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.

2014

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.

2012

3 Dec. 2012, v276

• Fixed bug in hgHubConnect that was preventing errors from showing up.
• Now using UDR for genbank transfer to euronode.
• Fixed genbank searching for assemblies without all_mrna table which used to silently fail.
• Fixed Table Browser to display only the uniProt and proteome databases, not swissProt and proteins.
• Reduced privileges for the default MySQL user (hguser) to accommodate requirements for MySQL 5.1 and 5.5.
• Fixed a bug in autoXml so that it works now with XML name spaces.
• Moved the full text index (trix) command line driver from one-shot to a real place in the source tree and gave it a better name and improved comments.
• Added bedDetail track type to allow composite trackDb configuration options.
• Added code from Robert Hubley to src/hg/liftUp/liftUp.c to allow lifting of RepeatMasker .align file types.
• Added dropdown items to 'Mirror' menu to enable users to switch between geographic mirror sites (US and Europe).
• Fixed display problem for VCFs with mixed haploid status (e.g. chrX).
• Fixed crash when per-chromosome BAM files are not available for all chroms.
• Hosting samtabix git repository at UCSC.
• Ongoing work on Variant Annotation Finder (added annoStreamBigBed).

5 Nov. 2012, v275

• Made errors in hub.txt and genome.txt show up as warnings in hgTracks.
• Changed pslToBed to set thickStart and thickEnd to chromStart for non-coding beds.
• Mapped all characters other than alnum, dash, and underbars to underbars in track names in track hubs.
• Changed bedExact library method to look at thickStart and thickEnd.
• New compilation option, now default at UCSC: instead of separately downloading, patching and building samtools and tabix, we can use the new samtabix package (https://github.com/AngieHinrichs/samtabix) which contains combined, pre-patched samtools and tabix. See kent/src/product/README.building.source.
• On details page for VCF data, if name looks like dbSNP or dbVar ID, make an external link.
• Fixed recently introduced liftOver bug for bedPlus data.
• Fixed HTML double-encoding problem in VCF details.
• Removed support for 32-bit CGI build.
• Released Track Database Definition Documentation (for generic trackDb settings and for Track Hubs).
• Fixed support for "parent" setting in superTrack child.

15 Oct. 2012, v274

• Improved display of VCF indel alleles in hgTracks & hgc.
• Prevent schema page crash for sparse bigBeds in hgTables (no sample rows from current chrom).
• Mod to bigBed lib: chop by tabs, not spaces (was causing incorrect example row display in hgTables).
• Fixed missing html in hgTables schema for bigDataUrl types and hub subtracks.
• Removed dependency on proteome.spXref2 table.
• Cleaned up gbSanity to not generate bogus errors.
• Display username in hgLogin forgot password confirmation message box.
• Found consistent cookie dates that makes making hgLogin logout work on Safari.
• Added blat repMatch default values for tileSizes 16 to 18, and incremented blat major version to 35x1.
• Set more liberal track limits for bigBed hgTracks.
• Added flushResults command to parasol.
• Fixed problem with missing PDF/PS link in hgGenome.
• Modified publications track to show publisher logos.

25 Sept, 2012, v273

• Added twoBitDup check to makeGenomeDb.pl.
• Fixed gateway page to avoid showing clades that have no browsers.
• Don't spam users on slow connections with ajax errors.
• liftOver feature addition: lifting large regions by end/restitching.
• Changed the printout of the data about the number of exons in a gene in hgGene.
• Ongoing work on documenting trackDb settings.
• Fixed bug for bigBeds in dense.
• Caught instances of extra spaces in URL for public track hubs.
• Fixed problems of duplicate genes in new refGene tables.

4 Sept, 2012, v272

• Table Browser bug fix for timeout situations.
• Refinements to description of SNP function codes (now displayed as SO terms).
• Modify hgLogin to use the sendmail to send mail to user.
• Add missing clause in like to fix problem with exact queries in non-knowGene assemblies.
• Added function to print out chrom ranges on summary zoom levels to bigBedInfo.
• Fixed Table Browser problem with getting schemas for very big bigBeds.
• Added support for items in Peak tracks, and use those items to match uniquely in item details display.
• When more than one record have exactly the same chrom, start, end, and name, now support displaying such multiples for *Peak and bigBed tracks.
• Added score-filtering to bigBed item click.

14 Aug, 2012, v271

• Added menus to all CGIs, use sans-serif fonts and change background of hgTracks.
• Merged gene suggest into the position/search box.
• Include description in gene suggest list.
• Enabled highlighting for genes chosen via gene suggest.
• Decommissioned the Proteome Browser.
• Fixed buffer size problem in bed validation in validateFiles.
• Small improvements to email logistics of hgLogin.
• Display Sequence Ontology (SO) terms instead of dbSNP-specific terms for functional effects on SNP details pages.
• Fixed bug for haplotype-clustering display of haploid VCF with lots of no-calls.
• Minor UI tweaks for BAM tracks.
• Fixed bug where dense subtracks with views could give misleading centerLabels.

24 July, 2012, v270

• Ongoing work on hgVarAnnogrator UI.
• Fixed BAM UI checkbox behavior.
• Improved botDelay to allow our own robots to run unbottlenecked via hg.conf setting bottleneck.except.
• Added support to return alignments for the whole genePred (CDS + UTR) not just the CDS regions.
• Fixed hgLogin bug -- Do not send user name to non-existent email address.
• Ongoing work on trackDb documentation.

