All File Changes

v267_base to v268_preview (2012-05-15 to 2012-05-22) v268

• python/lib/ucscGb/encode/mkChangeNotes.py
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    fixing for source tree restructure
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    removing raw from view name
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    fixing for source tree restructure
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 4, context: html, text, full: html, text
    fixing for source tree restructure
• src/hg/encode/raDiff/raDiff
  • lines changed 1, context: html, text, full: html, text
    changed over to new library
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    fixing for source tree restructure
• src/hg/encode/raMerge/raMerge
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    fixing for source tree restructure
• src/hg/hgLogin/hgLogin.c
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    Use safecpy when there are no format args for safef, to avoid stricter gcc compile warnings on Ubuntu.
  • lines changed 55, context: html, text, full: html, text
    hgLogin.c will not compile with openssl lib. See http://redmine.soe.ucsc.edu/issues/7824#note-6 for more detail.
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    Polish signup mail text.
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    Changed sed user name mail text.
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    Removed commented out code and corrected indent errors based on Code Review #7932 feedback from Brian.
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    Merge branch 'master' into chinhli-hgLogin-final
• src/hg/hgLogin/makefile
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    Remove -lcrypt -lssl from -L flag, See redmine 7955 and 7824 for more details
• src/hg/hgSession/hgSession.c
  • lines changed 4, context: html, text, full: html, text
    Removed commented out code and corrected indent errors based on Code Review #7932 feedback from Brian.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    show bigBed items in color when in dense (really fix #7272)
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    menuBar => printMenuBar to fix name collision with some new code
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 7, context: html, text, full: html, text
    Added a warning note (research use only) before the Go button inthe variant annotation integrator (#6152), per Jim's suggestion.
    
  • lines changed 10, context: html, text, full: html, text
    Moving hgVarAnnogrator's warning note to after the "Go" button per Jim's request. (#6152)
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 10, context: html, text, full: html, text
    Response to QA of redmine 7972. 1. Make Experiment Summary the first link off ENCODE portal for Mouse as with Human 2. Have links in help message refer to human or mouse as appropriate
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    Response to QA of redmine 7972. 1. Make Experiment Summary the first link off ENCODE portal for Mouse as with Human 2. Have links in help message refer to human or mouse as appropriate
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 43, context: html, text, full: html, text
    HTML cleanup. Axed nonsense attributes, comments, etc. Fixed one major bug where a </tr> was writen as <tr>.
  • lines changed 3, context: html, text, full: html, text
    Added fr3.
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    added hetGla1 assembly
• src/hg/htdocs/admin/jk-install.html
  • lines changed 121, context: html, text, full: html, text
    In mirror.html, replaced link to jk-install with link to source tree. Edited jk-install to point to source tree. (redmine #2511)
• src/hg/htdocs/admin/mirror.html
  • lines changed 12, context: html, text, full: html, text
    Added a note about new versions of MySQL disabling LOAD DATA LOCAL INFILE (redmine 7423)
  • lines changed 2, context: html, text, full: html, text
    In mirror.html, replaced link to jk-install with link to source tree. Edited jk-install to point to source tree. (redmine #2511)
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    Made change in wording suggested by Larry (redmine #7423)
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 730, context: html, text, full: html, text
    Cleaned up lots of html. Bag tags, nonsense attributes, etc. Added Fugu fr3 Credit. (sorry to put in the same commit)
  • lines changed 63, context: html, text, full: html, text
    added naked mole-rat credits
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    added hetGla1 credits
• src/hg/htdocs/goldenPath/help/bedgraph.html
  • lines changed 10, context: html, text, full: html, text
    Changed the coordinates in the example since they fell outside the range of chromosome 19 on hg19
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 1, context: html, text, full: html, text
    Changed the part that said sessions are not shared by default. By default, they *are* shared.
