All File Changes

v299_preview2 to v299_base (2014-04-21 to 2014-04-28) v299

• src/browserbox/README.txt
  • lines changed 4, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/browserbox/root/changes.txt
  • lines changed 3, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/browserbox/root/cleanVm.sh
  • lines changed 3, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/browserbox/root/cronUpdate.sh
  • lines changed 1, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/browserbox/root/mirrorTrack
  • lines changed 1, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/browserbox/root/updateBrowser.sh
  • lines changed 25, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/browserbox/usr/local/apache/htdocs/favicon.ico
  • lines changed 0, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/browserbox/usr/local/apache/htdocs/images/homeIconSprite.png
  • lines changed 0, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/browserbox/usr/local/apache/htdocs/style/gbib.css
  • lines changed 3, context: html, text, full: html, text
    cosmetic changes to make gbib more distinct from main site and also toremove links that direct user back to main site (unless required, like
    suggestion box), refs #12717
    
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 15, context: html, text, full: html, text
    Display "There is no file submitted by user@xyz.edu" messagewhen the user had not submit any file yet.
    
  • lines changed 1, context: html, text, full: html, text
    Change button label, Cricket request. refs Stanford RM #1372
  • lines changed 1, context: html, text, full: html, text
    Swapping label to match what's on ENCODE EDW beta site. Stanford RM #1372
• src/hg/hgCustom/hgCustom.c
  • lines changed 7, context: html, text, full: html, text
    some tweaks in response to code review. Provide a default assembly nameinstead of (null), and add default case to switches on enumerated typed
    variables. refs #13118
    
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 32, context: html, text, full: html, text
    grab the id's for the hubPublic table from the hubStatus table withoutchecking the remote location unless we haven't seen the hub before.
    
• src/hg/hgMirror/hgMirror
  • lines changed 25, context: html, text, full: html, text
    adding include file support to hgMirror
  • lines changed 5, context: html, text, full: html, text
    improving some comments in hgMirror
  • lines changed 6, context: html, text, full: html, text
    making hgMirror depend on a flag defined in hg.conf
  • lines changed 17, context: html, text, full: html, text
    refactoring some code of hgMirror into a function
  • lines changed 1, context: html, text, full: html, text
    fixing stupid typo
  • lines changed 12, context: html, text, full: html, text
    closing open cursors, hoping this helps against some errors on the box
  • lines changed 20, context: html, text, full: html, text
    as hgMirror is handling all the post-rsync changes to tables, need toadd a few rows for box-specific tracks on hg19
    
  • lines changed 2, context: html, text, full: html, text
    fixing small mysqldb and makefile bug
• src/hg/hgMirror/makefile
  • lines changed 2, context: html, text, full: html, text
    adding empty "clean" target
  • lines changed 4, context: html, text, full: html, text
    fixing small mysqldb and makefile bug
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 6, context: html, text, full: html, text
    compile-time option to add a password to some bigBed files for gbib-onlytracks, refs #11957
    
• src/hg/hgTracks/goldTrack.c
  • lines changed 4, context: html, text, full: html, text
    Added a trap for when map items are written outside the track they are supposed to be for. The trap is only on for genome-test and sandboxes. I found one bug with it: gold in dense had wild map item ending coordinates. Fixed. Redmine #13087
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    The doTrackMap look failed to calculate Y appropriately. This should be fixed. Redmine #13087
• src/hg/hgTracks/imageV2.c
  • lines changed 61, context: html, text, full: html, text
    Added a trap for when map items are written outside the track they are supposed to be for. The trap is only on for genome-test and sandboxes. I found one bug with it: gold in dense had wild map item ending coordinates. Fixed. Redmine #13087
  • lines changed 1, context: html, text, full: html, text
    Oops. Accidentally referenced my provate warnWithBacktrace. Still #13087
• src/hg/hgTracks/imageV2.h
  • lines changed 8, context: html, text, full: html, text
    Added a trap for when map items are written outside the track they are supposed to be for. The trap is only on for genome-test and sandboxes. I found one bug with it: gold in dense had wild map item ending coordinates. Fixed. Redmine #13087
• src/hg/hgTracks/multiWig.c
  • lines changed 10, context: html, text, full: html, text
    some tweaks in response to code review. Provide a default assembly nameinstead of (null), and add default case to switches on enumerated typed
    variables. refs #13118
    
  • lines changed 36, context: html, text, full: html, text
    make stacked wiggles grok the smoothing parameter, Fix autoscale to usethe windowingFunction to drive the autoScale.
    
  • lines changed 1, context: html, text, full: html, text
    stacked bar fixes, including javascript on the ui page
• src/hg/hgTracks/wigCommon.h
  • lines changed 4, context: html, text, full: html, text
    make stacked wiggles grok the smoothing parameter, Fix autoscale to usethe windowingFunction to drive the autoScale.
    
• src/hg/hgTracks/wigTrack.c
  • lines changed 4, context: html, text, full: html, text
    make stacked wiggles work in point mode
  • lines changed 70, context: html, text, full: html, text
    make stacked wiggles grok the smoothing parameter, Fix autoscale to usethe windowingFunction to drive the autoScale.
    