3 July, 2012, v269

• hgTables now properly filters on Ids and regions even if no field from primary table is in output or filter-tables.
• Added bottleneck delay to hgTracks.
• Added filtering fields in table browser for custom track bigWigs (by value, and limit on number).
• Added twoBitDup utility that warns if DNA sequences in 2bit are included more than once.
• Enabled genbank runs euroNode machine.
• New highlight mode in hgTracks used by GENCODE to highlight selected tracks.
• Fixed BAM tag-printing bug: signed 8-bit ints were displayed as unsigned.
• Fixed a stricter-gcc warning: string comparison using "==". Angie
• Added featureBits to the userApps delivery.
• Set the wikiTrack to be read-only optional via hg.conf variable.
• A little polish for the new login system.

12 June, 2012, v268

• New Login/Signup system for Sessions (hgLogin).
• Support for views for track type (Genome Variation Format) GVF.
• ENCODE Experiment Matrix for mouse data. This web application provides real-time table and matrix summary view of ENCODE data that is available at UCSC.
• hgTables now correctly filters on primary table identifiers even if no fields from the primary table are selected for output.
• Use hgFixed.trackVersion.version (if available) for 'Data Version' in hgc and hgTrackUi.
• Fixed hgEncodeVocab bug that failed to display Input when it was being treated as an Antibody.
• Mysql load error detection is now the default.
• Ongoing work on Variant Annotator.
• HapMap LD checkbox javascript bugfixes.
• Added support for per-chromosome big files for VCF db tracks (a la BAM).
• Fixed the script that generates the hgcentral.sql file on hgdownloads.
• Fixed bug in trackDb reading when "type bigBed" didn't have number of columns following it.

22 May, 2012, v267

• Improved cpgIsland script to allow kluster runs on assemblies with 100s of thousands of contigs.
• Fixed bug in gsBig.c program to eliminate its garbage temp files properly.
• Created new Login/Signup system: hgLogin.
• Added alwaysZero support to multiWig.
• Added "check all/clear all" buttons to transparent overlay tracks in the integrated regulatory ENCODE supertrack.
• Fixed missing "c=chromName" in many hgc URLs.
• Fixed missing "body" and "html" tags in mRNA details page.
• Ongoing work on hgVarAnnogrator UI: position input, store search spec in cart, handle back button.
• BAM UI bugfix - Global minimum alignment quality score is not reflected in the sub-tracks.
• Improved speed of Publications Marker Band track.
• Made sqlList dynamic arrays thread-safe but just as fast.
• Added keepalive call to prevent cgiApoptosis() from terminating a legitimately busy long-running process.

1 May, 2012, v266

• Moved copyright information from kent/src/README to kent/README since this is now the top level directory people check out.
• Updated style guide section of kent/src/README.
• Made programs to convert ENCODE cv.ra, metaDb table, and encodeExp table to a Django-managed database.
• Created verticalSplitSqlTable utility program to help normalize (in the relational sense) the antibody information from ENCODE.
• Created textBetween and replaceTextBetween command line utilities that let you extract or replace text between two strings.
• Fixed problem where context menu disappeared off the top of the screen.
• Continuing work on euroNode.
• Fixed problem where bigBeds weren't being shown properly.
• Disabled inPlaceUpdate when either left or center labels are turned off.
• Changed priorities for oligo and cutter track to ensure they appear after tracks which get the default of 100.
• Ongoing work on gpFx library to predict disruption of genePred given a variant.
• Tweak to OMIM generation to avoid checking a field that changes dramatically between versions.
• Variant annotation integrator: wig and VCF support, basic web UI, bugfixes, JSON parser.
• Checked in cpgIslandExt code into the kent source tree and fixed up to compile in this environment.
• Updated the doCpgIslands.pl script to use kluster runs to get done much faster and handle high contig count assemblies.
• Created ENCODE Data Matrix: A new set of web pages that display a real-time summary of ENCODE datasets in tabular and matrix format.
• Revamped validateFiles, bedToBigBed, hgLoadBed, and customTracks to use a shared validator routine. Enforces the BED standard.
• MySQL Local Data Infile loading now checks for mysql warnings and treats them as errors by default.

10 April, 2012, v265

• Changed PDF output to play down postscript.
• Fixed error in usage message in bedGraphToBigWig.
• Added stricter error checking to bulk mysql loaders (hgLoadBed, hgLoadMaf, hgLoadWiggle).
• Initial work on variant annotation integration tool.
• Fixed minor table browser display problem with BAM quality scores containing lthan or gthan.
• Fixed Table Browser bug where there is a table tag in trackDb.ra but no track tag of the same value.
• Fixed a bug where in wgEncodeRegTfbsClustered the score sometimes was larger than the max of the components visible on the details page.
• Added search-ability for tableName advanced track search.
• Removed search-ability for fileType, suppressed term info links in advanced track search.
• Ongoing work on alternate login system.
• Fixed score filtering on bigBed's that are bed9'S.
• Fixed Downloads link for ENCODE track where table and track name are not matching.
• Fixed problems with in-place update when center and left labels are turned off.
• Released ENCODE DataMatrix, displays real-time summaries of datasets.

13 March, 2012, v264

• Show message when there are too many Restriction Enzymes to show in the view.
• Improved reporting of warnings and errors in javascript client code.
• Added licensing URL to README.
• Fixed typo in gfServer error message.
• Fixed bug where table browser was showing wrong min/max for bigWigs.
• Minor performance improvement to pgSnp drawing code.
• Ongoing work on alternate login system.
• Ongoing work on track automation.
• More tweaks to hgTrackUi matrix.