• src/hg/htdocs/goldenPath/help/oligoMatch.html
  • lines changed 2, context: html, text, full: html, text
    Added line saying that IUPAC ambiguity codes may be used. Redmine #7913.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 44, context: html, text, full: html, text
    Initial check-in of trackDb settings documentation
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 4090, context: html, text, full: html, text
    Initial check-in of trackDb settings documentation
  • lines changed 32, context: html, text, full: html, text
    A bit better commenting and some work on the self-assembling toc.
  • lines changed 503, context: html, text, full: html, text
    A bit more cleanup of the rejected settings tables before inviting feedback.
  • lines changed 340, context: html, text, full: html, text
    Fixed a lot of anchor tags unclosed. Needed to allow TOC self-assembly to find hidden settings. This should work now, and the self-assembled TOC should prove almost as good as my manual one.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 370, context: html, text, full: html, text
    Initial check-in of trackDb settings documentation
  • lines changed 71, context: html, text, full: html, text
    A bit better commenting and some work on the self-assembling toc.
  • lines changed 17, context: html, text, full: html, text
    Fixed a lot of anchor tags unclosed. Needed to allow TOC self-assembly to find hidden settings. This should work now, and the self-assembled TOC should prove almost as good as my manual one.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 4213, context: html, text, full: html, text
    Initial check-in of trackDb settings documentation
• src/hg/htdocs/goldenPath/help/trackDb/trackDbTestBlurbs.html
  • lines changed 41, context: html, text, full: html, text
    Initial check-in of trackDb settings documentation
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 18, context: html, text, full: html, text
    Added a line specifying that fixedStep tracks must keep the same step size. Also fixed the example because it falls outside the range of hg19 chromosome 19. (redmine #7707)
  • lines changed 29, context: html, text, full: html, text
    Added new track options and descriptions (redmine #6866)
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 33, context: html, text, full: html, text
    updated name attribute for hetGla1 announcement
  • lines changed 26, context: html, text, full: html, text
    Added Fugu fr3 announcement. Added missing date to previous headline.
  • lines changed 1, context: html, text, full: html, text
    made correction to hetGla1 announcement
• src/hg/htdocs/images/home_icon_sprite_white.png
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    Adding image needed for new top glabal navigation menu.
• src/hg/htdocs/images/plusesign-main-menu.png
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    Added new plus sign image for use with new global nav menus.
• src/hg/htdocs/inc/global-nav-bar.inc
  • lines changed 106, context: html, text, full: html, text
    New html for global navigation bar.
• src/hg/htdocs/indexNews.html
  • lines changed 76, context: html, text, full: html, text
    changed release date for hetGla1
  • lines changed 24, context: html, text, full: html, text
    Added Fugu fr3 accouncement. Correct one word in previous title.
  • lines changed 1, context: html, text, full: html, text
    made a correction to hetGla1 announcement
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    Added nice_menu.css
• src/hg/htdocs/style/nice_menu.css
  • lines changed 429, context: html, text, full: html, text
    CSS needed for new dropdown menus. Some redundant code from Jabico, will need cleanup.
  • lines changed 2, context: html, text, full: html, text
    Changed path for two images to kent src dirs.
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    Fixed a line-height issue conflict with HGStyle.css. Needed to vertically align middle menu text.
• src/hg/inc/encode/wgEncodeGencodePdb.h
  • lines changed 1, context: html, text, full: html, text
    fixed typo in table description
• src/hg/inc/hgFindSpec.h
  • lines changed 1, context: html, text, full: html, text
    merge-and-squash dev branch hgFindSpecReleaseTag
• src/hg/inc/jsHelper.h
  • lines changed 17, context: html, text, full: html, text
    add jsonStringEscape; make .h header comments match .c file
• src/hg/js/hgVarAnnogrator.js
  • lines changed 91, context: html, text, full: html, text
    Fixed most jslint warnings - thanks Kate! (#6152)
• src/hg/js/jquery.plugins.js
  • lines changed 492, context: html, text, full: html, text
    Javascript needed for new global navigation menus with drop downs. Can also serve as a single plave to put all JQuery plugin code.
