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.

2011

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

Previous Releases

• Genome Browser Scale Bar (in Base Position track).