles are not available; by default, show alleles on + strand or if user clicks 'reverse', all on - strand (with option to revert to showing dbSNP's strand).
• Added functionality to details page for VCF data: if haplotype clustering is not enabled, don't show 'sorting order' option; show Hardy-Weinberg only when explicitly enabled since it's usually N/A.
• Finished work on the new repeat masker display.

29 July 2014, v303

• Changed all links in navigation bar and on static doc pages to relative links. This makes it so that it is no longer required to install the browser at the top level.
• Removed udcTimeout from the cart at end of hgTracks. This prevents this debugging tag from persisting and slowing down tracks involving bigDataUrls, and track hubs indefinitely.
• Created new program, expData, which takes in expression data and creates a binary tree using a hierarchical agglomerative clustering library. The output is a .json file type intended for d3 visualizations.
• Started work adding new Repeat Masker nesting visualization display code from Robert Hubley.
• Changed the sort order for assembly hubs. Sort according to the orderKey value on the order of databases in assembly hubs. The default is to list in the order in genomes.txt.
• Fixed a bug that listed unconnected unlisted hubs when a hub was broken.
• Refactored hubCheck to support HAL library.
• Fixed a problem where sessions on assembly hubs would not hold onto custom tracks.
• Added "retry hub" error message to hgHubConnect so broken hubs can be disconnected.
• Fixed bug where in some circumstances, users get a blank cookie value.
• Fixed bug in TF ChIP-seq track: suppress display of a motif for a TF peak whose highest-scoring motif lies outside the viewing window.
• Bug fixes for VAI tool: first character of symbolic alt alleles were sometimes skipped; trailing quote was not stripped from FILTER header lines' descriptions; incorrect calls for large deletion; was calling frameshift instead of stop_gained when insertion makes a stop codon.
• Ongoing work on VAI tool: moved regulatory data into own section, suppressed regulatory details from protein-coding consequence lines because they're in regulatory feature lines.
• Ongoing work on GBiB including installation helpers for Windows and OSX.

8 July 2014, v302

• Added regulatory consequence-calling to VAI using ENCODE Clustered TFBS and DNase.
• Fixed a bug in searching where supertracks were not displaying when a search term matched an item in the track.
• Cleaned up JavaScript code based on run through jshint.
• Fixed hgTrackUi to better support ranges in Filter settings.
• Fixed off-by-one pixel height problem with BED files generated by hgGenome.
• Fixed a bug where hiding a track in certain conditions resulted in an error.
• Updated trackDbDoc to make it clear that '-' are not allowed in track names.
• Added 2 new tokens for trackDb URL setting which are for clicked item start and end.
• Sped up image-only reload as seen on FireFox when there are many (50) tracks displayed.
• Added functionality to the chains display to make directional arrows visible more often.
• Added descriptionUrl to hubPublicCheck -addHub command.
• Enabled bigBed item search on native bigBed tracks.
• Ongoing work on GBiB.

17 June 2014, v301

• Enabled searching for tracks with Track Hubs.
• Added support for Watson/Crick mode (i.e. negative values wiggle data types).
• Added copyright notices to several source files.
• Made prototype Tukay plotter and bar grapher.
• Created a BAM filtering program and added to bamFile.c library.
• Created a convertor program: BAM to fastq.
• Added support for details page of in-progress DNase Combined Sites track.
• Created tool hgBedSources, to generate a bed file with id list and an id+name map file from input file of bed items + list of names.
• Changed ENCODE peaks display to be full height when no peak summit ('point source') is defined (when there is peak summit, the peak is full height and the remainder of the item is half height).
• Make-over for Track Hub Portal to make it more user-friendly.
• Fixed bug in border-case drawing problem with snake tracks (HAL data type).
• Added support for mafDot in trackDb to show "." if a base is identical to maf reference.
• Fixed some bugs in splitFileByColumn.
• Compiled source code on Mac OSX Mavericks and fixed issues.
• Edited htmlCheck so that it now tolerates missing HIDDEN and CHECKBOX input types.
• Added back missing dense mode left labels to pgSNP tracks.
• Fixed VAI so it ignores "variants" with no observed variation.
• Fixed VAI so that it stops trying to find a chrom that is not in the input file.
• Added support for assemblies with many sequences (> 100) to checkTableCoords.c.

27 May 2014, v300

• Added new feature: the ability to search track hub info pages.
• Fixed bug in hgTables where BAM position range was including an extra base to the left.
• Fixed duplicate labels in hgTracks when pgSnp and unclustered VCF were in full visibility mode.
• Resolved new compiler warnings for Mac OS X Mavericks (10.9).
• Added option to pslMap to limit mapping alignments to those prefixed with the corresponding input qName.
• Reconfigured hgTracks visibility updates by drop downs in track controls.
• Fixed a bug in the snakes display having to do with new compact mode.