• src/hg/js/jquery.validate.min.js
  • lines changed 51, context: html, text, full: html, text
    Adding validation plugin for client side form validation of new login screens.
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Added jquery.plugins.js
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    Added jquery.validate.min.js
• src/hg/lib/bbiChroms.as
  • lines changed 6, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls) - grabbed VCF fromNCBI using Aspera (ascp) -- 142GB!
    
• src/hg/lib/bbiChroms.sql
  • lines changed 12, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1 Variant Calls) - grabbed VCF fromNCBI using Aspera (ascp) -- 142GB!
    
• src/hg/lib/encode/wgEncodeGencodeExonSupport.sql
  • lines changed 1, context: html, text, full: html, text
    make index non-unique
• src/hg/lib/encode/wgEncodeGencodePdb.as
  • lines changed 1, context: html, text, full: html, text
    fixed typo in table description
• src/hg/lib/encode/wgEncodeGencodePdb.sql
  • lines changed 1, context: html, text, full: html, text
    fixed typo in table description
• src/hg/lib/gpFx.c
  • lines changed 60, context: html, text, full: html, text
    support for additional indel types in gpFx (#6152)
• src/hg/lib/hgFindSpecCustom.c
  • lines changed 14, context: html, text, full: html, text
    merge-and-squash dev branch hgFindSpecReleaseTag
• src/hg/lib/itemDetailsHtml.sql
  • lines changed 1, context: html, text, full: html, text
    allow multiple entries for an given item name
• src/hg/lib/jsHelper.c
  • lines changed 60, context: html, text, full: html, text
    add jsonStringEscape; make .h header comments match .c file
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 17, context: html, text, full: html, text
    support for additional indel types in gpFx (#6152)
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 12, context: html, text, full: html, text
    support for additional indel types in gpFx (#6152)
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    Prevent warning message about lack of special type support for views when type is gvf. (for #34)
• src/hg/lib/variant.c
  • lines changed 14, context: html, text, full: html, text
    support for additional indel types in gpFx (#6152)
• src/hg/lib/wikiLink.c
  • lines changed 4, context: html, text, full: html, text
    hgLogin.c will not compile with openssl lib. See http://redmine.soe.ucsc.edu/issues/7824#note-6 for more detail.
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 44, context: html, text, full: html, text
    Finished liftOver, N50 number tasks. Updating description html.
  • lines changed 12, context: html, text, full: html, text
    Finished N50 number tasks. Updating description html.
• src/hg/makeDb/doc/encodeDccHg19/gencodeV12.txt
  • lines changed 56, context: html, text, full: html, text
    load of GENCODE V12
  • lines changed 21, context: html, text, full: html, text
    load of GENCODE V12
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release3.notes
  • lines changed 793, context: html, text, full: html, text
    make release note
• src/hg/makeDb/doc/hg18.txt
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    Track #34: Updating hg18 too.
• src/hg/makeDb/doc/hg19.txt
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    Updated the contents of the hgnc table
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    Track #7964 (1000 Genomes Phase 1 Variant Calls) - grabbed VCF fromNCBI using Aspera (ascp) -- 142GB!
    
  • lines changed 31, context: html, text, full: html, text
    Track #34 (dbVar): data update from John Lopez at NCBI.
  • lines changed 47, context: html, text, full: html, text
    Track #34 (dbVar for human): added new dataset (nstd45, ISCA Curated).
