All File Changes

v264_preview2 to v264_base (2012-02-28 to 2012-03-06) v264

• python/virtual.txt
  • lines changed 4, context: html, text, full: html, text
    Added clarifications for python virtual environment use.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo. Added extra i.
• src/README
  • lines changed 3, context: html, text, full: html, text
    Adding licence URL to README.
• src/ai/wordChain/wordChain.c
  • lines changed 2, context: html, text, full: html, text
    Addig a few comments.
  • lines changed 113, context: html, text, full: html, text
    Commenting more, breaking a large function into two. Making it so that first word of nonsense output is random rather than the first word of the text.
• src/gfServer/gfServer.c
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in usage message.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUmMassWengTfbsValid.daf
  • lines changed 25, context: html, text, full: html, text
    Cleaning up the daf for UmassWeng
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUmassWengTfbsValid.daf
  • lines changed 25, context: html, text, full: html, text
    Cleaning up the daf for UmassWeng
  • lines changed 3, context: html, text, full: html, text
    Adding the new composite for UmassWendTfbsValid
• src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrHistone.daf
  • lines changed 3, context: html, text, full: html, text
    added treatment term
  • lines changed 2, context: html, text, full: html, text
    add treatment in the variables group
• src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrRnaSeq.daf
  • lines changed 6, context: html, text, full: html, text
    update with treatment term
  • lines changed 2, context: html, text, full: html, text
    add treatment in the variables group
• src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrTfbs.daf
  • lines changed 3, context: html, text, full: html, text
    added treatment term
  • lines changed 2, context: html, text, full: html, text
    add treatment in the variables group
• src/hg/encode/qaEncodeTracks2/makefile
  • lines changed 1, context: html, text, full: html, text
    moved over ot name qaEncodeTracks2
• src/hg/encode/qaEncodeTracks2/qaEncodeTracks
  • lines changed 78, context: html, text, full: html, text
    moved over ot name qaEncodeTracks2
• src/hg/encode/qaEncodeTracks2/qaEncodeTracks2
  • lines changed 78, context: html, text, full: html, text
    moved over ot name qaEncodeTracks2
  • lines changed 4, context: html, text, full: html, text
    changed usage to be correct
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 13, context: html, text, full: html, text
    changed hgLiftOver to only output message out multiple option not being suppported for the positions format ONLY if the input is positions format and if the multiple option is checked
• src/hg/hgTracks/simpleTracks.c
  • lines changed 6, context: html, text, full: html, text
    All pgSnp tables have a bin column, but loadPgSnp was not usinghAddBinToQuery to take advantage of it. It makes a difference when viewing a 1Mb region.
• src/hg/hgc/t2g.c
  • lines changed 1, context: html, text, full: html, text
    added a sqlReeResult after hiram code review
  • lines changed 3, context: html, text, full: html, text
    sorted t2g results by year now
• src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
  • lines changed 3, context: html, text, full: html, text
    Major refactoring. New JS file encodeMatrix.js will be shared by all 3 data matrix apps
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 4, context: html, text, full: html, text
    Migrate ChipMatrix to refactoring 1 (dataMatrix.js)
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
  • lines changed 1, context: html, text, full: html, text
    Migrate ChipMatrix to refactoring 1 (dataMatrix.js)
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 3, context: html, text, full: html, text
    Major refactoring. New JS file encodeMatrix.js will be shared by all 3 data matrix apps
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 1, context: html, text, full: html, text
    Major refactoring. New JS file encodeMatrix.js will be shared by all 3 data matrix apps
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 3, context: html, text, full: html, text
    Cleanup data summary app to use common code in encodeMatrix.js
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
  • lines changed 1, context: html, text, full: html, text
    Cleanup data summary app to use common code in encodeMatrix.js
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 4, context: html, text, full: html, text
    Added a line for CSHL Long RNA-seq (redmine #5986)
  • lines changed 8, context: html, text, full: html, text
    Added CSHL Long RNA-seq out of alphabetic order (redmine #5986)
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 2, context: html, text, full: html, text
    Added ENCODE Project Consortium as an author and added two more authors for a total of ten authors (redmine #6870)
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    Added new mm10 assembly
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    Added credits for new mm10 browser
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 106, context: html, text, full: html, text
    added snp135 annoucement and archived one other
  • lines changed 24, context: html, text, full: html, text
    Adding RGD Genes to the news. Commenting out mm10 announcement until later
• src/hg/htdocs/indexIntro.html
  • lines changed 1, context: html, text, full: html, text