6 May 2014, v299

• Created new display method: stacked overlay mode for multiWigs.
• Tuned performance of initial display of public hub list.
• Compacted the snakes/HAL display.
• Fixed multiple alignment tracks when viewed with the visibility set to squish.
• Fixed bug in main display, where items were being drawn in the wrong place due to a calculation error.
• Suppress "Variant Identifiers" option in VAI for assemblies without a SNP table.
• Fixed bug in hgc where printCustomTrackUrl was called twice for VCF/tabix.
• Fixed bug in hgc for pgSnp data types: don't look ahead to next exon from last exon.
• Detect but tolerate extra tab at end of line from 1000Genomes phase1 VCF files.
• Handle "chr"-less VCF files.
• Ongoing work on Genome Browser in a Box (GBiB) including committing all configuration files.

15 April 2014, v298

• Allow user to select which gene name to display in Ensembl Gene tracks.
• Fixed link to NCBI for hg19.
• Increased buffer size in hubConnect to deal with huge data sets.
• Ongoing work on Genome Browser in a Box (GBiB) including tweaks to VAI, hgLiftOver, and nib file access.
• Made the UI more user-friendly in the Hub Portal by making a click-able expansion of assembly lists.
• Fixed bug in which a symbolic position could get stuck in the cart.

25 March 2014, v297

• Added 100X zoom out button to main tracks image.
• Improved error messages for directly uploaded bigData Custom Tracks.
• Fixed broken VCF intersection in the Table Browser.
• Fixed custom coloring of SNPs by exceptions in hgTracks.
• Added support for (small) plain VCF custom tracks to the: Table Browser, Tracks page, details pages, VAI, and Custom Tracks.
• Trim identical bases on right of indel alleles to prevent false overlap in VCF files in: Tracks page, details pages, VAI.
• Fixed bug in GTF to genePred conversion where an assertion was triggered when the GTF had a spliced stop codon where the exon containing the first part of the stop codon only consisted of the stop codon bases.
• Altered the way ajax return from update of tracks in the hgTracks image is parsed.
• Added hgsid back into the hgTracks URL (as shortened by history plug-in).
• Simple change to prevent top menu from wrapping, which broke the menu.
• Added random session key for greater security of cart data.
• Added bottleneck delay to cartDump.
• Fixed GTF output from Table Browser with BAM Custom Tracks and hubs.
• Fixed bug in bedDetail that prevented long HTML fields.
• Ongoing work on Genome Browser in a Box (GBiB).

4 March 2014, v296

• Fixed two Custom Track issues regarding multiple threads.
• Fixed bug in lavToPsl that was clipping (#12727). Brian
• Fixed crash in multiWig if individual bigWig is not found (#12644). Brian
• Tweaked genePred reader to tolerate missing exon frames (#12674). Brian
• Fixed bug in bigWig summary calculations (#12558). Brian
• Fixed bug in drag-highlight that caused the gene name auto-complete dialog to appear beneath hgTracks images.
• Fixed a Mac-Safari specific bug in the right-click disable of drag-highlight.
• Fixed a problem with custom track bed detail files.
• Allow hubs to use pennant icon.
• Made improvements to hgc and hgTrackUi to support non-human SNPs.
• Ongoing work on Genome Browser in a Box (GBiB) including fixing bug in reading MAFs from stdin; fixing bug with lineFile seeks when on top of udc.

11 Feb 2014, v295

• New feature: highlight region in the main display.
• Fixed a bug in the main display when there is no P/Q arm information available.
• Automated part of our dbSNP process: locate NCBI assembly report file, use it to map RefSeq contig names to GenBank contig names.
• Changed hgTracks "refresh" behavior to scroll to top of page.
• Changed configure page to present all groups with unified column widths for cleaner look.
• Fixed hgTracks problem when "ruler" track is hidden.
• Fixed FireFox-only bug where back-button return to hgTracks page left visibility drop-downs disabled.
• Added a feature to snake tracks: it now draws a pale yellow bar when there are N's in the query.
• Fixed gff3ToPsl to handle NCBI's gff cigar format.
• Fixed Table Browser's gtf output to work with split-tables.
• Created special chromosome-ordering for hg38 which has many alternate chromosomes.
• Allow an FTP URL with an unencoded "+" character.
• Ongoing work to display of motifs in Transcription Factor cluster tracks.
• Ongoing work on Genome Browser in a Box (GBiB).

