Releases: ucscGenomeBrowser/kent
Releases · ucscGenomeBrowser/kent
v482 Genome Browser Software
This is the v482 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- Change the hubConnect page so it no longer redirects.
- Improving mouseover of genePred tracks, adding hint to zoom in more to show cDNA positions, and a link to a new doc html page that explains what we mean by "phase 0/1/2".
- Added right-click Track Description feature in hgTracks.js.
- BAM tracks now go into coverage mode if maxItems is exceeded. Also added a cap to the number of items that will be loaded (BAMMaxItems).
- It is now assumed that the RGB value in the ninth field of a bed should be treated as a color.
- Allow .bigBed file extension to work with featureBits.
- Fixed hgBlat table of alignments not available once browsing. This fixes both native blat track and ct blat track.
- Changes to our bottleneck system to better recognize and penalize heavy bot activity on our servers.
- Anti-bot work: wait for 10 seconds on. Added hg.conf that triggers apache log entry when a user arrives without cookies, and added bytedance bot to robots.txt.
- New tool tabToBed: give it a .tsv file and it will guess what the fields with chrom, start, end, name, or give it the names of these fields and it will make an .as file and a .bed file to make a bigBed from the .tsv.
- GBIC changes: a few small changes for OSX, adding freetype for all linuxes, fix straw.cpp for new g++, allow builds on the beta tag when not on the beta branch for mirrors, always use mariadb and removing mysql_config dependency, removing udr, always install curl just in case, redoing the whole Dockerfile using newer commands, address the root user problem for mariadb, and other changes.
- Fixed buffer overflow in fixed-size mouseover buffer by making it a bigger fixed size.
- "hubtools up" no longer re-uploads a file into Hubspace if it's already there.
- hgVai: fixed corner cases surfaced by running vai.pl on EVA snps (40 assemblies, 909M variants).
- Improvements to wuhCor1 big tree build process.
v481 Genome Browser Software
This is the v481 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- Fixed VCF does not work on extended case-color options in Get DNA for vcf, vcfTabix, and vcfPhasedTrio in hgc.
- Fixed instructions in hgCustom for URL-only custom tracks.
- Fixed broken html generation in hgTrackUi filterBy's.
- Made configuration instructions for URL-only custom tracks more obvious with red message at the top.
- Fixed mangled composite track UI when score filtering is disabled. This caused form and table begin/end mismatches. Also a little bit of movement of some inconsistent code to make it easier to understand where score fitler config is called.
- Added two new accessibility fonts.
- Fixed Table Browser filter error caused by not handling special case of tables with both db table and bigGenePred or bigBed.
- Fixed missing uri encoding in url for ajax callback in track collections js.
- hgVai: fixed corner case (insertion containing stop codon).
- Improvements to hgcentralTidy.c to better clean out hgcentral spam entries.
- Added botDelay to hgNear as a highly executed CGI on RR.
- Improvements to wuhCor1 big tree build process.
v480 Genome Browser Software
This is the v480 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- Users must now be logged in before using track collections.
- Enabled caching for hubApi.
- Implicitly convert ENST accessions to ENSP accessions during hgvs search if the hgvs term is a p. term.
- Interact tracks gain an option to suppress display of the details boxes. When displayed, those boxes are also larger now - easier to find and click on.
- Revision of the recently-added heatmap display style, with better support for heatmap legends and coloring.
- A thousand groups are now allowed in MAF displays, not just 20.
- hvGfx library fix - hvGfxCurve now correctly relocates points of the curve in reverse complement mode, so hic tracks in arc mode won't look like koosh balls anymore.
- More hubSpace prep for release: add search box for genome selection, row clicks either open the directory or select the row if it was a regular file, wording changes, install hook scripts into cgi-bin/loader, decode or encode file names more appropriately, especially if coming from hubtools, make spaces characters no longer allowed so apache can find the track files easier.
- Fixed memory bug in peakClusters.
- Fixed slNameSort in list.c for hubApi, refreshed expected output lists.
- Fixed bad slNameSort override in findCutters utility.
- AutoSql files that define arrays with a variable number of arguments can now use variables whose name starts with an underscore (obscure and unlikely to be used widely, but it works now).
- bedPartition - add options -minPartitionItems, -partMergeDist, and statistics output. The goal is to produce fewer, larger partitions, so that job startup overhead isn't greater than the runtime.
- Improvements to wuhCor1 big tree build process.
v479 Genome Browser Software
This is the v479 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- Added support for DropBox for hubs and custom tracks using byteranges.
- Added "view conversions" link to hgLiftOver output page to display conversions as html.
- hgSearch now uses chromAlias.
- First version of a positional heatmap track display that uses several extra fields in a bigBed. This is similar to the existing microarray track type, but should be more flexible (and supports multiple heatmaps in the same track).
