All File Changes

v272_base to v273_preview (2012-08-28 to 2012-09-04) v273

• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    Redmine 8961. Galt found this error and found the solution too. Big-beds in dense never support filtering and rely upon a summary query, rather then querying all items in the range.
• src/hg/hgTracks/menu.c
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    Added id to view menu list group for easier scripting and testing. Same change as made in globalNavBar.inc
• src/hg/htdocs/ENCODE/index.html
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    Minor reformatting and edits for clarity. Rename pubsMain.html to pubs.html so existing links (including outside site) navigate to new pubs landing page
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 1343, context: html, text, full: html, text
    Minor reformatting and edits for clarity. Rename pubsMain.html to pubs.html so existing links (including outside site) navigate to new pubs landing page
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    Typo fix. Thanks Steve H.
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 1375, context: html, text, full: html, text
    Minor reformatting and edits for clarity. Rename pubsMain.html to pubs.html so existing links (including outside site) navigate to new pubs landing page
• src/hg/htdocs/ENCODE/pubsMain.html
  • lines changed 48, context: html, text, full: html, text
    Minor reformatting and edits for clarity. Rename pubsMain.html to pubs.html so existing links (including outside site) navigate to new pubs landing page
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 1, context: html, text, full: html, text
    Made change suggested by Brian in code review (redmine #8941)
  • lines changed 9, context: html, text, full: html, text
    Minor reformatting and edits for clarity. Rename pubsMain.html to pubs.html so existing links (including outside site) navigate to new pubs landing page
• src/hg/htdocs/goldenPath/credits.html
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    minor grammar and typing fixed per code review; redmine 8859
• src/hg/htdocs/goldenPath/help/mysql.html
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    minor grammar and typing fixed per code review; redmine 8859
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 2, context: html, text, full: html, text
    Clarified 'subgroup' examples between hub and non-hub versions.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 644, context: html, text, full: html, text
    Renamed trackDbHubs.html to trackDbHub.html
  • lines changed 2, context: html, text, full: html, text
    Clarified 'subgroup' examples between hub and non-hub versions.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHubs.html
  • lines changed 644, context: html, text, full: html, text
    Created trackDbHubs.html at the urging of Ruihua. This may have to be redone when Donna does her final review of trackDbDoc.html. But since most of the verbiage is in the trackDbLibrary.shtml and is shared by both docs, Donna's edits will probably only affect that one common file.
  • lines changed 644, context: html, text, full: html, text
    Renamed trackDbHubs.html to trackDbHub.html
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 136, context: html, text, full: html, text
    Created trackDbHubs.html at the urging of Ruihua. This may have to be redone when Donna does her final review of trackDbDoc.html. But since most of the verbiage is in the trackDbLibrary.shtml and is shared by both docs, Donna's edits will probably only affect that one common file.
  • lines changed 123, context: html, text, full: html, text
    Clarified 'subgroup' examples between hub and non-hub versions.
  • lines changed 9, context: html, text, full: html, text
    Minor change to make names of subgroup and view examples more unified.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 10, context: html, text, full: html, text
    Added Craig Lowe pub.
• src/hg/htdocs/images/Alligator_Mississippiensis.jpg
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    gator photo from NASA Kennedy
• src/hg/htdocs/images/Ceratotherium_simum.jpg