21 February, 2012, v263

• Turned off chrom size checking for big* and bam files.
• Fixed out of memory error when doing sub-track merge in table browser.
• Fix missing "overlay type" control for multiWigs in hgTrackUi.
• Fixed IE8 problem with rightClick configure.
• Fixed bug with wiggle autoscaling when only one value is present in range.
• Fixed bug in table browser that crashed in bigWig dumps when data point limit reached.
• Allow mirror sites to have no hgFixed table.

31 January, 2012, v262

• Check for illegal chromosomes in bam and big* custom track loaders.
• Fix pack option missing from blat and some other tracks.
• Suppress too verbose messages generated by loading some bams.
• Add synonym for stop-loss SNPs, which appears in snp135 SNPs.
• Check syntax of urls in "add hubs" tab.
• Added a utility to check to see if a twoBit file has duplicated sequences.
• Support the nextItem button on custom bigBed tracks.
• New subtrack configuration feature.
• Fix to composite/view/subtrack inconsistencies bug.
• Fix to subtrack vis not getting to cart if populated by wrench-click.
• Fix to allow composites that are not packable.
• Fix to tolerate numeric trackDb tags in hgTrackUi.
• Fix to resize subtrack cfg box so that controls do not extend outside of it.
• Fixed bug in simple repeat automatic script.
• VCF: represent missing data properly in INFO and GT fields.

10 January, 2012, v261

• Small tweaks to VCF support.
• Ongoing work on (now 57-way) master phylo tree.
• Fixed js error-reporting.
• Internal utility for helping to determine the quality of an assembly.
• Turned on assembly name by default in Base Position track.
• Fixed Genome Graphs display.
• Made changes to genbank code to support small RNAs for the UCSC Genes pipeline.

2011

13 December, 2011, v260

• A little more polish for Data Hubs.
• Extend DNA case/color options to composite tracks.
• Support for VCF data format in main display, table browser, custom tracks, etc.
• Added monospace font option to phyloGif.
• Added angled text to the top of the matrices on hgTrackUi page (this results in the matrix being more narrow).

15 November, 2011, v259

• Fixed Table Browser to remove successive duplicates from joiner-generated list columns.
• Fixed some compiler warnings.
• Ongoing work to support VCF data type.
• Allow tracks of type bigBed to show colors in dense mode.
• Created workaround for Apache 2.2.21 problem.
• Remove "Enable advanced javascript features" option.
• Added progress meter for upload of large Custom Tracks.
• Added new UCSC exception flag for dbSNP: Inconsistent Alleles.
• Checking for non-standard characters in track names.
• Keep restricted tables off of DAS server.
• Small interface tweaks to Data Hub page.
• Added extraFields support for bigBeds in hgc.

25 October, 2011, v258

• Ongoing work on VCF support.
• More polish for Data Hubs.
• Automated OMIM updates.
• Tweaked to in-place updating in hgTracks.
• Added API to return browser image via URL.
• Changed default text alignment to left rather than full.

27 September, 2011, v257

• Ongoing work on supporting VCF+tabix format.
• More polish for Data Hubs.
• Fixed bigWigMerge bug.
• Stared work to minify java script.
• Prep top blue navigation bars for web redesign.
• Disable in-place navigation if advanced java script features are turned off.

8 September, 2011, v256

• Ongoing work on supporting VCF+tabix format.
• Added 4k readAhead buffer to UDC for speed-up.
• Final touches on drag-n-zoom anywhere in image.
• Final touches on drag-scroll x1.
• Tweaks to UDC BAM fetch.
• Small UI improvements to Track Data Hubs.
• Started work to support returning browser image via URL.
• Automatically re-size the browser image to fit the internet browser.

17 August, 2011, v255

• Lots of features and speed-up to UDC.
• Several performance measurements and enhancements.
• Automatically fit browser image to screen.
• Fixed right-click for bigWigs not retaining vertical viewing max.
• Ongoing work on supporting VCF+tabix format.
• Accept BAM files with wildcards.
• Enabled parallel loading of tracks using bigDataUrl.
• Added product ordering link for IKMC entries when available.
• Started implementing drag-n-zoom anywhere in image.
• Started implementing drag-scroll x1.
• Enabled context menu (right click) on Firefox3/4 + Mac OS X.

28 July, 2011, v254

• Completed release 1 of Data Hubs.
• Added parallel-fetch loading of remote bigDataUrl tracks using pthreads.
• Ongoing work to support VCF+tabix file format.
• Fixed intersections for bigWigs in Table Browser.
• Tweaks to pslCDnaFilter program.
• Fixed hgTracks to draw very large items when zoomed way in.
• Fixed pgSnp to recognize a two-base deletion as a frame shift.
• Working on in-place updating.

5 July, 2011, v253

• Ongoing work on data hub.
• Fixed logic problem where aligned mRNAs were showing up in Unaligned list after search.
• Tweaked hgSuggest to choose normal chroms over haps and randoms.
• Disallowed file references in bigDataUrl.
• Allowed bigWig files to close after being loaded.

14 June, 2011, v252

• Ongoing work on data hub.
• Ongoing work to support VCF file format.
• Switched from HMTL v3.1 to V4.0 transitional.
• More support for microarray tracks.
• Fixed bug with right-click and mean+whiskers view.
• Fixed color-by-strand bug that was not working in BED8.
• Fixed GTF Table Browser output for the case where start/stopcodons sometimes span introns.
• Fixed case where CGIs were staying open too long and causing RR nodes to crash.
• Drag-n-drop of tracks in image now drag contiguous set of subtracks if dragging side button.

