Genome Browser Software Features: Difference between revisions

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== 4 Oct, 2010 v241 ==
== 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 ==
== 20 Sept, 2010 v240 ==

Revision as of 23:16, 28 October 2010

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.

8 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.

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

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

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

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

Previous Releases

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