Genome Browser Software Features (2008-2012)

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This page contains a list of major new software features found in the UCSC Genome Browser: 2008-2012. The most recent features are always at the top of the page.

Contents

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

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