All File Changes

v300_preview to v300_preview2 (2014-05-05 to 2014-05-12) v300

• src/hg/encode3/eap/lib/resetDb
  • lines changed 48, context: html, text, full: html, text
    Adding Long RNA-seq pipeline software and updated a few existing software entries.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 1, context: html, text, full: html, text
    Open floodgate for edwSubmit to digest dm3 and ce10 data.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 3, context: html, text, full: html, text
    Merged two functions for EDW web autorefresh
  • lines changed 12, context: html, text, full: html, text
    Suppress menu of users for non-admins.
  • lines changed 1, context: html, text, full: html, text
    Layout alignment tweak
  • lines changed 16, context: html, text, full: html, text
    Persist the EDW browse max sub count display variable across CGIs via cookie. refs Stanford 1372
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 4, context: html, text, full: html, text
    Fix for page 'jumping' on autorefresh in edwWeb CGIs. Simple approach (save scroll position in cookie) may suffice. Stanford #1372
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 1, context: html, text, full: html, text
    Open floodgate for edwSubmit to digest dm3 and ce10 data.
  • lines changed 15, context: html, text, full: html, text
    Fix for page 'jumping' on autorefresh in edwWeb CGIs. Simple approach (save scroll position in cookie) may suffice. Stanford #1372
• src/hg/hgMirror/makefile
  • lines changed 5, context: html, text, full: html, text
    the standard build needs compile and install rules refs #13064
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    take out imageMap x coordinate check that Tim added
• src/hg/hgTracks/simpleTracks.c
  • lines changed 14, context: html, text, full: html, text
    Fixing pgSnp full-mode duplicate label bug noticed by Matt. pgSnpdraws its own labels inside pgSnpDrawAt(). makeActiveImage calls
    doLeftLabels which draws the full-mode left labels -- unless there is
    a track->drawLeftLabels, in which case doOwnLeftLabels is used to
    call track->drawLeftLabels after drawing items. My solution for now
    is to give pgSnp a no-op track->drawLeftLabels to prevent the usual
    full mode left labels. It would be nice to move the label-drawing
    code out of pgSnpDrawAt and into pgSnpLeftLabels, but that would take
    a lot more dev & testing effort.
    refs #9329 notes 58, 60, 62
    
  • lines changed 146, context: html, text, full: html, text
    making some changes to bacEnds tracks code to allow change of tablename. Removing some code which is not necessary anymore as a result.
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 1, context: html, text, full: html, text
    fix crashing bug in snakes introduced long ago, but given a new killinglicense by recent changes to compact snakes.
    
