All File Changes

v273_preview to v273_preview2 (2012-09-04 to 2012-09-11) v273

• src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
  • lines changed 3, context: html, text, full: html, text
    added in switch to not append wikiBaseUrl if it was already there
• src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease
  • lines changed 15, context: html, text, full: html, text
    made this a little more usable
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 9, context: html, text, full: html, text
    Making bigBed able to filter in dense when zoomed in by making it dynamic with regards to maxItems
  • lines changed 1, context: html, text, full: html, text
    removing arbitrary limit on bigBed -- let users have more control
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    Making bigBed able to filter in dense when zoomed in by making it dynamic with regards to maxItems
  • lines changed 2, context: html, text, full: html, text
    removing arbitrary limit on bigBed -- let users have more control
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    fixing Cosmic genome position to add chr prefix to chromosome name since data came from Ensembl
• src/hg/htdocs/ENCODE/analysis.html
  • lines changed 131, context: html, text, full: html, text
    Early version of Analysis page
  • lines changed 19, context: html, text, full: html, text
    Input from Ian Dunham. Review from Brian Lee
  • lines changed 1, context: html, text, full: html, text
    Fix FTP to analysis package
  • lines changed 19, context: html, text, full: html, text
    Corrections to Analysis portal page, after QA review
  • lines changed 2, context: html, text, full: html, text
    One more description tweak from QA
  • lines changed 3, context: html, text, full: html, text
    Change references to Nature supplementary info and code bundles, input from Ian Dunhams. #8877
  • lines changed 88, context: html, text, full: html, text
    Made changes and cleaned up the html (redmine #8877)
  • lines changed 90, context: html, text, full: html, text
    Made corrections and cleaned up the html (redmine #8877)
  • lines changed 1, context: html, text, full: html, text
    Fix URL to supplemenetary info on ANalysis page
  • lines changed 2, context: html, text, full: html, text
    More URLS fixed
  • lines changed 3, context: html, text, full: html, text
    Take link off temporarily as it's the first one on the page and its asking for a password. Nature mag will need to fix
  • lines changed 7, context: html, text, full: html, text
    Sanitized email addresses and reactivated the first link to the Nature site (redmine #8877)
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 4, context: html, text, full: html, text
    Adding html snippit for new track on ENCODE mouse downloads for Univ Wash DGF (Release1) RM#3631
• src/hg/htdocs/ENCODE/index.html
  • lines changed 110, context: html, text, full: html, text
    Update News, and add links to Analysis page
  • lines changed 12, context: html, text, full: html, text
    breaking new news item into 100 char lines so easier to edit, not to code reviewer, don't review this for content since I haven't made the necessary edits yet, redmine 9001
  • lines changed 155, context: html, text, full: html, text
    adding italics around journal names and fixing typo (theese to these) in new Sept 5 news item, removing old news items (older than Aug 9), shortening the latest 3 news items and directing to newsarchives to read more, redmine 9001
  • lines changed 3, context: html, text, full: html, text
    gave special website a name (per Kate) and made it a link to the URL, redmine 9001
  • lines changed 28, context: html, text, full: html, text
    reinstating Aug 28 news item per Kate's request, redmine #9001
• src/hg/htdocs/ENCODE/integrativeAnalysis/VM/index.html
  • lines changed 1, context: html, text, full: html, text
    Remove 5 sec delay on referrer page for ENCODE virtual machine page at Galaxy. #8740
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 161, context: html, text, full: html, text
    adding all the items from the ENCODE/index.html page except tommorrow's new Sept 5 news item to the news archives, redmine 9001
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 2, context: html, text, full: html, text
    Tiny changes to some settings that I noticed while helping Erik Larsson set up his hub.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 2, context: html, text, full: html, text
    Tiny changes to some settings that I noticed while helping Erik Larsson set up his hub.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    Tiny changes to some settings that I noticed while helping Erik Larsson set up his hub.
• src/hg/lib/web.c
  • lines changed 4, context: html, text, full: html, text
    only show clades for databases that are active redmine 8846
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromFaire.release2.notes
  • lines changed 5, context: html, text, full: html, text
    updated notes
• src/hg/makeDb/doc/hg19.txt
  • lines changed 49, context: html, text, full: html, text
    Track #8886 (Add new Denosiva dataset to browser): Added VCF tracksfor Denisova and 11 modern humans. Have draft description for
    Denisova, still need to write one for modern humans (if we offer
    those... leave up to 1000 Genomes or track hub???). Have makeDb
    template for analysis files (fetched files, need to trackify them).
    