21 Jan 2014, v294

• Allow colons in both HTTP and FTP URLs.
• In support of the back button, added the assembly, organism and position to the URL.
• Fixed a bug where sort was alphabetical on numeric values. This caused tracks to jump to unexpected places in the display image.
• Reversed table name check strategy: check normal name first, split tables last.
• Fixed BAM display where color-by-tag was turning blue in large regions.
• Fixed VCF reader to not require '=' in metadata lines in versions before 4.1.
• Added paste/upload options to VAI: accepts rs# IDs.
• Created New tool for bigWig manipulation: bigWigCat.
• Sped up the Table Browser by fetching only the list of chromosomes used by the table instead of all chromosomes.
• Changed Genbank's alignment strategy to remove recognition of repeat-masked sequence.
• Ongoing work on Genome Browser in a Box (GBiB) including a new CGI: hgMirror.

2013

16 Dec 2013, v293

• Added support for back-button in hgTracks; it now supports history of "positions". Track configuration settings will only reflect current settings.
• Allowed track hubs to be more forgiving of poorly-formatted lines in txt file.
• Fixed a bug in maf frames builder where blocks of one base were being ignored.
• Fixed net.c for FTP subtleties regarding url-encoding and the leading slash in the path requested.
• Fixed a new problem in hgTables caused by a recent bugfix to gffOut. This ensures that the exonCount, exonStarts, and exonEnds match.
• Fixed bug seen only in IE10: white-on-white text in site menus and black-on-blue group headers.
• Minor change to support non-standard UWash Exome Variants VCF data in hgTracks display tool tip.
• Fixed https access problem with ENCODE Experiment matrix.
• Added build scripts to the source tree that were local files in the build account.
• Added generic scripts for all the steps of trash cleaning for mirror site users.
• Ongoing work on VAI: Fixed incorrect use of NMD_transcript_variant: it means 'variant in a transcript that is already subject to NMD, not that the variant causes NMD; Added ability to paste in rs# IDs as variants to annotate; Cleaned up logic for detecting/adding extra left base for indel in VCF; Added hgTrackUi links for tracks offered by hgVai; User request: don't truncate alt allele column so short; Made per-gene-track Artificial Example Variants (not only per-region); Added comment method to annoFormatters; Added comment about no items in region.
• Enabled hyperlinks output for bedGraph and microarray tracks from Table Browser.
• Extended base/difference-coloring code to support LRG Regions, LRG transcripts.
• Ongoing work on Genome Browser in a Box (GBiB).

19 Nov 2013, v292

• Added support for display of motifs in Transcription Factor cluster track, and other factorSource type tracks.
• Set network default read write timeout for tcp connections to 2 minutes.
• Fixed case where strand output in liftOver could be wrong when multiple flag was used with bed6 strands and it hit multiple chains.
• Added IUPAC support to the oligoMatch utility.
• Fixed the hgTables gtf-output frame column, at least for tables that have exonFrames column available like refGene and other genePredExt tables.
• Fixed bug in genePredCheck to recognize case-sensitive chrom names.
• Started work on fixing bugs in source tree so that it can be build on new Mac OSX compiler.
• Ongoing work to support HAL and halSnakes in assembly hubs.

29 Oct 2013, v291

• Fixed ajax code to be tolerant of ISPs that strip newlines from content.
• Fixed a problem where hub assembly lists were not nicely wrapping on hub portal page.
• Removed an invalid assert in Gene Haplotypes feature that assumed that if only one haplotype is found, it is the reference haplotype.
• Rewrote some of makeTrackIndex: replaced mdb and cv access with the lib routines that are much more efficient.
• Fixed a bug (and added tests) in pslOpen that would hang on files with only comments.
• Changed "genes" field in gwasCatalog to a longblob from a varchar(255).
• Updated build system to automatically detect MySQL libraries and build environment.
• Fixed several bugs in anno* libs found by Case Western team.
• Tweaked search position for Artificial Example Variants.
• Updated links to new Galaxy server from Table Browser.
• Ongoing work to support HAL and halSnakes in assembly hubs including adding a chromosome color mode for HAL snakes and adding MAF output in Table Browser for HAL data type.