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    rhino photo from wikicommons user Esculapio
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 9, context: html, text, full: html, text
    Added ids to menu groups for easier scripting and selenium testing.
• src/hg/js/autocomplete.js
  • lines changed 8, context: html, text, full: html, text
    don't report ajax errors (#8816)
• src/hg/makeDb/doc/cerSim1.txt
  • lines changed 422, context: html, text, full: html, text
    initial makeGenomeDb done
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release3.notes
  • lines changed 103, context: html, text, full: html, text
    updating notes for haib tfbs
  • lines changed 11, context: html, text, full: html, text
    updated notes to reflect restored table
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrHistone.release3.notes
  • lines changed 1539, context: html, text, full: html, text
    createing notes file
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDgf.release1.notes
  • lines changed 340, context: html, text, full: html, text
    creating notes file
• src/hg/makeDb/doc/papAnu2.txt
  • lines changed 572, context: html, text, full: html, text
    Initial browser build of baboon papAnu2.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding cerSim1 white rhino redmine 8752
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    add ignore
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    fixup spaces to tabs
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    oops... checked this in without tabs
• src/hg/makeDb/genbank/src/copy/gbCopyStep
  • lines changed 1, context: html, text, full: html, text
    testing adding a sleep after each rsync for euronode weirdness in connection
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    adding definition for cerSimNames white rhino redmine 8752
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Removing missing protocol reference
• src/hg/makeDb/trackDb/gator/allMis1/description.html
  • lines changed 2, context: html, text, full: html, text
    slightly less wide gator photo from NASA Kennedy
  • lines changed 2, context: html, text, full: html, text
    reference photo to NASA source
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 24, context: html, text, full: html, text
    fixed double compression on CSHL long human, mdb has new md5s/filenames to reflect these changes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 102, context: html, text, full: html, text
    fixing metaData stuff
  • lines changed 207, context: html, text, full: html, text
    renaming bad experiment
  • lines changed 117, context: html, text, full: html, text
    fixing metaDb and adding last peak files
  • lines changed 241, context: html, text, full: html, text
    metaDb corrections
  • lines changed 12, context: html, text, full: html, text
    fixed revoke messages
  • lines changed 7, context: html, text, full: html, text
    reloaded metadata and revoke message
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 31, context: html, text, full: html, text
    added Tranche hashes back into mdb for the UNC BSU tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtGenc.ra
  • lines changed 49, context: html, text, full: html, text
    added Tranche hashes back into mdb for the UNC BSU tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 8399, context: html, text, full: html, text
    fixed double compression on CSHL long human, mdb has new md5s/filenames to reflect these changes
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 23039, context: html, text, full: html, text
    Staging HAIB TFBS (Release 3) on beta (redmine #6772)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    revoked a table too early and too well, that i need to modify the public metadata for release purposes, this is an unsed control that is being revoked in the newest release
  • lines changed 2, context: html, text, full: html, text
    Revert "revoked a table too early and too well, that i need to modify the public metadata for release purposes, this is an unsed control that is being revoked in the newest release"
    This reverts commit 7092f1b0c2d7d0d4fbd1c71e1ddbc8ce538decbd.
    