• src/hg/makeDb/doc/papAnu2.txt
  • lines changed 17, context: html, text, full: html, text
    Finished papAnu2 genscan.
• src/hg/makeDb/doc/sarHar1.txt
  • lines changed 15, context: html, text, full: html, text
    Finished sarHar1 ensGene v68 upgrade.
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added cerSim1.
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added cerSim1.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Adding antibody validation docs to CV
  • lines changed 2, context: html, text, full: html, text
    Adding cell line protocol to CV
  • lines changed 1, context: html, text, full: html, text
    Adding antibody validation doc to CV
  • lines changed 94, context: html, text, full: html, text
    Registering new antibodies and adding validation docs
  • lines changed 2, context: html, text, full: html, text
    Adding a label for the Bcells
  • lines changed 2, context: html, text, full: html, text
    Fixing bugs in validation doc presentation
  • lines changed 41, context: html, text, full: html, text
    Adding antibody validation docs, registering new antibody, fixing lab names, vendorNames, vendorIds, adding comments
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 182, context: html, text, full: html, text
    Copying alpha CV to beta
• src/hg/makeDb/trackDb/human/hg19/dhcVcfDenisovaPinky.html
  • lines changed 88, context: html, text, full: html, text
    Track #8886 (Add new Denosiva dataset to browser): Added VCF tracksfor Denisova and 11 modern humans. Have draft description for
    Denisova, still need to write one for modern humans (if we offer
    those... leave up to 1000 Genomes or track hub???). Have makeDb
    template for analysis files (fetched files, need to trackify them).
    
