All File Changes

v327_preview2 to v327_base (2016-01-04 to 2016-01-11) v327

• src/browserbox/root/.my.cnf
  • lines changed 11, context: html, text, full: html, text
    updating GBIB hg.conf so that it allows local adaptations in
    hg.conf.local, refs #16616
    
• src/browserbox/root/updateBrowser.sh
  • lines changed 132, context: html, text, full: html, text
    major change to gbib update script, refs #16616
    
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
  • lines changed 8, context: html, text, full: html, text
    updating GBIB hg.conf so that it allows local adaptations in
    hg.conf.local, refs #16616
    
• src/browserbox/usr/local/apache/cgi-bin/hg.conf.local
  • lines changed 2, context: html, text, full: html, text
    updating GBIB hg.conf so that it allows local adaptations in
    hg.conf.local, refs #16616
    
• src/hg/hgMenubar/makefile
  • lines changed 1, context: html, text, full: html, text
    Updating relative path calculation to support root-level resource paths beginning with //
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 25, context: html, text, full: html, text
    Fixing bug where user comes in with no cookies and clicks GenomeBrowser menu link to go straight to hgTracks. I needed to call the cart function for more cases, not just the lastDbPos. I also got rid of the 2 goto statements and labels.
    
  • lines changed 11, context: html, text, full: html, text
    Fixing sub-issue # 107 in RM 12242, crashed if certain conditions caused vis changes during track-load. Work around for now is to just clone all tracks for all windows instead of only cloning non-hidden tracks.
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Updating name of link as per Todd Lowes request, refs #16601
    
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 2, context: html, text, full: html, text
    Small unnoticeable test change to ENCODE FAQ page
    
  • lines changed 2, context: html, text, full: html, text
    Small unnoticeable return test change to ENCODE FAQ page
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    Adding approved change to FAQ to specify what BED represents
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #16596
    
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 257, context: html, text, full: html, text
    Restructuring multi-region help doc, most of the text itself hasn't changed, just where it is. refs #16565
    
  • lines changed 128, context: html, text, full: html, text
    Switching order sections on multiregion doc, refs #16565
    
  • lines changed 78, context: html, text, full: html, text
    adding more to multi-region help doc, refs #16565
    
  • lines changed 32, context: html, text, full: html, text
    Adding explanation of custom regions to help doc, refs #16565
    
  • lines changed 61, context: html, text, full: html, text
    More help doc work, refs #16565
    
  • lines changed 38, context: html, text, full: html, text
    Added some pictures to the help doc, only viewable from my sandbox though, other minor changes as well, refs #16565
    
  • lines changed 115, context: html, text, full: html, text
    Most pictures present, doc almost fully fleshed out, refs #16565
    
  • lines changed 152, context: html, text, full: html, text
    Almost finished with rough draft, just need one final picture, refs #16565
    
  • lines changed 25, context: html, text, full: html, text
    Rough draft finished for multiregion doc, refs #16565
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #16596
    
  • lines changed 45, context: html, text, full: html, text
    added snp144 announcement
    
• src/hg/htdocs/indexNews.html
  • lines changed 2, context: html, text, full: html, text
    Changes based on CR, refs #16596
    
  • lines changed 83, context: html, text, full: html, text
    added snp144 announcement
    
  • lines changed 6, context: html, text, full: html, text
    made correction and added post to archives section
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v327
    
• src/hg/lib/annoStreamDb.c
  • lines changed 3, context: html, text, full: html, text
    Removing duplicate definition of NOSQLINJ - thx Galt. refs #16515
    
• src/hg/makeDb/doc/ci2.txt
  • lines changed 32, context: html, text, full: html, text
    ci2 to ci3 liftOver for ci3 browser release refs #16628
    
• src/hg/makeDb/doc/ci3/initialBuild.txt
  • lines changed 471, context: html, text, full: html, text
    in the pushQ refs #16628
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    add missing table for pubsMarkerAnnot table in all.join, refs #16610
    
  • lines changed 3, context: html, text, full: html, text
    clean joinerCheck on ci3 refs #16628
    
• src/hg/makeDb/schema/joiner.doc
  • lines changed 3, context: html, text, full: html, text
    adding a small note to the all joiner readme file, as it took me a while
    to find the command to update my all.joiner file. no redmine.
    