8 Oct 2013, v290

• Added db.neverLocal to hg.conf to help mirrors debug their mysql problems.
• Fixed a problem with Ubuntu and other systems where load data LOCAL infile has been disabled by default for mysql clients.
• Improved mysql setup documentation regarding both setting the default storage engine to myisam and turning on local-infile in my.cnf.
• Improved paraFetch timeouts and retries.
• Improved hdb.c and hgc to handle bed4 and bed9 when element has size=0 start==end such as a SNP insertion point.
• Fixed a couple of small issues with the login code.
• Added new options to pslCDnaFilter to ignore introns and repeat masked sequence.
• Fixed bug in pslMap where mappings would be missed if multiple mapping alignments mapped to the same rangetree node.
• Added support for version numbers in genbank tables.
• Fixed bug in bigBed item search (bad allocation in bPlusTree code).
• Ongoing improvements to the VAI.
• Ongoing work to support HAL and halSnakes in assembly hubs.

17 Sept 2013, v289

• Fixed item search code.
• Allow hgVai to accept assembly hubs but bow out if no gene track exists.
• Fixed crash in Human Proteins hgc page.
• Fixed a table browser crash when switching to an assembly that didn't have a track group.
• Changed dbList in hubStatus table to be a blob; 255 chars was not big enough.
• Fixed hgLogin buffer overflow error.
• Ongoing work to support HAL and halSnakes in assembly hubs.
• Ongoing work on hgVai.

26 Aug 2013, v288

• Fixed bug in hgLogin, set realName with same value as userName when creating account.
• Fixed HTML encoding in hgLogin.
• Reordered the fields the same way for display of bigBed and BED tracks.
• Fixed noScoreFilter for bigBed to work properly.
• Tuned the performance for the track and file search.
• Fixed lack of base-difference colors in hub BAM tracks and even native BAM tracks that didn't have a whole bunch of extra trackDb settings.
• Fixed hgVai when specifying region with VCF input.
• Fixed hgVai to support assemblies with no SNP tracks.
• Ongoing work on annoStreamDb: use mysql to sort incrementally-updated GenBank tables; fix to support assemblies with thousands of sequences.
• Ongoing work to support HAL and halSnakes in assembly hubs.

5 Aug 2013, v287

• Improved performance of hgTracks search and hgFiles search.
• Added support for 'factorSource' file format.
• Added support for displaying external html pages directly in details pages (iframeUrl and iframeOptions in trackDb settings).
• Removed hard-coded http string from hgLogin and hgSession.
• Changed hgGene to not set the chromosome position in the cart.
• Ongoing work to allow visualization of nested Repeat Masker tracks.

15 July 2013, v286

• Made the userApps easier to build.
• Added Ensembl navigation link to assemblies as appropriate.
• Fixed hgConvert so that it doesn't die if the other assembly is not in dbDb.
• Released final version of the Variant Annotation Integrator (hgVai) and documentation.
• Fixed text display for warning in hgVai and hgTables.
• Used the new NCBI link to display GeneReviews article.
• One more anti-spam trick for hgUserSuggestion.
• Fixed buffer overflow in hgTracks.
• Handle HTTPS for redirects between UCSC and other official mirror sites like genome-euro.
• Fixed obscure bug in dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
• Fixed a minor bug in pushCarefulMemHandler mutex handling.

25 June 2013, v285

• Released new CGI to act as a Suggestion Box.
• Released new CGI for Variant Annotation Integrator.
• Released new Assembly Hubs feature.
• Simplified process for users to download and/or compile utilities.
• Allowed mutex to work with multiple threads.
• Removed calls that caused duplicate warn handler pop underflow errors.
• Performance enhancements for track search functionality.
• Fixed gene details links to InterPro (#11078) and TreeFam.
• Added new utility: bigWigCorrelate.
• Added multi-view composite support for type pgSnp.
• Ongoing work on bigBed Item Search.

3 June 2013, v284

• Released Gene Haplotype Alleles section for gene details pages, hg19.
• Added features for Publications track: color by topic, impact factor or year, sped it up, various IDs on main table (for VEP), allow OCRed images.
• Added trix search and bigBed item search for track hubs.
• Ongoing work on simplifying the build and number of utilities.
• Ongoing work on Variant Annotation Integrator: hgVai.

13 May 2013, v283

• Added support for HTTPS in hgSession.
• Allowed CGI timing function to be controlled via options in hg.conf file.
• Continued improvements to makefile system; destination binaries now depend upon their objects and the libraries.
• Fixed wigColorBy bug hgTracks right-click update.
• Fixed clipping error in anti-aliased lines that could cause crash.
• Fixed bug in handling of right-click on a hub track.
• Fixed bug in updating hubStatus table with longLabel.
• Fixed a buffer flow problem which caused a crash for bigWig custom tracks.
• Fixed some problems with spaces in labels in bigBeds.
• Sped up bigBed's handling of long records.
• Fixed link from gene details page to Interpro.
• Ongoing work on Variant Annotation Integrator.
• Ongoing work on Assembly Hubs.
• Ongoing work on Gene Haplotype Alleles feature.