17 May, 2011 v251

• Ongoing work on data hub.
• Ongoing work to support VCF file format.
• Fixed BLAT segfault for maxIntron <= 11 when tileSize <= 11
• Created a hard fail if CGIs can't find correct version of js or css files.
• Switched HTML from DOCTYPE 3.2 to 4.01 Transitional.
• Streamlined hgLiftOver CGI.

26 April, 2011 v250

• Ongoing work on data hub.
• Fixed bedRemoveOverlap program for 32-bit machines.
• Updated paraFetch and paraSync to support option which only downloads newer files.
• Switched the order of chains/nets to phylo order.
• Fixed error found when viewing zoomed-out microarray tracks.
• Ensure that the appropriate track is visible when a user selects something from the gene search box.
• Ongoing work on UCSC Genes update, hg19.
• Fixed small error in GTF output from Table Browser.

4 April, 2011 v249

• New track type: vcfTabix (bigDataUrl type of track).
• Ongoing work on VCF customFactory + track handler.
• Fixed GTF output in Table Browser.
• BAMs fully supported in Table Browser.
• New utility: bigWigMerge.
• More work on File Search functionality.
• Fixed instance where display mode collapsed to dense.
• Fixed Table Browser bug where selected fields stuck when switching tracks.
• Repaired details page for custom BAM tracks.
• Added support to allow chimp chr2 chain/nets on human browser to draw in two colors.
• Fixed wrapping top blue navigation bar.
• Ongoing work on data hub.
• Added botDelay to hgGene CGI.
• Ongoing work on VCF parser.
• Fixed blat crashing bug.
• Allow SSIs in description page html.
• Display one mapBox per row in BAM files if there are too many items.

14 March, 2011 v248

• Ongoing work on data hub.
• Adding support for bamWigs.
• Added support in Table Browser for BAMs.
• Ongoing work to support VCF filetype.
• Prevent topbar from wrapping on narrow displays.
• Supporting SSI-like syntax for track html files in hgTrackDb.
• Added new utility to check if two columns look joinable in a database.
• Right-click now highlights found item in hgTracks.
• Utility to convert BEDs to pseudo-PSLs.
• Improve performance of genbank alignments.

18 Feb, 2011 v247

• Ongoing work on data hub.
• Added support for new track type: GVF.
• Created example script to run a stand-alone lastz/chain procedure on two genomes without UCSC environment.
• Allow user to auto-set the width of the hgTracks image to width of browser window.
• Modified refSeqGet to return results in a predictable order to minimize test failures when database changes.
• Small tweaks to Track Search GUI.
• Label exon numbers from right to left when on reverse strand.
• Ongoing work for support of new OMIM tracks.
• Added Table Browser support for BAM files.
• Added support for zoom-to-codon, and zoom-to-exon.
• Fixed memory corruption on very long GFF attribute columns.
• Cleaned up error message in Custom Tracks for pgSnp type.
• Revamped 'data last updated' times for hgc and hgTrackUi.
• Automated NCBI Incident DB update procedure.
• Added Zoom To Codon and Zoom To Exon to context menu.

31 Jan, 2011 v246

• Ongoing work on data hub.
• Accommodate systems that do not have samtools installed.
• Fixed right-click menu for micro-array tracks.
• Started work on File Search.
• Tightened down Custom Track html upload process.
• Fixed small bugs in Table Browser with bigBed/bigWig file types.
• New utility: bedRemoveOverlap.
• Resolved conflict between right-click menu and wiki track items.

10 Jan, 2011 v245

• Bug fix for tdbQuery.
• ENCODE DocID work.
• Enabled release tags in include statements in trackDb.
• New trash-cleaning scripts.
• Ongoing work on right-click functionality.
• Added support for "downloads-only" style tracks.
• Removed GIF support from kent library, PNG support assumed.
• Made display smarter about very dense BAMs.
• Assign ids in seq and extFile tables locally rather than globally.
• New CFI hgFileUi for composites with downloadable files.
• New utility: paraSync (like rsync with paraFetch to easily mirror a bunch of directories via http, https, or ftp over tcp).
• Fixed bug where drag-n-zoom in ideogram was not available when cytoBand track was on.

2010

13 Dec, 2010 v244

• Automated the dbSNP process: doDbSnp.pl.
• Ongoing work on ENCODE docId.
• Automated process for checking and building DECIPHER data updates.
• Fixed ruler problems in V2 image.
• Added tooltip to OMIM, hg18, hg19.
• Enabling search using OMIM ID in the URL.
• Fixed subtle bug in visiGene so that link from images to hgGene function correctly.
• Enabled right-click menu.
• Added support for GFF3 discontinuous features.

15 Nov, 2010 v243

• Fixed Table Browser: GTF lines with start > end.
• hg19 snp131 Coding SNPs.
• Fixed alignment numbering when "viewing parts of alignment".
• Added some js to Gene Sorter for instant changes.
• Added IP logging option to gfServer.
• Prototype of phoneHome function.
• Created ability for an assembly to not have a BLAT server.
• Fixed: mRNA non-synonomous codons don't work when genome is a stop.
• Final polish on Track Search tool.
• Fixed warning message in bigWig when viewing region without data.

18 Oct, 2010 v242

• Allow js browser access to DAS.
• Improved handling of multiTracks.
• BAM: range settings for shading alignment quality and base quality.
• ENCODE metaData work.
• Speeding up Table Browser for scaffold-based assemblies.
• Ongoing work on Track Search tool.
• Force browser reload for style sheets.