    Change the server detect line so that the TEST text appears on both .soe. and .cse. urls per redmione 7108
• src/hg/htdocs/indexNews.html
  • lines changed 44, context: html, text, full: html, text
    added snp135 annoucement and archived one other
  • lines changed 92, context: html, text, full: html, text
    Added new mm10 announcement, collapsed old announcement, removed archived annoucement
  • lines changed 85, context: html, text, full: html, text
    Adding RGD Genes to the news. Commenting out mm10 announcement until later
• src/hg/htdocs/style/encodeProject.css
  • lines changed 3, context: html, text, full: html, text
    Search panel cosmetics/usability - break out style for instructions, use italics for action/verb
  • lines changed 0, context: html, text, full: html, text
    Migrate ChipMatrix to refactoring 1 (dataMatrix.js)
• src/hg/inc/liftOver.h
  • lines changed 11, context: html, text, full: html, text
    changed hgLiftOver to only output message out multiple option not being suppported for the positions format ONLY if the input is positions format and if the multiple option is checked
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v264
• src/hg/js/encodeChipMatrix.js
  • lines changed 295, context: html, text, full: html, text
    Migrate ChipMatrix to refactoring 1 (dataMatrix.js)
  • lines changed 67, context: html, text, full: html, text
    Factoring out a bit more shared code
• src/hg/js/encodeDataMatrix.js
  • lines changed 350, context: html, text, full: html, text
    Major refactoring. New JS file encodeMatrix.js will be shared by all 3 data matrix apps
  • lines changed 8, context: html, text, full: html, text
    Migrate ChipMatrix to refactoring 1 (dataMatrix.js)
  • lines changed 1, context: html, text, full: html, text
    Correct app name in comment header
  • lines changed 67, context: html, text, full: html, text
    Factoring out a bit more shared code
• src/hg/js/encodeDataSummary.js
  • lines changed 161, context: html, text, full: html, text
    Cleanup data summary app to use common code in encodeMatrix.js
• src/hg/js/encodeMatrix.js
  • lines changed 157, context: html, text, full: html, text
    Major refactoring. New JS file encodeMatrix.js will be shared by all 3 data matrix apps
  • lines changed 1, context: html, text, full: html, text
    Migrate ChipMatrix to refactoring 1 (dataMatrix.js)
  • lines changed 62, context: html, text, full: html, text
    Factoring out a bit more shared code
• src/hg/js/encodeProject.js
  • lines changed 1, context: html, text, full: html, text
    Search panel cosmetics/usability - break out style for instructions, use italics for action/verb
  • lines changed 75, context: html, text, full: html, text
    Major refactoring. New JS file encodeMatrix.js will be shared by all 3 data matrix apps
  • lines changed 49, context: html, text, full: html, text
    Migrate ChipMatrix to refactoring 1 (dataMatrix.js)
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    Major refactoring. New JS file encodeMatrix.js will be shared by all 3 data matrix apps
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    "Error(s)" => "Warning/Error(s)" (#6842)
• src/hg/lib/liftOver.c
  • lines changed 26, context: html, text, full: html, text
    changed hgLiftOver to only output message out multiple option not being suppported for the positions format ONLY if the input is positions format and if the multiple option is checked
• src/hg/lib/omim2gene.as
  • lines changed 8, context: html, text, full: html, text
    more changes to otto-mate the OMIM load (#6943)
• src/hg/lib/omim2gene.sql
  • lines changed 15, context: html, text, full: html, text
    more changes to otto-mate the OMIM load (#6943)
• src/hg/lib/omimGeneSymbol.sql
  • lines changed 13, context: html, text, full: html, text
    more changes to otto-mate the OMIM load (#6943)
• src/hg/logCrawl/encodeUserDbCrawl/encodeUserDbCrawl.c
  • lines changed 17, context: html, text, full: html, text
    Separating out encode tracks from others statistically a little better.
• src/hg/makeDb/doc/dm3.txt
  • lines changed 69, context: html, text, full: html, text
    redmine ToDo #7177 droVir2 to dm3 liftover.
• src/hg/makeDb/doc/droVir2.txt
  • lines changed 29, context: html, text, full: html, text
    redmine ToDo #7177 droVir2 to dm3 liftover.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV11.release1.notes
  • lines changed 76, context: html, text, full: html, text
    Adding the V11 notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromDnase.release2.notes
  • lines changed 326, context: html, text, full: html, text
    updateing notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release4.notes
  • lines changed 1908, context: html, text, full: html, text
    first draft of notes for UwDnase
• src/hg/makeDb/doc/fr3.txt
  • lines changed 2, context: html, text, full: html, text
    note lifted fr2 ensGene for the 8way annotation
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 1, context: html, text, full: html, text
    correct the WGS NCBI URL
• src/hg/makeDb/doc/hg18.txt
  • lines changed 18, context: html, text, full: html, text
    Track #7090 (ISCA update): dbVar kindly re-dumped their ftp filesafter b0b found that the files were missing the Parent attribute; reloaded data.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    Added a comment to hg19 GWAS Catalog section to make it more clearthat it depends on hg18 GWAS Catalog having just been built, because it uses an assembly-independent file from the hg18 build dir. Thanks Brian for alerting me that this wasn't clear.
