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.

2016

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.