- hubCheck now checks that subtracks have the same group setting as their parent to enforce implicit group correctness when the group setting is not set at the right level.
- Added the db parameter to async hgTracks image updates to band-aid the multiple tabs with different genomes but same hgsid confusion.
- hubApi can detect if the genome argument is an assembly hub.
- hubApi getData endpoint can detect if requested tracks are in a track hub and retrieve them without explicitly setting hubUrl argument.
- Increased the number of split tables allowed.
- Improvements to wuhCor1 big tree build process.
v478 Genome Browser Software
This is the v478 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- Added sort option to bedToBigBed utility.
- Added a cart rewrite for the new Splicing Impact supertrack.
- Explain how to download big* files on the Table Browser schema page.
- Added support for quickLifting mySQL beds, including custom tracks.
- Added ability to turn off table name based handling in CGIs per track will default to type based handling.
- Do not create a hub on invocation of hgCollection. This should reduce number of empty hubs.
- Fixed another prop() vs attr() jquery upgrade bug, this time when turning on subtracks.
- Fixed minor hgTracks imageV2 bug - add one only if we are drawing center labels.
- hgConvert will now report when it's unable to find a chain file instead of crashing (this is very rare).
- GBiB will now update from a frozen binary set until we make it compatible with our new compilation setup.
- sqlTableSize return value switched from int to long type to support tables with more than 2^31 rows.
- Removed sandbox commands from our mariadb table dumps for better compatibility with older mariadb and mysql installations.
- Proof of concept preview of contributed tracks to GenArk hubs working out of /gbdb/ hierarchy.
- Working toward getting GenArk hubs to function out of the /gbdb/ local filesystem.
- Fixed file path security concern in hgEncodeVocab.
- Improvements to wuhCor1 big tree build process.
v477 Genome Browser Software
This is the v477 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- Filename now used as custom track shortLabel when uploading a custom track, rather than "User supplied data".
- hgTrackUi and composites: set parent to pack if a child is un-hidden, set children to pack if parent is un-hidden.
- Fixed ClinVar coloring for CNVs.
- Compile user download on Ubuntu using standard static where possible using Docker.
- Add very old program tabFmt to tree due to popular demand.
- Started using a new version of RepeatMasker (v4.1.7-p1) and a new version of windowMasker (v28.0.11) for GenArk browser build.
- Improved source tree build using more static libraries, fewer dynamic libraries: libz.a libm.a.
- Improvements to wuhCor1 big tree build process.
v476 Genome Browser Software
This is the v476 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- Feaure ‘Right click > hide other tracks’ and ‘hide’ now hide the parent instead of the last child. This means that you can no longer have tracks in the track list that have no subtracks shown.
- First major commit of hubspace.
- Update browserSetup.sh after running it on Rocky 9.5 in vm on hgwdev.
- Fix for https cert locations on Ubuntu/Debian, and updated https whitelist with a fresh scan of last year's log of the RR and official mirrors.
- Various fixes to address compiling on the new Rocky 9 OS.
- Edge and Safari have a 32k cart string size limit. We now work around that.
- Fixed code that chops strings so as not to call ArraySize with NULL.
- Ported hgBeacon to python3.
- Make sure jquery library is included in iframes for hubCheck on the hub development tab.
- Work on making HAL build-compatible.
- Add a version of stringify (stringifyEz) that is in an interpreted language so it does not have to be built first and in the path. Useful if building just parts of the tree.
- Fixing issues in the source tree for the transition to newer linux version, more static libraries, fewer dynamic libraries.
- Preparations are underway to host all of the GenArk assembly hubs in the /gbdb/ hierarchy to eliminate the dependency on hgdownload service.
- Fixed up crash bug in findMotif program when missing arguments.
- Improvements to wuhCor1 big tree build process.
v475 Genome Browser Software
This is the v475 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- 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 records. Removed -partSize, which just groups by number of partitions and was not useful. It is replaced by -partMergeSize, to allow for merging partitions within a certain distance.
- Fixes for openssl3.
- CGI version now shows up on the configuration page.
v474 Genome Browser Software
This is the v474 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- 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)
- Making sure that hgGeneGraph is not spawning more and more dot programs
- Rework the use of /scratch/tmp /data/tmp and /dev/shm temporary filesystems in the automated pipelines to accommodate new cluster machines
- Fixup security points in the assembly request CGI script that is sending emails
- hgPhyloPlace: add option for subtree JSON files to persist instead of being cleared after 2 days
v473 Genome Browser Software
This is the v473 release of the UCSC Genome Browser. A summary of the relevant code changes includes:
- 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" op 3CFC tion on GBiBs since they don't have an API available.
- More work on right-click - hide all other tracks.
- Continuous GenArk process improvements.