• src/hg/hgc/hgc.c
  • lines changed 96, context: html, text, full: html, text
    making some changes to bacEnds tracks code to allow change of tablename. Removing some code which is not necessary anymore as a result.
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Added calMil1 release to the news, credits, etc.
  • lines changed 7, context: html, text, full: html, text
    Releasing criGri1, eriEur2 and taeGut2 (redmine #6506,9419,10190)
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 64, context: html, text, full: html, text
    Added calMil1 release to the news, credits, etc.
  • lines changed 184, context: html, text, full: html, text
    Releasing criGri1, eriEur2 and taeGut2 (redmine #6506,9419,10190)
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 14, context: html, text, full: html, text
    Changes based on Code Review, refs #13191
• src/hg/htdocs/goldenPath/help/hgQuickStartHub.html
  • lines changed 327, context: html, text, full: html, text
    Adding first draft of Quick Start Guide to Hubs
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 1, context: html, text, full: html, text
    adding announcement about stacked wiggle feature, plus fixing some other little documentation things, refs #11630
  • lines changed 1, context: html, text, full: html, text
    Removing extra word in stacked wiggle documentation
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 1, context: html, text, full: html, text
    adding announcement about stacked wiggle feature, plus fixing some other little documentation things, refs #11630
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 27, context: html, text, full: html, text
    adding announcement about stacked wiggle feature, plus fixing some other little documentation things, refs #11630
  • lines changed 29, context: html, text, full: html, text
    Added calMil1 release to the news, credits, etc.
  • lines changed 77, context: html, text, full: html, text
    Releasing criGri1, eriEur2 and taeGut2 (redmine #6506,9419,10190)
• src/hg/htdocs/images/hubDirectoryImage.jpg
  • lines changed 0, context: html, text, full: html, text
    Adding image for first draft of Quick Start Guide to Hubs
• src/hg/htdocs/images/stackedMultiWig_screenshot.png
  • lines changed 0, context: html, text, full: html, text
    adding announcement about stacked wiggle feature, plus fixing some other little documentation things, refs #11630
• src/hg/htdocs/indexNews.html
  • lines changed 90, context: html, text, full: html, text
    adding announcement about stacked wiggle feature, plus fixing some other little documentation things, refs #11630
  • lines changed 83, context: html, text, full: html, text
    Added calMil1 release to the news, credits, etc.
  • lines changed 83, context: html, text, full: html, text
    Releasing criGri1, eriEur2 and taeGut2 (redmine #6506,9419,10190)
• src/hg/htdocs/style/encode3.css
  • lines changed 3, context: html, text, full: html, text
    Removing font-face rule for fontawesome that refers to local font/ dir as we're getting this font remotely (and I haven't figured out how to override font-face rule). Avoids file not found in Apache log. refs Stanford #1372
• src/hg/htdocs/style/encode3Ucsc.css
  • lines changed 1, context: html, text, full: html, text
    Tweak layout so submit buttons align vertically with text input control. refs Stanford #1372
  • lines changed 12, context: html, text, full: html, text
    Suppress access to images not used (avoid apache log errs). refs Stanford #1372
  • lines changed 4, context: html, text, full: html, text
    Layout alignment tweak
• src/hg/js/ajax.js
  • lines changed 2, context: html, text, full: html, text
    Rewrote the car variable queuing routines, fixing one bug and ensuring the vars are updated at window unload event as a last resort. Also changed a couple stray undeclared vars that use strict found. Redmine 13164.
• src/hg/js/hgTracks.js
  • lines changed 139, context: html, text, full: html, text
    Rewrote the car variable queuing routines, fixing one bug and ensuring the vars are updated at window unload event as a last resort. Also changed a couple stray undeclared vars that use strict found. Redmine 13164.
  • lines changed 1, context: html, text, full: html, text
    Need to mark page as dirty when vis changes via drop-down, even if refresh isn't set. Redmine 13164.
  • lines changed 26, context: html, text, full: html, text
    Replaced Object.keys() which may not be supported by some browsers and moved three utility type scripts from cart to utils.js. Redmine 13164.
• src/hg/js/utils.js
  • lines changed 26, context: html, text, full: html, text
    Replaced Object.keys() which may not be supported by some browsers and moved three utility type scripts from cart to utils.js. Redmine 13164.
• src/hg/lib/wiggleCart.c
  • lines changed 8, context: html, text, full: html, text
    delete warning for wiggle min/max that was only output on hgwdev.
• src/hg/makeDb/doc/rn5.txt
  • lines changed 1214, context: html, text, full: html, text
    Adding entries for rn5 conservation subtracks. refs #8212
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes15.csh
  • lines changed 9, context: html, text, full: html, text
    load hgBlastTab in other species
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 5, context: html, text, full: html, text
    Added criGri1, eriEur2 and taeGut2 (redmine #6506,9419,10190)
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 5, context: html, text, full: html, text
    Added criGri1, eriEur2 and taeGut2 (redmine #6506,9419,10190)
  • lines changed 1, context: html, text, full: html, text
    Added calMil1 to RR genbank update list
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 6, context: html, text, full: html, text
    Added overrides and updated assembly versions for addition of new chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 6, context: html, text, full: html, text
    Added overrides and updated assembly versions for addition of new chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/human/hg19/evsEsp6500.html
  • lines changed 1, context: html, text, full: html, text
    fixing spelling mistake on EVS details page, refs #9329
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    removing release tags from EVS track before release, refs #9329
  • lines changed 1, context: html, text, full: html, text
    Fixed the start token for the EVS variants URL. Unfortunately the start and end tokens get filled in with window coordinates and not item coordinates. Sigh. Redmine 9329.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwg.ra
  • lines changed 5, context: html, text, full: html, text
    Tweak track shading for DHS Master track in progress. refs #1320.
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 393, context: html, text, full: html, text
    Adding description page for rat 13way. refs #8212
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    allowing some changes to the bacEnds tracks
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    allowing some changes to the bacEnds tracks
  • lines changed 8, context: html, text, full: html, text
    adding Augustus gene predictions refs #13088
• src/hg/makeDb/trackDb/turkey/melGal1/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    Moved information from this file into the higher-level directory file (redmine #10190)
• src/hg/makeDb/trackDb/turkey/melGal1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Added overrides and updated assembly versions for addition of new chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra
  • lines changed 16, context: html, text, full: html, text
    Added overrides and updated assembly versions for addition of new chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo link (redmine #10190)
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo link (redmine #10190)
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    don't run proteins/spToDb tests, as they are not built
• src/hg/protein/spToDb/makefile
  • lines changed 1, context: html, text, full: html, text
    force tests to look in BINDIR for spToDb
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v300 preview2

• lines changed: 3293
• files changed: 65