Genome Browser Software Features
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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.
2012
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
27 February, 2009 (v201)
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.
31 October, 2008 (v194)
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
22 September, 2008 (v191)
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