Genome Browser Software Features: Difference between revisions
From genomewiki
Jump to navigationJump to search
(v235) |
(v236) |
||
Line 1: | Line 1: | ||
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. | 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. | ||
== 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 == | == 12 July, 2010 v235 == |
Revision as of 20:45, 21 July 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.
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).