• src/hg/makeDb/genbank/doc/initial-load.html
  • lines changed 6, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/align-genbank
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/build-genbank
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/build.crontab
  • lines changed 19, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/ccds-import
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/hgdownload-copy
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/hgnfs1-copy
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/hgwdev-dbload
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/hgwdev.crontab
  • lines changed 16, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/etc/mkdownload
  • lines changed 2, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/makefile
  • lines changed 2, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
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    work around #! file path size limit
• src/hg/makeDb/genbank/src/align/gbAlignStep
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    removed outdate /cluster/genbank reference
• src/hg/makeDb/genbank/src/align/gbPython
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    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/src/ccds/README
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    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
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    remove temporary files as we go
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    oops, fix error in last commit. Need to pass $keep into dbLoad function
• src/hg/makeDb/genbank/src/extFileUpdate/extFileTool
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    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/src/lib/py/genbank/GbIndex.py
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    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/src/process/gbMkOrganismList
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
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    work around #! file path size limit
• src/hg/makeDb/genbank/src/repair/extFileFindLost
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/src/repair/repairMgcOrfeome
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
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    work around #! file path size limit
• src/hg/makeDb/genbank/tests/tools/getTblOverhead
  • lines changed 3, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/tests/tools/modifyTablesTemplate
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/tests/tools/optimizeTables
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/genbank/tests/tools/updateCdnaInfoMolColumn
  • lines changed 1, context: html, text, full: html, text
    moved gbroot to /hive/data/outside/genbank
• src/hg/makeDb/hgFindSpec/hgFindSpec.c
  • lines changed 104, context: html, text, full: html, text
    merge-and-squash dev branch hgFindSpecReleaseTag
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
  • lines changed 91, context: html, text, full: html, text
    Finished liftOver, N50 number tasks. Updating description html.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    fixed transcript genc v7 -> v10 tag error
  • lines changed 54, context: html, text, full: html, text
    added some of the BTOs for cell lines. I havent done everything yet though
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    adding in views plussig and minussig
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    Approved changes from beta to public. Also fixed some issues in alpha. Redmine #7931.
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    Fixed miss-spelled file name extension, found by weekly link checker.
  • lines changed 11, context: html, text, full: html, text
    Fixing orderUrls in cv
  • lines changed 5, context: html, text, full: html, text
    Adjusting some labels in the CV
  • lines changed 18, context: html, text, full: html, text
    added more BTO terms to cell lines. still not done
  • lines changed 7, context: html, text, full: html, text
    Removed version stanza as this is not being used at the moment.
  • lines changed 72, context: html, text, full: html, text
    Adding termIds and termUrls to CV
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 73, context: html, text, full: html, text
    Updating beta cv
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 150, context: html, text, full: html, text
    Approved changes from beta to public. Also fixed some issues in alpha. Redmine #7931.
  • lines changed 1, context: html, text, full: html, text
    removed provisional tag.
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    Fixed broken link found by link checker.
  • lines changed 1, context: html, text, full: html, text
    Fixed miss-spelled file name extension, found by weekly link checker.
• src/hg/makeDb/trackDb/grcIncidentDb.html
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    Moved some periods outside the hyperlinks
• src/hg/makeDb/trackDb/human/hg18/burgeRnaSeqGemMapperAlign.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/ceuBcellRNASeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/fantomCageGraphTop.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeqRelease2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeqRelease3original.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMapRelease2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeqProv.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeqRelease1.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseqRelease2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleRNAseq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/burgeRnaSeqGemMapperAlign.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/ctgPos.html
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    Fixed broken links
• src/hg/makeDb/trackDb/human/hg19/gap.html
  • lines changed 4, context: html, text, full: html, text
    Fixed broken links
• src/hg/makeDb/trackDb/human/hg19/gold.html
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    Fixed broken links
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 217, context: html, text, full: html, text
    fixed last donorId merge issue.
  • lines changed 96, context: html, text, full: html, text
    missing one in name only, and forgot ot add trackDb last time
  • lines changed 223, context: html, text, full: html, text
    changing all polyA pluses to dateunrestricted = 2012-05-14 if it was 05-16 or after
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    added in missing attic statements
  • lines changed 775, context: html, text, full: html, text
    correcting the plus/minus raw signals to no raw
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    more last second fixes. (attic items, label stuff)
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    added in last expIds and some objType corrections
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 926, context: html, text, full: html, text
    lots of metaDb updates, almost all script generated
  • lines changed 103, context: html, text, full: html, text
    renamed monocytes and corrected metadata to not have donor id anymore. also removed some attic tracks from the trackDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 40, context: html, text, full: html, text
    added md5sum's and meta-data for AWG.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 129, context: html, text, full: html, text
    Added last submission for Histone track. Redmine #7510.