  • lines changed 4, context: html, text, full: html, text
    Track #8886 (new Denisova): added comment about missing data as suggested by Ed.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 87, context: html, text, full: html, text
    added accession numbers for HAIB array data (yay!)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 65, context: html, text, full: html, text
    added accession numbers for HAIB array data (yay!)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
  • lines changed 75, context: html, text, full: html, text
    added accession numbers for HAIB array data (yay!)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    adding in missing date unrestricted
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 5, context: html, text, full: html, text
    updated md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 8, context: html, text, full: html, text
    Matt added some Restricted Until dates (redmine #6772)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 23043, context: html, text, full: html, text
    Staging on public HAIB TFBS (Release3) RM#6772
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwRepliSeq.ra
  • lines changed 17, context: html, text, full: html, text
    Updating md5sum metaData for Univ Wash Repli-Seq for RM#8477
• src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
  • lines changed 86, context: html, text, full: html, text
    Track #8886 (Add new Denosiva dataset to browser): Added VCF tracksfor Denisova and 11 modern humans. Have draft description for
    Denisova, still need to write one for modern humans (if we offer
    those... leave up to 1000 Genomes or track hub???). Have makeDb
    template for analysis files (fetched files, need to trackify them).
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Track #8886 (Add new Denosiva dataset to browser): Added VCF tracksfor Denisova and 11 modern humans. Have draft description for
    Denisova, still need to write one for modern humans (if we offer
    those... leave up to 1000 Genomes or track hub???). Have makeDb
    template for analysis files (fetched files, need to trackify them).
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Renaming wgEncodeUncBsuProtGenc.release1.ra to have no release1 in the name
  • lines changed 2, context: html, text, full: html, text
    Staging on public HAIB TFBS (Release3) RM#6772
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.html
  • lines changed 240, context: html, text, full: html, text
    adding in first version of release 3 html
  • lines changed 32, context: html, text, full: html, text
    qa fixes for haib tfbs
  • lines changed 2, context: html, text, full: html, text
    fixed more html stuff
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 839, context: html, text, full: html, text
    massive label changefest
  • lines changed 22, context: html, text, full: html, text
    qa fixes for haib tfbs
  • lines changed 8, context: html, text, full: html, text
    more short label stuff
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
  • lines changed 52, context: html, text, full: html, text
    first pass at comments
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html
  • lines changed 1, context: html, text, full: html, text
    Adding in a release note about the Tranch Hash data and the proteocommons as well as making the data display in the downloads dir
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra
  • lines changed 2, context: html, text, full: html, text
    Adding in a release note about the Tranch Hash data and the proteocommons as well as making the data display in the downloads dir
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.html
  • lines changed 229, context: html, text, full: html, text
    Renaming wgEncodeUncBsuProtGenc.release1.ra to have no release1 in the name
  • lines changed 2, context: html, text, full: html, text
    Adding in a release note about the Tranch Hash data and the proteocommons as well as making the data display in the downloads dir
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.ra
  • lines changed 149, context: html, text, full: html, text
    Renaming wgEncodeUncBsuProtGenc.release1.ra to have no release1 in the name
  • lines changed 2, context: html, text, full: html, text
    Adding in a release note about the Tranch Hash data and the proteocommons as well as making the data display in the downloads dir
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.html
  • lines changed 4, context: html, text, full: html, text
    Small edit to match wording of hgc details for view description of rawScore, UNC BSU Proteogenomics (Release1) RM#8419
  • lines changed 12, context: html, text, full: html, text
    Adding language from hgc details page to view configuration description following Katrina's advice for UNC BSU Prot (Release 1) RM#8419
  • lines changed 7, context: html, text, full: html, text
    Making changes to mm9 UW DGF html & hg19 UNC BSU Prot html as per code review RM#8993
  • lines changed 229, context: html, text, full: html, text
    Renaming wgEncodeUncBsuProtGenc.release1.ra to have no release1 in the name
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
  • lines changed 149, context: html, text, full: html, text
    Renaming wgEncodeUncBsuProtGenc.release1.ra to have no release1 in the name
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 18, context: html, text, full: html, text
    Adding in the md5sums
  • lines changed 17, context: html, text, full: html, text
    added md5sums to CaltechHist
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 43, context: html, text, full: html, text
    Fixing the treatment none to be consistent, cleaning up the matrix commands
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechHist.ra
  • lines changed 17, context: html, text, full: html, text
    added md5sums to CaltechHist
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 43, context: html, text, full: html, text
    Restaging metaData for Univ Wash DGF (Release1) RM#3631
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging on public UW DGF (Release 1) RM#3631
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 10189, context: html, text, full: html, text
    Releasing CSHL Long RNA-seq (Release 3) to the RR (redmine #8652)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrHistone.ra
  • lines changed 6566, context: html, text, full: html, text
    Releasing LICR Histone (Release 3) to the RR (redmine #7501)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 3725, context: html, text, full: html, text
    Staging on public UW DGF (Release 1) RM#3631
  • lines changed 43, context: html, text, full: html, text
    Restaging metaData on public for Univ Wash DGF (Release1) RM#3631
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging on public UW DGF (Release 1) RM#3631
  • lines changed 2, context: html, text, full: html, text
    Releasing CSHL Long RNA-seq (Release 3) to the RR (redmine #8652)
  • lines changed 2, context: html, text, full: html, text
    Releasing LICR Histone (Release 3) to the RR (redmine #7501)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra
  • lines changed 3, context: html, text, full: html, text
    changed defaults on the mm9 licr track, so no grey checkbox
  • lines changed 406, context: html, text, full: html, text
    fixed more label issues
  • lines changed 7, context: html, text, full: html, text
    fixed bone marrow labels
  • lines changed 20, context: html, text, full: html, text
    fixed brain and olfact labels
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.html
  • lines changed 1, context: html, text, full: html, text
    Making changes to mm9 UW DGF html & hg19 UNC BSU Prot html as per code review RM#8993
  • lines changed 1, context: html, text, full: html, text
    Correcting Data Release information for UW DGF (Release 1) RM#3631
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 116, context: html, text, full: html, text
    Fixing the treatment none to be consistent, cleaning up the matrix commands
  • lines changed 24, context: html, text, full: html, text
    Removing maxItems
  • lines changed 5, context: html, text, full: html, text
    Changing the sort order for B-cells
  • lines changed 5, context: html, text, full: html, text
    Adding diff to specific short labels
  • lines changed 1, context: html, text, full: html, text
    Did not mean to add maxWindowsToDisplay back in
• src/hg/near/hgNear/advFilter.c
  • lines changed 7, context: html, text, full: html, text
    add titles (and corresponding cart open) to fix hgNearRobot errors
• src/hg/near/hgNear/afiAli.c
  • lines changed 1, context: html, text, full: html, text
    add titles (and corresponding cart open) to fix hgNearRobot errors
• src/hg/near/hgNear/getSeq.c
  • lines changed 14, context: html, text, full: html, text
    add titles (and corresponding cart open) to fix hgNearRobot errors
• src/hg/near/hgNear/hgNear.c
  • lines changed 8, context: html, text, full: html, text
    add titles (and corresponding cart open) to fix hgNearRobot errors
• src/hg/near/hgNear/hgNearData/Mouse/gnfMouseAtlas3.html
  • lines changed 1, context: html, text, full: html, text
    fix an encoding problem
• src/hg/near/hgNear/search.c
  • lines changed 1, context: html, text, full: html, text
    add titles (and corresponding cart open) to fix hgNearRobot errors
• src/hg/near/hgNear/userSettings.c
  • lines changed 8, context: html, text, full: html, text
    add titles (and corresponding cart open) to fix hgNearRobot errors
• src/hg/utils/automation/ensGene/hg19.ensGene.ra
  • lines changed 2, context: html, text, full: html, text
    filtered out HSCHR6_1 and use a new 68 lift file.
• src/hg/utils/automation/ensGene/sarHar1.ensGene.ra
  • lines changed 3, context: html, text, full: html, text
    Finished sarHar1 ensGene v68 upgrade.
• src/hg/utils/automation/ensGene/taeGut1.ensGene.ra
  • lines changed 1, context: html, text, full: html, text
    Finished taeGut1 ensGene v68 upgrade.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v273 preview2

• lines changed: 48069
• files changed: 112