    It broke things worse.
    
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromDnase.ra
  • lines changed 4540, context: html, text, full: html, text
    Releasing Duke DNaseI HS (Release 3) to the RR (redmine #7962)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Releasing Duke DNaseI HS (Release 3) to the RR (redmine #7962)
  • lines changed 2, context: html, text, full: html, text
    Staging HAIB TFBS (Release 3) on beta (redmine #6772)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 244, context: html, text, full: html, text
    fixing labels for flo and adding back in moissing control
  • lines changed 10, context: html, text, full: html, text
    renaming bad experiment
  • lines changed 32, context: html, text, full: html, text
    fixing metaDb and adding last peak files
  • lines changed 139, context: html, text, full: html, text
    cleaning up for pushQ
  • lines changed 6, context: html, text, full: html, text
    pulling unused control
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    changed view range to start at 0
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    changed default limit to 0 ont he low end
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.html
  • lines changed 3, context: html, text, full: html, text
    update rawScore definition
  • lines changed 2, context: html, text, full: html, text
    modify rawScore definition
  • lines changed 49, context: html, text, full: html, text
    Making changes to UNC BSU Proteogenomics (Release 1) RM#8419 to make more readable
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding rhino cerSim1 to the build
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 2, context: html, text, full: html, text
    column titles were in the wrong place
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 203, context: html, text, full: html, text
    run encodeRenameObj on ESE14 cell exp where the age and strain were run during submission
  • lines changed 223, context: html, text, full: html, text
    run encodeRenameObj for exp with ESE14 whose age and strain were wrong during submission
  • lines changed 60, context: html, text, full: html, text
    update age and strain for the entries of ESE14 after running encodeRenameObj
  • lines changed 73, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 49, context: html, text, full: html, text
    encodeMkFilesList update
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 33, context: html, text, full: html, text
    changed some files in mm9 UwDnase to fix the double compression issue for this track
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging on beta Univ Washington DNaseI DGF (Release 1) RM#3631
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrHistone.ra
  • lines changed 6566, context: html, text, full: html, text
    Staging LICR Histone (Release 3) on beta (redmine #7501)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHist.ra
  • lines changed 73, context: html, text, full: html, text
    Staging Stanford Yale Histone mm9 on beta to update MetaData RM#8913
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 3725, context: html, text, full: html, text
    Staging on beta Univ Washington DNaseI DGF (Release 1) RM#3631
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 5, context: html, text, full: html, text
    changed some files in mm9 UwDnase to fix the double compression issue for this track
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHist.ra
  • lines changed 73, context: html, text, full: html, text
    Staging on public Stanford Yale Histone (Release 2) metaData update RM#8913
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging on beta Univ Washington DNaseI DGF (Release 1) RM#3631
  • lines changed 2, context: html, text, full: html, text
    Staging LICR Histone (Release 3) on beta (redmine #7501)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.html
  • lines changed 1, context: html, text, full: html, text
    update release notes
  • lines changed 13, context: html, text, full: html, text
    fix some editing stuff
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra
  • lines changed 20, context: html, text, full: html, text
    run encodeRenameObj on ESE14 cell exp where the age and strain were run during submission
  • lines changed 5, context: html, text, full: html, text
    added strain in file sort, dimension box
  • lines changed 1, context: html, text, full: html, text
    update age selection
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    remove trailing whitespace using cat input.txt | sed 's/[ |t]*$//'
  • lines changed 3, context: html, text, full: html, text
    set default subtrack for display
  • lines changed 134, context: html, text, full: html, text
    modify short labels
  • lines changed 12, context: html, text, full: html, text
    set default display
  • lines changed 7, context: html, text, full: html, text
    fix shortlabels
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.html
  • lines changed 6, context: html, text, full: html, text
    added release note
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    Making small punctuation changes, double quotes/reference parenthesis, for Univ Wash DNaseI DGF (Release1) RM#3631
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 4, context: html, text, full: html, text
    set default display for different views, fix typo in long label
  • lines changed 5, context: html, text, full: html, text
    added dimensionBox, edit file sort list
  • lines changed 92, context: html, text, full: html, text
    clean up long labels
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    fix long labels in response to Brian's comment #3631 note 72
  • lines changed 112, context: html, text, full: html, text
    fixed long and short labels
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    testing age option box
• src/hg/makeDb/trackDb/pubs.html
  • lines changed 1, context: html, text, full: html, text
    camel-case PubMed
• src/hg/makeDb/trackDb/rhino/cerSim1/description.html
  • lines changed 63, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rhino/cerSim1/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rhino/cerSim1/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rhino/cerSim1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial contents from makeGenomeDb.pl
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 7, context: html, text, full: html, text
    Query the trackVersion table to find what is previous ensGene version.
• src/hg/utils/automation/ensGene/mm10.ensGene.ra
  • lines changed 7, context: html, text, full: html, text
    Use ens,68.lft to lift random ensembl name to ucsc name for mm10.
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 6, context: html, text, full: html, text
    adding twoBitDup check
• src/product/README.debug
  • lines changed 20, context: html, text, full: html, text
    added Angie's information on for the browser to use GET
• src/utils/bigBedInfo/bigBedInfo.c
  • lines changed 1, context: html, text, full: html, text
    took out a superfluous external declaration via code review (#8945)
• src/utils/qa/weeklybld/buildEnv.csh
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    v273 preview1
• src/utils/qa/weeklybld/buildZip.csh
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    Removing 'README.txt' which had been forced into the root of the zip file at Max's request. He now points out that it is unnecessary since the 'README' at the kent root is enough direction.
• src/utils/qa/weeklybld/makeZip.csh
  • lines changed 3, context: html, text, full: html, text
    Removing 'README.txt' which had been forced into the root of the zip file at Max's request. He now points out that it is unnecessary since the 'README' at the kent root is enough direction.

• lines changed: 57059
• files changed: 112