4 Oct, 2010 v241

• Added new track type, bedDetail, to custom and built-in tracks.
• Added pgSnp (personal genome SNPs) as custom track type.
• Edited madeGenomeDb script to turn the quality track into a bigWig instead of wiggle.
• Ongoing work on Track Search tool.

20 Sept, 2010 v240

• Provided access control of some tables in the Table Browser.
• Fixed snp131Clinical's missing-func item, hg19.
• Added PSL configuration for multi-view tracks.
• Ongoing work on v2.0 image.

7 Sept, 2010 v239

• New trackDb setting 'tableBrowser off' which prevents hgTables from displaying a track.
• fix bug in gtpToGenePred where insertions between multiple bases of stop codon generated incorrect frame.
• Optimized ENCODE pipeline downloading for gzipped files.
• Made chains for GRCh patches, hg19.
• Started work on ENCODE-specific style sheet.
• Ongoing work on Track Search tool.

23 August, 2010 v238

• Fixed doSameSpeciesLiftOver script so that blat chunk will not exceed 5000.
• More fine-tuning of multi-wiggle display.
• Ongoing work on GUI 2.0.
• Drag-reorder functionality going live.
• Ongoing work on Track Search tool.
• Stop opening an SQL connection for each seq retrieved by the Table Browser.

9 August, 2010 v237

• New utility: gff3ToPsl, converts GFF3 files with CIGARs in GAP attributes.
• Fixed bug in doSameSpeciesLiftOver.
• Added sqlDump to assist in debugging connection cache/profile problems.
• Better handling of uniProt connection for hgNear GO column.
• useCount CGI.
• Address problem of hgTables consuming all available sockets before TIME_WAIT period by using the connection cache.
• Ongoing work on web 2.0 GUI.

26 July, 2010 v236

• Change quality tracks to bigWigs going forward.
• Fixed color drawing in psl tracks.
• Autodetecting PNG,SSL,BAM to help mirror sites.
• paraFetch for ENCODE pipeline.
• Ongoing work on Track Search feature.
• Ongoing GUI 2.0 work.

12 July, 2010 v235

• Enabled clicking in dense mode to switch to pack mode.
• More multiWig work.
• Changed all on-the-fly images from GIF to 32-bit PNG.
• Use painter's algorithm for mRNA track.
• Starting work on supporting remote tracks.

28 June, 2010 v234

• PNG 32-bit color for multiWiggles.
• More tweaks due to git source control switch.
• Ongoing work on multiWiggles.
• New CGI: hgTrackRender.
• Skip browser and track lines at the beginning of bedGraphs and wigs when creating bigWigs.
• Halved calls to botDelay when BLATting multiple sequences.
• Ongoing work on Track Search.
• Ongoing work on metadata table.

11 June, 2010 v233

• Gracefully handle case of code being compiled without USE_BAM=1.
• Utility: tagAlignToSAM.
• Fixed wiki track so that it displays even when not logged in.
• Extended wiggle whiskers to work with log transforms.
• Made wigEncode default the span to the stepSize in fixedStep wigs.
• Ongoing work on multiWiggle display.
• Starting work on Track Search tool.
• Fixed problem where hgTrackUi was giving a null for the sortOrder of tracks with no dimensions.
• New hgTrackUi drop-down list.
• Provide helpful explanation of bigWig and BAM schema.
• PNG 32-bit color for multiWiggles.
• Set up the make so that trackDb also builds metaDb (if needed).
• wigToBed program.
• Program to submit ENCODE data to GEO.
• Program to lift blat subrange queries - pslLiftSubrangeBlat.

(v231) released in conjunction with v232

• Created multiwig data type.
• Started work on 32-bit color to support multiwigs.
• Allow hgNear to handle special characters more gracefully.
• Refactoring to split the trackDb.tableName field into separate track and table fields.
• Changed 'subtrack' to 'parent' in all trackDb.ra files.
• Removed all_mrna and all_est tracks from scaffold databases, since they will use mrna and est tracks instead.
• Working on holding metadata in a metaDb table instead of trackDb.
• Created converter for tagAlign to SAM format.
• Fix to isPcr for primers that match but dangle off the ends of the chrom.
• More work on GUI V2.
• Added composite filter boxes.
• Added support for integration between the TB and GREAT tool at Stanford.
• Augmented bigBed schema output.
• Fixed Genome Graphs so that it works properly for tracks with views.
• Support for text2genome track.
• Added support for a JSON based API to the browser.
• Fixed gff3ToGenePred program.
• More polish for the matrix trackUi pages.

10 May, 2010 (v230)

• Added BAM setting to inhibit the option to color items.
• Ongoing work on multiWiggle display.
• Started work on BAM sequence validator.
• First pass at automated data pipeline for browser.
• Ongoing work on rgba graphics in display.
• Cleaned up some autoSql so that descriptions can be properly displayed in schema.
• Enabled indel display controls for BAM tracks.
• Added support for integration between the TB and GREAT tool at Stanford.
• Tweaked Genome Graphs to handle sparse variableStep wiggles better.
• Fixed Custom Tracks to more gracefully handle invalid bigDataUrls.
• Ongoing work on regulatory track.
• Tweaks to fonts so that Table Browser correlate function can use them.
• Removed xenoRefSeq link to aligned org browser if it doesn't have RefSeq enabled.
• Switch blue for purple for query-insertion-at-end, more easy to distinguish from green for polyA.