  • lines changed 15, context: html, text, full: html, text
    Track #7090 (ISCA update): dbVar kindly re-dumped their ftp filesafter b0b found that the files were missing the Parent attribute; reloaded data.
  • lines changed 17, context: html, text, full: html, text
    added isca update to Aggregate subtracks
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 3, context: html, text, full: html, text
    Set default position to an area contains RHOG chr14:70,034,487-70,048,046
• src/hg/makeDb/doc/rn4.txt
  • lines changed 221, context: html, text, full: html, text
    cleaning up hgNear tables for rgdGene2
• src/hg/makeDb/schema/all.joiner
  • lines changed 80, context: html, text, full: html, text
    Adding the GencodeV11 to all.joiner
• src/hg/makeDb/trackDb/chimp/panTro2/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/chimp/panTro2/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/cow/bosTau4/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/cow/bosTau4/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 6, context: html, text, full: html, text
    Added more to 6 treatment descriptions.
  • lines changed 12, context: html, text, full: html, text
    Added 1 age and 1 treatment for Ren lab.
  • lines changed 13, context: html, text, full: html, text
    provisional labels for terms of type mapAlgorithm
  • lines changed 16, context: html, text, full: html, text
    provisional labels for terms of type age
  • lines changed 12, context: html, text, full: html, text
    added provisional labels for terms of type seqPlatform
  • lines changed 36, context: html, text, full: html, text
    removed dots from tags of recently scraped cell lines
  • lines changed 8, context: html, text, full: html, text
    Fixes found in code review Redmine 7133 1. Fixed the labels of diffProtA to be protocl instead of protein 3. Changed tissue catilage to tissue cartilage
  • lines changed 30, context: html, text, full: html, text
    Fixed naming of differentiaion protocols to match diffProtA naming schema.
  • lines changed 3, context: html, text, full: html, text
    Renamed diffDMEM_7d to follow differntiation protocol treatments.
  • lines changed 1, context: html, text, full: html, text
    Fixed special Beta character to use html formating. Fixes in Code Review. Redmine #7133.
  • lines changed 6, context: html, text, full: html, text
    Fixed the vendorId and labels for BRG1 and INI1 which were switched.
  • lines changed 17, context: html, text, full: html, text
    Removed BMDM, as this is not a cell line, but a differentiation of Bone Marrow.
  • lines changed 2, context: html, text, full: html, text
    Shortened tag so that table names will fit table limit.
  • lines changed 2, context: html, text, full: html, text
    Shortened term for diffProt7d, doesn't follow convention, but is the only way to fit.
  • lines changed 19, context: html, text, full: html, text
    Removing Provisional Tags
  • lines changed 12, context: html, text, full: html, text
    Fixing merge conflict
  • lines changed 52, context: html, text, full: html, text
    Finally submitting T98G cell line so I uncommented it
  • lines changed 77, context: html, text, full: html, text
    Adding Treatment Stanzas and Moving 4OHTAM to Alphabetize
  • lines changed 14, context: html, text, full: html, text
    provisional labels for strains
  • lines changed 4, context: html, text, full: html, text
    provisional labels for categories
  • lines changed 4, context: html, text, full: html, text
    provisional labels for attic
  • lines changed 1, context: html, text, full: html, text
    noting that all attic labels are provisional
  • lines changed 10, context: html, text, full: html, text
    provisional labels for protocols
  • lines changed 2, context: html, text, full: html, text
    provisional labels for restrictionEnzymes
  • lines changed 5, context: html, text, full: html, text
    provisional labels for regions
  • lines changed 5, context: html, text, full: html, text
    Removed duplicate registration of Bone_marrow_derived_macrophage_differentiation to diffProtD_7d.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 1680, context: html, text, full: html, text
    Copying alpha cv.ra over to beta. Many additions and changes!