22 April 2013, v282

• Overhauled makefile system.
• Created a secure and sharable sendmail utility: mailViaPipe (and used it for hgLogin).
• Fixed bug with cookies in hgLogin.
• Found and fixed a problem with excessive activity in custom tracks by adding a 1000 track limit per submission.
• Added anti-alias lines to browser image.
• Added udcDir option to twoBit utilities.
• Created new utility (bedScore) that assigns (or transforms) score field in BED files, based on values in a selectable column of the file, using user choice of 4 algorithms.
• Started work on a tag-storm format (hierarchical .ra) for use in storing metadata.
• Ongoing work on annoGrator (AVI)
• Refactored and extended gadPos program to use Gencode as another gene symbol lookup.
• Ongoing work on euroNode.

1 April 2013, v281

• Reduced memory use of pslMap by up to two orders of magnitude.
• Added hints about how to improve browser images for publications.
• Fixed bug where session custom tracks are clobbered when original hgsid session modifies CTs.
• Added support for HGVS's chromosome range format with "_".
• Changed the transparency so that it shows up in PDF, and also can be normalized when we add more cell lines.
• Fixed a bug where sometimes zoom summaries would not be written out by bedGraphToBigWig.
• Ongoing work on Variant Annotation Integrator tool: bugfixes, baseline VEP-formatted output.
• Ongoing work on faux centromere generation code.
• Ongoing work on assembly hubs.

11 March 2013, v280

• Fixed problem in hub support for 'parent' setting when used by superTrack 'children'.
• Fixed right-click getDna link to use session ID and database.
• Several display and usage improvements to GENCODE track.
• Started work on transparency code.
• Ongoing work on Variant Annotation Integrator tool.
• Support drag-select in ideogram even if it has only one bar.
• Initial work on Assembly Hubs.

19 Feb. 2013, v279

• Added maxWindowToDraw to dense VCF tracks' trackDb entries.
• New error check in checkTableCoords to avoid segfault on bogus bed12.
• Added missing implementation of TB paste/upload IDs for bigBed.
• Smartened up hgFileUi to recognize when ENCODE restriction timestamps are in effect.
• Enlarged buffer that overflowed with huge trackUi matrices.
• Fixed sort by metadata ordering in the 'Assayed cells' section of details page of Clusters tracks.
• Performance improvement to genbank dumps of all assembly table status dumps: added sleeps.
• Fixed error in bedToPsl.
• Fixed udc cache location problem related to saved sessions and early cart processing.
• Fixed bigBedIntervalQuery and hgc to not drop 0-length items (insertions).
• Fixed invalid assert in hgTrackUI JavaScript code that caused weird error messages for certain tracks.
• Ongoing work on Variant Annotation Finder.
• Ongoing work on Gene Alleles.
• Ongoing work on Haplosufficiency Map.
• Ongoing work on faux centromere generation code.

29 Jan. 2013, v278

• Continued work on faux-centromere generation code.
• Fixed bedGraphToBigWig to make it handle large input better.
• Added CGI timing measurement for all CGIs to apache error_log.
• When Apache kills timed-out CGIs, we now trap SIGTERM and call exit to allow atexit to clean up.
• euroNode/mirrors menu: Added support for database table-based GUI menu items.
• Fixed unitProt's links back to the Genome Browser.
• Removed link to the no longer maintained Stanford SOURCE database from refGene and few other places.
• Increased limit of trackDb.txt file to 64Mb.
• Made Genbank tracks fail more gently when sequence is missing (ie. when updates are turned off).
• Tweaks to VCF: tolerate Complete Genomics's AN=0 records.
• Accommodate missing name/ID in DGV track details page.
• Fixed Table Browser to display example identifiers on paste/upload page for bigBed data type.
• Changed hgc peak cluster handler to sort on metadata.
• Changed hgTrackUi subtrack list default to 'all' if there is no matrix.

7 Jan. 2013, v277

• Continued work on Variant Annotation Finder (added bigWig support).
• Added code to re-try a hub with an error message after a hg.conf configurable amount of time has passed.
• Fixed a problem in the table browser when track hubs have tables with dots in them.
• Used threads to process bigDataUrl customTracks in parallel.
• Set CHARSET=iso-8859-1 for all hgLogin forms.
• Fixed bug in searching for cytoBand identifiers on mouse browsers.

Visit the Genome_Browser_Software_Features_(2008-2012) page for features released in the 2008-2013 time frame.