26 April, 2010 (v229)

• Tweaks to MAF output from Table Browser.
• Fixed links from gene pages to upgraded Stanford SOURCE website.
• Fixed display bug in wiggle whiskers when value is near zero.
• Fixed bedGraphToBigWig and bedToBigBed display at high zoom levels.
• Starting work on makeItems type custom tracks.
• Allowing as few as 2 characters for gene suggestion box.
• Fixed GTF output from Table Browser.
• Full support for the new metaTbl based metadata for ENCODE tracks.
• Added support for http(s) proxy for big* and BAM.

12 April, 2010 (v228)

• Made the blue for CDS query-insertion-at-end darker and bluer.
• Allow long strings in Custom Track names.
• Added verbose output to joinerCheck.
• Automated generation of ENCODE release text file.
• Changed gene search box to accept a minimum of 2 chars.
• Set label width to 1/2 the image size if it's sized too large.
• Fixed GCC portability issues.
• Added support for BAM in multi-view composite tracks.
• Added support for profiles in hg.conf.
• Small tweaks to the display of DGV track.
• Renamed komp to ikmc as requested by contributor Carol Bult.
• Added a couple of tests for bigWig and BAM.
• Work on the ENCODE validation program.
• Added more font sizes to hgTracks display.
• Added support to darken colors in hgTracks display.
• Fixed overlapSelect bug.
• Fixed point peaks, they are 1-based.

31 March, 2010 (v227)

• BAM track improvements.
• Fixed bigBed details display error.
• Tweaked hgSuggest.
• Fix regCluster program to break up clusters that are weakly linked.
• New program, regBedStats, to calculate stats for groups of bed files.
• Put code in place to support clusters of tables.
• Move some javascript code into c to speed handling massive images.
• Some tweaks to V2 image.
• Put udc underneath samtools' network code.
• Fixed problem of tables displaying in reverse-order in Table Browser.
• Fixed mafSplit program (which was clipping off the first base of every split).
• Added lots of code and textual support for mirror sites.
• Enabled mirror sites to choose a different default genome.
• Created new script to auto-generate ENCODE change notes.
• Tweaks to gff3ToGenePred program.
• Added metadata table.

8 March, 2010 (v226)

• Allow all Custom Track types access to hgTrackUi.
• Restrict BED details from bigBed to first 6 fields on bigBed details page.
• Fixed hgPal output from Table Browser.
• More work on BAM/SAM display.
• Changes to hgTrackDb to allow for three-state release.
• More shine for V2 GUI.

22 February, 2010 (v225)

• New CGI: hgSuggest - gene search autocomplete.
• Limit Custom Track names to 128 characters.
• Removed 50 item restriction for drawing stacked bars in Personal Genome track.
• Improved error message for GTF output from Table Browser.
• Added hook for specifying a search type in URL.
• Fixed multiz configuration for codon translation.
• Cleaned up pslUniq program.
• Set default clade to mammal if not found in the gateway.
• Do not let the wiki track error if the genomewiki goes away.
• Made a single file rewriter for view-in-the-middle, for mirror sites that have their own trackDb.ra files.
• Getting rid of settingsByView stuff in tdbQuery.
• Some tweaks to bigBed: fixed memory leak, etc.
• Fixed bigBed so that it works in dense mode on a clean cart and it works with custom tracks.
• New program: blastXmlToPsl.
• Tweaks and additions to the matrix and check boxes in hgTrackUi.
• Fix to BAM display: handle soft-clipping when fetching query sequence.

8 February, 2010 (v224)

• Microarray tracks and custom microarray tracks now support the "expColor" trackDb setting which can be various color combinations.
• Changed ENCODE Regions label in Table Browser to ENCODE Pilot Regions.
• Removed score filter from bigBed.
• Fixed bug - we used incorrect gap penalties to calculate chain score in window.
• Fixed big* programs so that while you have to be sorted within a chromosome, the chromosomes themselves need not be sorted.
• Rough prototype for search tracks.

25 January, 2010 (v223)

• A little cleanup of BAM display before official release
• New utilities: encodePatchTdb, wigToBedGraph
• Added longLabel tooltips for links in track controls
• Added configuration option for the width of the label area
• autoSql now generates tab file load functions for "object" data types
• Removing Custom Tracks within Sessions that have not been used within 4 months
• Fixed bug that caused us to errAbort if cookie string ends with ';'

12 January, 2010 (v222)

• More support for BAM and remote files
• Allow whisker plots to display colors for positive and negative values
• Add sequence count to chromInfoPage
• Merged in view-in-the-middle code branch for trackDb*ra files
• encodePatchTdb program
• Ongoing work on right-click image menu
• Removed fixed-length restriction on size of item names
• Modified extFile updating to match new server configuration
• Changed content-type for DAS results to text/xml

2009

18 December, 2009 (v221)

• More support for SAM and BAM.
• Turn autoScale on by default for Custom Tracks.
• Make sure hgCustom doesn't fail if remote file is missing.
• Fixed bug in propagating view level radio button configuration to the subtracks.
• Fixed bug in center label toggle seen on mrna track when Next Item is off.
• Interleave accesses from two open udcFile handles to the same part of a URL/file.
• Add support for SAM and BAM files to ENCODE validator.
• Fixed neg-strand issue for PCR psl output.
• Catch (big*, bam) loader when it tries to open a missing file.
• More work on right-click menu for Imagev2.
• Fixed bug in matrix (plus/minus buttons were failing when no matrix exists).
• Tied the chrom image drag-jump feature to advanced Javascript features.
• Work on flat tracks for subtrack drag-reorder.

