v473 Genome Browser Software

This is the v473 release of the UCSC Genome Browser. A summary of the relevant code changes includes:

• Fix density mode for vcfTabix.
• Fix problem with hubUrl being trashed if Genark hub was specified as db.
• Ongoing work on behaving rationally when certain limits are exceeded in hgTracks.
• Primer3 outlink from hgGene now gets +-200bp flanking seq around the first and last exon to design primers around the exons.
• Fix freeType and Postscript handling to deal with UTF-8 encoded strings.
• Adapting the tutorial reminder to say where users can find the tutorial if they click it away now.
• Right click - move to top respects the ruler track.
• Click OK when "enter" key is pressed on trackUi dialog box.
• Now we just filter all the types, like BLATs guess, which makes them consistent and correct, the same as the default behavior it always had.
• The configuration page for some track types can include a selector to change the track color, but the selectors for subtracks of a composite were all being placed in the configuration block of the first subtrack. They are now distributed among the subtracks.
• Don't show download link to big* files on the table browser for non-distribution tracks.
• Fixed jQuery upgrade bugs: group drag and drop of tracks, drop-down checklist position, checkboxes marked as change during a form submit.
• Disable the "download track data in window" option on GBiBs since they don't have an API available.
• More work on right-click - hide all other tracks.
• Continuous GenArk process improvements.

v472 Genome Browser Software

This is the v472 release of the UCSC Genome Browser. A summary of the relevant code changes includes:

• Added new options to the right-click menu: hide all others, move to top, move to bottom
• Upgraded jQuery and jQuery-ui to the latest versions
• Force all tracks into coverage mode if 32K image size would otherwise be exceeded
• Users can now specify their parallel load timeout value
• Added (i) icons to table browser to better indicate you can mouseover for help text
• The hgLiftOver CGI and the command-line liftOver tool now include an option to keep a copy of the positions from the input file in the lifted output (for formats like BED, genePred, and others that include an item name field or something similar). This should help keep track of which items get mapped where for some users
• Various improvements to both the hgGateway search and new GenArk search
• Amino acid display now only shows up at base level
• Made the two reset genome browser links in the menu the same.
• Performance improvements for Hi-C tracks (and anything else that uses fakeCurl) - we now do a better job of re-using an existing udc handle for a series of requests on the same file. This should also fix some issues associated with having "too many file handles" open when viewing multiple Hi-C files at once
• The option to change some track draw colors is now available on their hgTrackUi page as well as the pop-up configure box in the main browser, and that option remembers what color was previously chosen for that track
• Repair for being unable to change decoration draw modes in the UI (an important variable wasn't being set)
• GBiC now attempts to repair tables it fetches from UCSC's servers before using them
• liftOver and hgLiftOver no longer leave temp files around when lifting coordinates in position format (chr:start-end)
• hgTables identifiers buttons fix - hubs call these functions with a NULL conn, needed to add a check for call with NULL conn identifiers getXrefInfo function
• hgSession backup.c Rocky 9 tar now requires the command line option --exclude before the parameter "."
• GBIB: Fixed MySQL trackDb tables before accessing them (MySQL tables on hgdownload are often in a crashed state)
• Ongoing work on hubtools: make hub.txt given a directory tree with big* files, first try at upload into hub space
• Continuous GenArk process improvements

Update: This release was amended to include a fix for a javascript issue where checkbox changes were not being registered, and dropbox menu options were misplaced on the screen.