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.

8 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).