  • lines changed 17, context: html, text, full: html, text
    Removing Provisional Tags
  • lines changed 2, context: html, text, full: html, text
    Moving comment out of description field
• src/hg/makeDb/trackDb/dog/canFam2/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/dog/canFam2/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 2, context: html, text, full: html, text
    fixup phastCons8way/fish.mod link
• src/hg/makeDb/trackDb/fugu/fr3/description.html
  • lines changed 12, context: html, text, full: html, text
    fixup sample search items for Fugu gateway page
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding basic metaDb for GencodeV11
  • lines changed 1, context: html, text, full: html, text
    adding haib bisulfite into makefile
  • lines changed 1, context: html, text, full: html, text
    This file needs to go to for the UmassWengTfbsValid
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV11.ra
  • lines changed 261, context: html, text, full: html, text
    Adding basic metaDb for GencodeV11
  • lines changed 69, context: html, text, full: html, text
    Adding expIds, accessions, and md5sums. Removing the Freeze information at request of lab
  • lines changed 17, context: html, text, full: html, text
    Adding the subId
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylWgbs.ra
  • lines changed 69, context: html, text, full: html, text
    added in new tracks to new wgbs track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 197, context: html, text, full: html, text
    replaced K562 experiment
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUMassWengTfbsValid.ra
  • lines changed 76, context: html, text, full: html, text
    Adding the new composite for UmassWendTfbsValid
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 181, context: html, text, full: html, text
    added in expIds
  • lines changed 521, context: html, text, full: html, text
    fixing gzip md5 debacle
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 83, context: html, text, full: html, text
    fixing control ids
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging UMAss 5C on beta, redmine# 225
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUmassDekker5C.ra
  • lines changed 988, context: html, text, full: html, text
    staging UMAss 5C on beta, redmine# 225
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUw5C.ra
  • lines changed 39, context: html, text, full: html, text
    Updated metadata with Mar 2012 Freeze date (redmine #6581)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 2112, context: html, text, full: html, text
    Staging UW DNase I HS (Release 4) on beta (redmine #6035)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwTfbs.ra
  • lines changed 83, context: html, text, full: html, text
    Matt made some changes to the metadata (redmine #6323)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 14306, context: html, text, full: html, text
    Releasing Broad Histone (Release 2) to the RR (redmine #4145)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 18218, context: html, text, full: html, text
    Releasing HAIB TFBS (Release 2), redmine# 4487
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUncBsuProt.ra
  • lines changed 15, context: html, text, full: html, text
    Updated metadata with Mar 2012 Freeze date (redmine #6581)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUw5C.ra
  • lines changed 39, context: html, text, full: html, text
    Updated metadata with Mar 2012 Freeze date (redmine #6581)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwAffyExonArray.ra
  • lines changed 33, context: html, text, full: html, text
    Updated metadata with Mar 2012 Freeze date (redmine #6581)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 2112, context: html, text, full: html, text
    Releasing UW DNase I HS (Release 4) on the RR (redmine #6035)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwTfbs.ra
  • lines changed 149, context: html, text, full: html, text
    Releasing UW CTCF Binding (Release 3) to RR (redmine #6323)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    Removed override redirect to temporary html file, as track is about to be released.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Getting rid of the last .new file
  • lines changed 2, context: html, text, full: html, text
    Fixes for Redmine #2606 1. Made patch.ra for wgEncodeUw5C to allow for leakof track within new supertrack. 2. Updated shortlabel to be consistent with wgEncodeUmass5c Redmine #225
  • lines changed 2, context: html, text, full: html, text
    Staging UW DNase I HS (Release 4) on beta (redmine #6035)
  • lines changed 2, context: html, text, full: html, text
    Releasing HAIB TFBS (Release 2), redmine# 4487
  • lines changed 2, context: html, text, full: html, text
    Releasing UW CTCF Binding (Release 3) to RR (redmine #6323)
  • lines changed 2, context: html, text, full: html, text
    Releasing Broad Histone (Release 2) to the RR (redmine #4145)
  • lines changed 3, context: html, text, full: html, text
    Adding the new composite for UmassWendTfbsValid
  • lines changed 1, context: html, text, full: html, text
    staging UMAss 5C on beta, redmine# 225
  • lines changed 2, context: html, text, full: html, text
    Releasing UW DNase I HS (Release 4) on the RR (redmine #6035)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html
  • lines changed 1, context: html, text, full: html, text
    Updated release date to be March. Redmine #4145
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 378, context: html, text, full: html, text
    Adding the Tap information
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
  • lines changed 5, context: html, text, full: html, text
    Fixing the Data Release Policy for GENCODE
  • lines changed 1, context: html, text, full: html, text
    Changing release policy again.