  • lines changed 108, context: html, text, full: html, text
    Fixed ordering of cells. Added expId, dccAccession and controlId. Also added md5sums. Redmine #7510.
  • lines changed 4, context: html, text, full: html, text
    Updated files based on remapping. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 135, context: html, text, full: html, text
    Added submissions for tfbs track. Redmine #7827.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 111, context: html, text, full: html, text
    added md5sum's and meta-data for AWG.
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUmassDekker5C.ra
  • lines changed 5, context: html, text, full: html, text
    Releasing patch for Uw5C & UmassDekker5C, redmine# 7245
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUw5C.ra
  • lines changed 5, context: html, text, full: html, text
    Releasing patch for Uw5C & UmassDekker5C, redmine# 7245
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 5, context: html, text, full: html, text
    Releasing patch for Uw5C & UmassDekker5C, redmine# 7245
  • lines changed 2, context: html, text, full: html, text
    Added alpha tag for release 3 of sydh tfbs track.
  • lines changed 1, context: html, text, full: html, text
    load of GENCODE V12
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
  • lines changed 37, context: html, text, full: html, text
    more last second fixes. (attic items, label stuff)
  • lines changed 2, context: html, text, full: html, text
    last second label and trackDb and html fixes before qa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 18, context: html, text, full: html, text
    missing one in name only, and forgot ot add trackDb last time
  • lines changed 154, context: html, text, full: html, text
    took off non -needed defaults
  • lines changed 41, context: html, text, full: html, text
    more defaults and fixed some trackDb view settings
  • lines changed 505, context: html, text, full: html, text
    fixed long labels
  • lines changed 505, context: html, text, full: html, text
    error in scriptRevert "fixed long labels"
    
    This reverts commit 096150cca51933453918b37f6ae17981950905a3.
    
  • lines changed 1, context: html, text, full: html, text
    fixed a label error
  • lines changed 693, context: html, text, full: html, text
    fixed labels
  • lines changed 373, context: html, text, full: html, text
    corrected labels for raw sig to sig
  • lines changed 271, context: html, text, full: html, text
    more last second fixes. (attic items, label stuff)
  • lines changed 613, context: html, text, full: html, text
    short labels
  • lines changed 135, context: html, text, full: html, text
    short labels part deux
  • lines changed 867, context: html, text, full: html, text
    last second label and trackDb and html fixes before qa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 789, context: html, text, full: html, text
    lots of structural changes to trackDb to make it work, and corrected tag errors
  • lines changed 0, context: html, text, full: html, text
    getting rid of uneeded whitespace
  • lines changed 130, context: html, text, full: html, text
    renamed monocytes and corrected metadata to not have donor id anymore. also removed some attic tracks from the trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeExonArraySuper.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
  • lines changed 1, context: html, text, full: html, text
    load of GENCODE V12
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Setting the defualt to hide from dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
  • lines changed 1, context: html, text, full: html, text
    load of GENCODE V12
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.html
  • lines changed 345, context: html, text, full: html, text
    load of GENCODE V12
  • lines changed 3, context: html, text, full: html, text
    load of GENCODE V12
  • lines changed 5, context: html, text, full: html, text
    documenting lifting chrM GENCODE annotations
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.ra
  • lines changed 223, context: html, text, full: html, text
    load of GENCODE V12
  • lines changed 69, context: html, text, full: html, text
    load of GENCODE V12
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
  • lines changed 1, context: html, text, full: html, text
    Setting the defualt to hide from dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
  • lines changed 1, context: html, text, full: html, text
    Setting the defualt to hide from dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Setting the defualt to hide from dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 1, context: html, text, full: html, text
    Setting the defualt to hide from dense
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
  • lines changed 6, context: html, text, full: html, text
    Fixing typos and grammer found in QA review
  • lines changed 3, context: html, text, full: html, text
    Trying to clean up PET Cluster paragraph
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.release3.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibShRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 6, context: html, text, full: html, text
    Adding in the visibility defaults per katrina request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release2.ra
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    Adding the allButton to the alpha release
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
  • lines changed 4, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html
  • lines changed 4, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html
  • lines changed 1, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.release2.ra
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    Shortening the short label for GENCODE
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.html
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
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    Updated long and short labels. Also updated track description about the new experiments found in this release. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra
  • lines changed 16, context: html, text, full: html, text
    Added last submission for Histone track. Redmine #7510.
