All File Changes

v322_preview to v322_preview2 (2015-08-31 to 2015-09-07) v322

• src/hg/hgMirror/hgMirror
  • lines changed 23, context: html, text, full: html, text
    fixing a bug on gbib where hgMirror can't write tempfiles due to
    insufficient rights. refs #15963
    
• src/hg/hgSession/hgSession.c
  • lines changed 55, context: html, text, full: html, text
    Another pass at #6551. Put default visibilities in the cart at session
    save. On session load hide any tracks that are default visibile, but
    aren't mentioned in the cart.
    
• src/hg/hgTracks/chainTrack.c
  • lines changed 2, context: html, text, full: html, text
    prevent NULL pointer dereference in some unusually chains (no redmine)
    
• src/hg/hgTracks/extTools.c
  • lines changed 32, context: html, text, full: html, text
    Removing the 'send to' menu and replacing it with a javascript-based
    dialog that closes itself. Also fixing a small bug with the / key on
    firefox for the shortcuts. refs #15113
    
  • lines changed 8, context: html, text, full: html, text
    Check whether local file "extTools.ra" exists before calling printExtMenuData and showing the keyboard shortcuts for it.
    
• src/hg/hgTracks/extTools.h
  • lines changed 3, context: html, text, full: html, text
    Removing the 'send to' menu and replacing it with a javascript-based
    dialog that closes itself. Also fixing a small bug with the / key on
    firefox for the shortcuts. refs #15113
    
  • lines changed 3, context: html, text, full: html, text
    Check whether local file "extTools.ra" exists before calling printExtMenuData and showing the keyboard shortcuts for it.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    Removing the 'send to' menu and replacing it with a javascript-based
    dialog that closes itself. Also fixing a small bug with the / key on
    firefox for the shortcuts. refs #15113
    
  • lines changed 9, context: html, text, full: html, text
    Check whether local file "extTools.ra" exists before calling printExtMenuData and showing the keyboard shortcuts for it.
    
• src/hg/hgTracks/menu.c
  • lines changed 13, context: html, text, full: html, text
    adding a sub-menu to the View menu, refs #15113
    
  • lines changed 71, context: html, text, full: html, text
    Removing the 'send to' menu and replacing it with a javascript-based
    dialog that closes itself. Also fixing a small bug with the / key on
    firefox for the shortcuts. refs #15113
    
  • lines changed 25, context: html, text, full: html, text
    moveing ext tools menu upwards and adding sep line, as per Jim's
    suggestions, refs #15113
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 30, context: html, text, full: html, text
    Look for trackDbSetting "trackHandler" in lookupTrackHandler instead of looking it up at the end of lookupTrackHandlerClosestToHome after modifying tdb. That was losing child trackHandler settings.
    
• src/hg/htdocs/style/nice_menu.css
  • lines changed 10, context: html, text, full: html, text
    moveing ext tools menu upwards and adding sep line, as per Jim's
    suggestions, refs #15113
    
• src/hg/htdocs/training/index.html
  • lines changed 3, context: html, text, full: html, text
    adding back link to UC Davis Bioinformatics
    
• src/hg/inc/cart.h
  • lines changed 7, context: html, text, full: html, text
    Another pass at #6551. Put default visibilities in the cart at session
    save. On session load hide any tracks that are default visibile, but
    aren't mentioned in the cart.
    
• src/hg/js/README
  • lines changed 3, context: html, text, full: html, text
    Removing the 'send to' menu and replacing it with a javascript-based
    dialog that closes itself. Also fixing a small bug with the / key on
    firefox for the shortcuts. refs #15113
    
• src/hg/js/hgTracks.js
  • lines changed 66, context: html, text, full: html, text
    Removing the 'send to' menu and replacing it with a javascript-based
    dialog that closes itself. Also fixing a small bug with the / key on
    firefox for the shortcuts. refs #15113
    
• src/hg/js/install.mk
  • lines changed 7, context: html, text, full: html, text
    Added 'top' target for faster development of top-level .js files
    (i.e. skip all of the new subdirs).
    