7 December, 2009 (v220)

• Updates and fixes to the pslCDnaGenomeMatch program.
• Fixed up hgTrackDb program and made it stop building trackDb table when it encounters an error.
• Clean-up of settings in trackDb.ra files.
• Added options to hgTrackDb to query values in .ra files.
• New utility for querying trackDb.ra files: raSqlQuery.
• Performance improvements to net.c/udc.c (for fetching block-compressed data).
• Small tweaks to "whiskers" wiggle display.
• Ongoing work on right-click code for browser image.
• Tweaks to parasol.
• Added program to get consistent versions of refSeq data from genbank.
• Removed js enforcement of viewRange limits.
• Added compression to bigBed and bigWig files.
• Allowing display of compressed bbi files.
• New display for wiggles: mean+whiskers.
• Added new display framework that flattens image and breaks into pieces.
• Changed 'Enable drag-zoom' to 'Enable advanced javascript features'.
• Allowing 5-dimension matrices on configure page.
• Started simplification of wiggleCart code and trackDb viewLimit settings.
• BAM display minor bugfixing (composite tracks, mates farther outside window).

17 November, 2009 (v219)

• Made a few fixes to next-item functionality
• Ongoing work on BAM file support
• Fixed some maf problems
• Fixed bug with computing mean query size
• Fixed png portability problems
• Added transform function for wiggles
• Set correct clipping rectangle in hgTracks/expRatioTracks.c
• Fixed problem with chainNet composite UI
• More work on bigWig

2 November, 2009 (v218)

• More work on BAM display
• Updated VisiGene for hg19
• Ignore drag activity in mini-button
• Fixed jumping coordinates in drag-n-zoom
• Tune-up for gbSanity tool
• Added support for new 3-way matrix check-boxes
• Created converter for 5C data (matrix) to bed
• New utility to do renaming of all sequences in fasta file
• More features for matrix configuration (moved Z-dimension outside matrix, added counts)

19 October, 2009 (v217)

• General tidying of Custom Track code
• Added support for bam as a custom track type
• Refactoring to avoid custom track bottleneck
• Allowing blat and gfServer to share some code
• Fixed some 3D matrix plus-minus button problems for Safari and IE8
• webUserAdmin program
• Fixed bedItemOverlapCount for 32-bit machines
• Allow import of type bedGraph custom tracks in Genome Graphs
• Fixed wigAsciiToBinary - was missing overlapping check for fixedStep

5 October, 2009 (v216)

• Allow alwaysZero for wigs to be set in trackDb, off by default
• A few fixes to the liftOver program
• Created special links to NCBI and ENSEMBL for older human assemblies
• Error checking in hgCustom for bigBed/bigWig files
• Added Affy Exon data back to UCSC Gene details pages
• Fixed compiler warnings from gcc 4.3.3
• Fixed hgCustom error that caused segfault on solaris
• New program: convert pairedTag file into a bed12
• New program: convert tagAlign file into a bed12
• Fixed bedItemOverlapCount program
• Fix composite chain/net display with split tables
• Fixed problem with bigWig on scaffolded assemblies
• Appended unique identifier to custom track names

21 September, 2009 (v215)

• Removing broken clip option from big* programs (replaced with separate bedClip utility)
• Added function to get list of database profile names
• Added scripts for auto update lsSnpPdb
• Allow fancy (jscript) clicking on cytoband image
• Setting up BAM type for display
• Added option to big* programs to specify cache location for remote files
• More work on web 2.0 GUI
• Fixed bug for Conservation track species selection
• Added "Always include zero" option to wiggle track configuration pages

9 September, 2009 (v214)

• Use GIF's Graphic Control Extension to make images background color transparent
• Added support for composite tracks to default to yellow bar when zoomed out too far
• Browser display speed-up efforts
• Tweaked error handling for CTs
• Changed bedToBigBed to multi-pass design to conserve memory
• Tuned code for speed
• Tweaking SNP-mapping pipeline
• Fine-tuning bigWig program
• Web 2.0 GUI work

(v213) released in conjunction with v214

• Added conditional use (USE_PNG) of external library libpng (http://libpng.org/pub/png/, sourceforge) to write memgfx images in the PNG format instead of GIF
• Use width 60 for protein codons, and 50 for nucleotides when displaying psl results
• Fixes to parasol
• Don't display Ensembl protein links for non-coding genes
• Fixed bigBed display error
• Added back in lost functionality: next/previous item for Custom Track
• Don't enforce double- or int-checking on numeric sql fields because the filter inputs can be ranges too
• Added support for new trackDb setting maxWindowToDraw
• Rename for bigBed and bigWig for dataUrl (which was already in use) to bigDataUrl
• More tweaks to bigBed and bigWig programs
• Added initial implementation of gff3ToGenePred converter
• Don't allow chain item to draw white with normalize score
• Remove multi-view settings from the table browser 'merge' function

10 August, 2009 (v212)

• Fixed memory leak in hgLiftOver
• Adding haval, an md5 alternative
• Refactoring bedGraphToBigWig
• Fixed bug when doing stranded overlap with PSLs
• Fixed null pointer and memory leak in MAF display
• More support for BAM and SAM
• Edits to hgCustom to support two uses of dataUrl
• webBlat fixes
• Fix compiler error for bedToBigBed

27 July, 2009 (v211)

• New improved background runner for ENCODE submissions
• Disable next/previous item on tracks of type bigBed
• Fix to Table Browser for bedGraph tables in 'bed format' output
• Ongoing tweaks to multi-view configuration
• Added functional annotations including mapped coords to snp125
• Fixed redundant message in identifier search in Table Browser
• Fixed SNP details page if SNP is a large insertion
• Fixed hgPal default species
• Enabled code to be built on SOLARIS system
• Re-enabled drag-and-zoom feature for browsers with AppleWebKit (>=531)
• Allow TransMap tracks to work as composite tracks
• Fixed ENCODE download page to not show 'restricted until' dates if they are in the past