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    Updated long and short labels. Also updated track description about the new experiments found in this release. Redmine #7510.
  • lines changed 6, context: html, text, full: html, text
    Fixed ordering of cells. Added expId, dccAccession and controlId. Also added md5sums. Redmine #7510.
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    Updated files based on remapping. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html
  • lines changed 3, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.html
  • lines changed 177, context: html, text, full: html, text
    Added submissions for tfbs track. Redmine #7827.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra
  • lines changed 19, context: html, text, full: html, text
    Added submissions for tfbs track. Redmine #7827.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
  • lines changed 31, context: html, text, full: html, text
    Fixed broken links
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.html
  • lines changed 32, context: html, text, full: html, text
    Fixed broken links
  • lines changed 2, context: html, text, full: html, text
    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html
  • lines changed 2, context: html, text, full: html, text
    Releasing patch for Uw5C & UmassDekker5C, redmine# 7245
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
  • lines changed 1, context: html, text, full: html, text
    Releasing patch for Uw5C & UmassDekker5C, redmine# 7245
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
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    Releasing patch for Uw5C & UmassDekker5C, redmine# 7245
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.patch2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
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    Releasing patch for Uw5C & UmassDekker5C, redmine# 7245
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.release2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.html
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release3.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release4.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release2.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/hg19Patch2/gap.html
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    Fixed broken links
• src/hg/makeDb/trackDb/human/hg19Patch2/gold.html
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    Fixed broken links
• src/hg/makeDb/trackDb/human/hgIkmc.html
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    Fixed broken links
• src/hg/makeDb/trackDb/human/ntModernHumans.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/ntSssSnps.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/ntSssTop5p.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/human/ntSssZScorePMVar.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/loadTracks
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    merge-and-squash dev branch hgFindSpecReleaseTag
• src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
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    removed extra space next to mitochondrial link
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    Correct the N50 number (1603177).
• src/hg/makeDb/trackDb/mouse/komp.html
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    Fixed broken links
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
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    added accession numbers for mm9 Caltech RNA seq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
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    added accession numbers back into LicrRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
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    set UCC accession of MEL/DMSO_2.0pct/Input/IgG-rat (wgEncodeEM002782) as the controlId of MEL, DMSO_2.0pct, IgG-rab sample, see note 57, redmine 5397
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra
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    turn on alignment track, add html entry in top stanza
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    added html entry in top stanza, turned on alighment, signal track not displyed as no agreement was reached on how to display (Venkat), cleaned up labels
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.html
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    update release note
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    update release note
• src/hg/makeDb/trackDb/ntSeqContigs.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/makeDb/trackDb/ntSeqReads.html
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    Removed extra '../..' which was causing error messages in broken link reports
• src/hg/utils/automation/gvfToBed8Attrs.pl
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    Track #34 (dbVar for human): added new dataset (nstd45, ISCA Curated).
• src/hg/utils/automation/loadCosmic.pl
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    support gzipped data dump because COSMIC is now gzipping them
• src/product/README.mysql.setup
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    Added a note about new versions of MySQL disabling LOAD DATA LOCAL INFILE (redmine 7423)
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    Made change in wording suggested by Larry (redmine #7423)
• src/utils/qa/qaGbTracks
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    Got rid of most of the globals, except in the tableList processing.
• src/utils/qa/weeklybld/buildEnv.csh
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    v268 preview1

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