• src/hg/makeDb/trackDb/drosophila/droEre1/description.html
  • lines changed 4, context: html, text, full: html, text
    Bad url to 2005 fly assembly. Contact not replying, removing link. No Redmine.
    
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 7, context: html, text, full: html, text
    Adjusting default priorities for hg38 tracks, refs #15680
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    hiding snp142 track by default, releasing new snp144 track
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Updated old url to avoid redirect. refs #16581
    
• src/hg/makeDb/trackDb/xenTro/xenTro7/description.html
  • lines changed 1, context: html, text, full: html, text
    Changes based on CR, refs #16596
    
• src/hg/mouseStuff/chainToPsl/tests/expected/example1.psl
  • lines changed 1, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/mouseStuff/chainToPsl/tests/expected/example1.psl.gz
  • lines changed 0, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/mouseStuff/chainToPsl/tests/expected/example2.psl
  • lines changed 1, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/mouseStuff/chainToPsl/tests/expected/example2.psl.gz
  • lines changed 0, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/mouseStuff/chainToPsl/tests/input/example1.chain
  • lines changed 98, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/mouseStuff/chainToPsl/tests/input/example1.chain.gz
  • lines changed 0, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/mouseStuff/chainToPsl/tests/input/example2.chain
  • lines changed 98, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/mouseStuff/chainToPsl/tests/input/example2.chain.gz
  • lines changed 0, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/mouseStuff/chainToPsl/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    Replaced test files with compressed versions, refs #16588
    
• src/hg/utils/automation/blastz-normalizeLav
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/blastz-run-ucsc
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/constructLiftFile.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/alternatesAgp.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/compositeAgp.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/compositeFasta.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/gatewayPage.js
  • lines changed 26, context: html, text, full: html, text
    fixups for code review refs #16589
    
• src/hg/utils/automation/genbank/gatewayPage.pl
  • lines changed 3, context: html, text, full: html, text
    fixups for code review refs #16589
    
• src/hg/utils/automation/genbank/ncbiToUcsc.sh
  • lines changed 5, context: html, text, full: html, text
    fixups for code review refs #16589
    
• src/hg/utils/automation/genbank/noStructureAgp.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/noStructureFasta.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/sorttable.js
  • lines changed 495, context: html, text, full: html, text
    fixups for code review refs #16589
    
• src/hg/utils/automation/genbank/unlocalizedAgp.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/unlocalizedFasta.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/unplacedAgp.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/genbank/unplacedFasta.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/grcIncidentDb.pl
  • lines changed 2, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/gwUploadFile
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/ucscCompositeAgp.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/automation/unplacedWithChroms.pl
  • lines changed 1, context: html, text, full: html, text
    /bin/env is only on centOS more generic and widely available is /usr/bin/env no redmine
    
• src/hg/utils/makeTableList/makeTableList.c
  • lines changed 9, context: html, text, full: html, text
    add hgFixed etc only when -all has been specified for makeTableList, no redmine
    
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    adding bigPslToPsl and pslToBigPsl to the utils build refs #15067
    
• src/lib/filePath.c
  • lines changed 22, context: html, text, full: html, text
    Updating relative path calculation to support root-level resource paths beginning with //
    
• src/product/ex.hg.conf
  • lines changed 4, context: html, text, full: html, text
    add documentation about the trackLog option refs #16617
    
• src/utils/bigWigAverageOverBed/bigWigAverageOverBed.c
  • lines changed 5, context: html, text, full: html, text
    make -minMax option to bigWigAverageOverBed work on empty ranges. #16580
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v327 final build refs #16513
    
• src/utils/twoBitDup/twoBitDup.c
  • lines changed 14, context: html, text, full: html, text
    usefult to have the unique keys in hand to compare two genome assemblies refs #16589
    

• lines changed: 2557
• files changed: 74