• src/hg/js/makefile
  • lines changed 4, context: html, text, full: html, text
    Added 'top' target for faster development of top-level .js files
    (i.e. skip all of the new subdirs).
    
• src/hg/lib/annoStreamDb.c
  • lines changed 41, context: html, text, full: html, text
    Discard large-bin items that fall on or after nextChunkStart because they
    will break the (chrom, chromStart) sorting order if they are also to the
    right of small-bin items on or after nextChunkStart -- and they will appear
    again in the next chunk of rows.
    
    Also a couple other fixes for problems found while debugging:
    - there was a spot where I forgot to restart merging after calling
    resetMergeState (when moving on to the next chrom in a genome-wide query)
    - in mergeRow, don't resetMergeState until both big and small queues are empty
    
    refs #15953
    
• src/hg/lib/cart.c
  • lines changed 37, context: html, text, full: html, text
    Another pass at #6551. Put default visibilities in the cart at session
    save. On session load hide any tracks that are default visibile, but
    aren't mentioned in the cart.
    
  • lines changed 1, context: html, text, full: html, text
    oops... bug fix for #6551 and existing sessions
    
• src/hg/makeDb/doc/genomeInformationSites.txt
  • lines changed 17, context: html, text, full: html, text
    correct source site and information site for the nematodes refs #15209
    
• src/hg/makeDb/doc/genomeSourceSites.txt
  • lines changed 17, context: html, text, full: html, text
    correct source site and information site for the nematodes refs #15209
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 6, context: html, text, full: html, text
    make keys check for ornAna1 clean refs #15796
    
• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    ensGene search rules good for dm6 too refs #15796
    
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    ensGene search rules good for dm6 too refs #15796
    
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.ra
  • lines changed 31, context: html, text, full: html, text
    improve fugu ensGene search rules refs #15796
    
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    improve fugu ensGene search rules refs #15796
    
• src/hg/makeDb/trackDb/human/stsMap.html
  • lines changed 1, context: html, text, full: html, text
    Fixing link on STS marker description page, refs #15524
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Add trackHandler settings for snp144* tracks.
    
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    improve ensGene name search refs #15796
    
• src/hg/makeDb/trackDb/sgpGene.html
  • lines changed 16, context: html, text, full: html, text
    Changes to SGP Genes track description page based on feedback from data provider, refs #13214
    
• src/hg/mouseStuff/chainToPslBasic/chainToPslBasic.c
  • lines changed 96, context: html, text, full: html, text
    added a easy to use chainToPsl program
    
• src/hg/mouseStuff/chainToPslBasic/makefile
  • lines changed 3, context: html, text, full: html, text
    added a easy to use chainToPsl program
    
• src/hg/mouseStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    added a easy to use chainToPsl program
    
• src/hg/utils/hubPublicCheck/hubPublicCheck.c
  • lines changed 4, context: html, text, full: html, text
    make hubPublicCheck put out empty string ("") for missing descriptionUrl
    instead of "(null)" #15932
    
• src/lib/annoGrateWig.c
  • lines changed 25, context: html, text, full: html, text
    If querying in a region, restrict wiggle values to the part of the region
    that overlaps the primary item, don't just use the bounds of the db rows
    that overlap start/end of region.
    fixes #15952
    
• src/lib/annoGrator.c
  • lines changed 1, context: html, text, full: html, text
    If querying in a region, restrict wiggle values to the part of the region
    that overlaps the primary item, don't just use the bounds of the db rows
    that overlap start/end of region.
    fixes #15952
    
• src/utils/bigWigMerge/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    Set verbose level to 0 so we don't get informational messages cluttering up stderr.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v322 preview2 refs #15948
    

• lines changed: 789
• files changed: 42