14 July, 2009 (v210)

• Made several fixes to the code so that it compiles properly on Solaris
• Synchronized hgPal with composite multiz tracks
• Fix to allow bigBed files to work with the filter feature in the Table Browser
• Fix to bedToBigBed so that it handles the color field (without needing an associated .as file)
• Added support for BAM (compressed alignments) files as a native track type
• Fixes and error checking for phyloTree CGI
• Removed the build of genbank from standard build (for mirrors' sake)
• Reworked the java warning message to accept "complicated" messages

26 June, 2009 (v209)

• Made cart error message more informative
• Added support for bigBed and bigWig
• Turned Base Position Track scale bar on by default
• Extended Table Browser filter so that it automatically includes linked tables specified in trackDb
• Turn off drag-n-zoom by default Safari and Chrome because it doesn't work under WebKit

15 June, 2009 (v208)

• Truncate long chrom names if they overwrite mini-buttons
• Added database name to hgTracks header
• Enabled using hgsqlrr (sql database for RR machines)
• Changes to coloring of tracks in hgTracks to support new data types
• Added cache to avoid repeated databases queries for organism name for xeno items (4.28x speedup)
• Turned chain/net into an optional composite track

29 May, 2009 (v207)

• Added debugging hook for command-line reproduceable forms
• Work on UDC (URL data cache for bigWig/bigBed)
• Fixed blastz automation to tolerate empty results when running lineage-specific repeats and tolerate previously existing results
• Tweaking dimension-Z for multi-view configuration
• Store last position in cart in case new position is invalid
• Optimized the saving of CTs within Sessions
• Display sequence different to the genome using a bed or bigBed which has the sequence in the name (e.g. tagAlign) in a similar manner to PSL
• Added new base color options for hgTracks

15 May, 2009 (v206)

• Fixed a couple off-by-one problems with insertion lines on the right end of CDS
• Fixed performance/memory leak for bedList
• Fixed bug where exons within 3 bases of the start of a chromosome are rendered in solid yellow
• hgTracks cart cleanup
• Changes to details pages for displaying ENCODE metadata
• Fixed bug in hgTracks for rendering colored bars on blat and pcr results

1 May, 2009 (v205)

• Increased size for table names of composite tracks to accommodate long ENCODE table names
• New file types: bigBed and bigWig
• Initial implementation of gff3 parser

17 April, 2009 (v204)

• Fixed off-by-one error that caused blue insert line to be drawn 1 base to the left of the end of + strand items
• Fix to Table Browser schema for subtrack tables
• Fixed Table Browser to allow show schema to work properly for non-genome databases
• Set USE_SSL=0 be the default since some mirror sites have difficulty
• Added numeric field validation by javascript to hgTracks
• Added numeric field validation by javascript to Table Browser
• Extended BLAT to accept long chrom names (e.g. chrNN_something)
• Fixed many instances of Table Browser using composite table when subtrack table is needed

3 April, 2009 (v203)

• added color-by-gray-scale option to Net track configuration (in addition to existing color-by-chromosome)
• new output type in Table Browser for microarray tracks: microarray tissue names

13 March, 2009 (v202)

• changed PCR display to indicate the location of primers

12 February, 2009 (v200)

• turned on drag-and-zoom feature by default
• fixed navigation to Ensembl when their chromosome names are different than ours

30 January, 2009 (v199)

• introduced multi-view track configuration

16 January, 2009 (v198)

• added drag-and-zoom feature to image (hgTracks)
• changed default image width from 620 pixels to 800 pixels
• added expand all / collapse all buttons for groups on hgTracks
• import marker-value pairs into Genome Graphs to get a custom marker column in the Gene Sorter
• Table Browser sped up when large number of ID names are uploaded/pasted

2008

19 December, 2008 (v197)

• Turned on by default the "next/previous exon navigation"

5 December, 2008 (v196)

• (partial list)
• hgPcr expanded to include UCSC Genes amplification for human and mouse (jumps across introns).

18 November, 2008 (v195)

• Session tool UI changes.
• Session tool gives error message when a session is given an existing name.
• Option to not color chains in the Chain track.
• Option to filter chains in the Chain track on a particular chromosome.

16 October, 2008 (v193)

• Added next/previous item capability to Custom Tracks.
• Added MAF r lines to indicate how MAF regions were defined.
• Automatic updates to upstream FASTA and MAF files.

3 October, 2008 (v192)

• New CGI: hgPal

9 September, 2008 (v190)

• Added MAF as custom track type

22 August, 2008 (v189)

• Fixed snp128 and snp129, so Table Browser filter doesn't show misleading choices.
• Fixed PDF/PS output to not include hidden BLAT results.

8 August, 2008 (v188)

• Added links to other organisms' browsers and DNA from Conservation track details page.

28 July, 2008 (v187)

• Added next-item feature to BED tracks with less than 9 columns
• Always show the "hide all" button even if the track control display is turned off.

11 July, 2008 (v186)

• Display the "hide all" button even if the track control display is turned off
• Added check for custom track existence when saving a session
• Added next-item feature to BED tracks with less than 9 columns
• New link in xenoRefGene details page to browser for other species
• New "D" (DNA) link on Conservation track details page for all species

27 June, 2008 (v185)

• Position/Search box now allows a single-base search (e.g. chr3:12345)

16 June, 2008 (v184)

• Added support for MAF-formatted custom tracks.
• java script now can collapse control button groups without server round trips