  • lines changed 9, context: html, text, full: html, text
    fix up some compiler warnings
  • lines changed 6, context: html, text, full: html, text
    stacked bar fixes, including javascript on the ui page
  • lines changed 8, context: html, text, full: html, text
    make sure that stacked wiggles are not set to mean+whiskers
• src/hg/htdocs/ENCODE/index.html
  • lines changed 3, context: html, text, full: html, text
    Making corrections from code review refs# 13108
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    Making corrections from code review refs# 13108
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 1, context: html, text, full: html, text
    updating docs to reflect final location of files, refs #11957
  • lines changed 9, context: html, text, full: html, text
    adding section about increasing memory to doc, refs #11957
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    Making corrections from code review refs# 13108
  • lines changed 1, context: html, text, full: html, text
    Adding missing tag per code review, refs #13109
• src/hg/htdocs/indexNews.html
  • lines changed 10, context: html, text, full: html, text
    Making corrections from code review refs# 13108
• src/hg/htdocs/style/encode3Ucsc.css
  • lines changed 7, context: html, text, full: html, text
    Fix EDW web layout problem (nav bar overlapping content) found by Chin
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v299
• src/hg/js/hui.js
  • lines changed 40, context: html, text, full: html, text
    stacked bar fixes, including javascript on the ui page
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    moving cgiApoptosis call to a better place which should work in mostCGIs.
    
• src/hg/lib/cgiApoptosis.c
  • lines changed 2, context: html, text, full: html, text
    adding browserbox name to cgiApoptosis again, it mysteriously disappeared
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    make hg.conf option false by default after comment from Braney
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    stacked bar fixes, including javascript on the ui page
  • lines changed 6, context: html, text, full: html, text
    make sure that stacked wiggles are not set to mean+whiskers
  • lines changed 1, context: html, text, full: html, text
    oops... a little fix to javascript used on wiggle ui
• src/hg/makeDb/doc/encode3/tools.txt
  • lines changed 497, context: html, text, full: html, text
    Sharing build notes for ENCODE3 analysis tools
  • lines changed 1, context: html, text, full: html, text
    Add path info
  • lines changed 44, context: html, text, full: html, text
    Adding doc for installation of ENCODE analysis pipeline tools
  • lines changed 645, context: html, text, full: html, text
    Kate's earlier check-in contained some of my not-ready-for-prime-time tesing. I have removed most of that and replaced it with the actual installs and index generations.
• src/hg/makeDb/doc/ochPri3.txt
  • lines changed 1650, context: html, text, full: html, text
    done and in the pushQ 007235 refs #9347
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Adding all.joiner entry in tablesIgnored for espEvs6500 table, refs #9329
  • lines changed 15, context: html, text, full: html, text
    adding ochPri3 refs #9347
• src/hg/makeDb/trackDb/alpaca/vicPac2/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/birds/melUnd1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/birds/melUnd1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/birds/melUnd1/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/cow/bosTau3/description.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
  • lines changed 1, context: html, text, full: html, text
    Turning conservation track back on.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Qian at UWash created a new URL for us that will resolve rsID or position if rsID is invalid. #9329.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.html
  • lines changed 1, context: html, text, full: html, text
    Making corrections from code review refs# 13108
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 8, context: html, text, full: html, text
    Turning on TFBS clustered motif track as default display refs# 12551
• src/hg/makeDb/trackDb/sloth/choHof1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/sloth/choHof1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/sloth/choHof1/gold.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/ucscToINSDC.html
  • lines changed 4, context: html, text, full: html, text
    Removing GRCh38 link, replacing with generic NCBI link
• src/hg/makeDb/trackDb/worm/caeRem2/ctgPos2.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/worm/caeRem2/description.html
  • lines changed 5, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/worm/caeRem2/gap.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makeDb/trackDb/worm/caeRem2/gold.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on choHof1, caeRem2, melUnd1, bosTau3, vicPac2 description pages
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    adding hgMirror to top-level cgi target, to get it onto hgdownload.thanks to a new hg.conf option, it will not run on the RR.
    
• src/hg/protein/spToDb/expected/test1/accToKeyword.txt
  • lines changed 7, context: html, text, full: html, text
    fix the spToDb tests to reflect an earlier commit to spToDb.c
• src/hg/protein/spToDb/expected/test1/keyword.txt
  • lines changed 7, context: html, text, full: html, text
    fix the spToDb tests to reflect an earlier commit to spToDb.c
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 5, context: html, text, full: html, text
    fixup misspelling and location of period refs #11681
• src/inc/common.mk
  • lines changed 11, context: html, text, full: html, text
    compile-time option to add a password to some bigBed files for gbib-onlytracks, refs #11957
    
• src/product/ex.hg.conf
  • lines changed 26, context: html, text, full: html, text
    documenting the gbib hg.conf options, in case that mirrors want to usethem. refs #11957
    
• src/utils/methylateGenome/methylateGenome.c
  • lines changed 14, context: html, text, full: html, text
    rewrote the logic of methylateGenome to use some stuff in dnautil.h
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v299 preview2
  • lines changed 3, context: html, text, full: html, text
    v299 final build

• lines changed: 3499
• files changed: 88