  • lines changed 48, context: html, text, full: html, text
    Changes according to ticket 6775
  • lines changed 6, context: html, text, full: html, text
    Fixes for Steve in #6775
  • lines changed 5, context: html, text, full: html, text
    A few more refinements on punctuation and wording for ticket 6775
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra
  • lines changed 2, context: html, text, full: html, text
    Commenting out a few tags that seem unused
  • lines changed 1, context: html, text, full: html, text
    Changing the green for non-coding to be brighter
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
  • lines changed 13, context: html, text, full: html, text
    added in html
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
  • lines changed 44, context: html, text, full: html, text
    added in new tracks to new wgbs track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
  • lines changed 48, context: html, text, full: html, text
    replaced K562 experiment
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.new.ra
  • lines changed 343, context: html, text, full: html, text
    Getting rid of the last .new file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release2.ra
  • lines changed 343, context: html, text, full: html, text
    Getting rid of the last .new file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed shortlabel to be less than 17 characters. Redmine #225.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassWengTfbsValid.html
  • lines changed 84, context: html, text, full: html, text
    Adding the new composite for UmassWendTfbsValid
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassWengTfbsValid.ra
  • lines changed 11, context: html, text, full: html, text
    Adding the new composite for UmassWendTfbsValid
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.patch.ra
  • lines changed 12, context: html, text, full: html, text
    Fixes for Redmine #2606 1. Made patch.ra for wgEncodeUw5C to allow for leakof track within new supertrack. 2. Updated shortlabel to be consistent with wgEncodeUmass5c Redmine #225
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Fixes for Redmine #2606 1. Made patch.ra for wgEncodeUw5C to allow for leakof track within new supertrack. 2. Updated shortlabel to be consistent with wgEncodeUmass5c Redmine #225
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.html
  • lines changed 25, context: html, text, full: html, text
    qa fixes for uw dnase
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    changing release date to match month
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    qa fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra
  • lines changed 3, context: html, text, full: html, text
    shortening too long of short label
  • lines changed 15, context: html, text, full: html, text
    qa fixes for uw dnase
  • lines changed 1, context: html, text, full: html, text
    fixed html code for label
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    changing scorefilter to 0
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    changing scorefilterlimit to 500
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    correcting html entity
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    changed tag for MONOCD14
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    fixed alphabetization of cell lines
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    fixing the alphabetizion again for dashes
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    qa fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.html
  • lines changed 1, context: html, text, full: html, text
    changing release date to match month
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    this one didn't need the date change
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.ra
  • lines changed 1, context: html, text, full: html, text
    fixed some stuff according to QA
• src/hg/makeDb/trackDb/human/iscaComposite.alpha.html
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    Deleted old iscaComposite.html file, and renames new 'alpha' one to iscaComposite.html.
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 7, context: html, text, full: html, text
    Deleted old iscaComposite.html file, and renames new 'alpha' one to iscaComposite.html.
• src/hg/makeDb/trackDb/human/trackDb.ra
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    removed release tags for 2 new isca subtracks that are to be released today.
• src/hg/makeDb/trackDb/mouse/mm10/description.html
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    Updated sample query
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    add good search rule for gold table to fine all fragment names
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 3, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 101, context: html, text, full: html, text
    Added updated expIds and accessions after adding age to the expVars. Redmine 5394.
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    update metaDb with new datasets submitted after the first release and before 02/16/12
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
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    Fixing the lab, cell, and dataType to match our CV
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 1771, context: html, text, full: html, text
    Added 15 experiments to track. Redmine #4468.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging CSHL Long RNA-Seq (Release 1) on RR (redmine #5986)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 7265, context: html, text, full: html, text
    Staging CSHL Long RNA-Seq (Release 1) on RR (redmine #5986)
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging CSHL Long RNA-Seq (Release 1) on RR (redmine #5986)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    Changed link from hgdownload-test to hgdownload. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra
  • lines changed 132, context: html, text, full: html, text
    clean up long labels
  • lines changed 131, context: html, text, full: html, text
    clean up long labels
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    clean up long labels
  • lines changed 131, context: html, text, full: html, text
    redmine #5393, note #72, add age to shortlabel, replace all the tissue/cell types with abbreviation
  • lines changed 274, context: html, text, full: html, text
    updatenew cell type, age, histone modification with new submission
  • lines changed 154, context: html, text, full: html, text
    Added in missing treatment in the subGroup line that was forgotten in commit 98353eb7fbf5b2f0c5a2e3ee07c7e4f680181206.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra
  • lines changed 76, context: html, text, full: html, text
    clean up long labels
  • lines changed 39, context: html, text, full: html, text
    updatenew cell type, age, histone modification with new submission
  • lines changed 76, context: html, text, full: html, text
    Added in missing treatment in the subGroup line that was forgotten in commit 98353eb7fbf5b2f0c5a2e3ee07c7e4f680181206.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra
  • lines changed 88, context: html, text, full: html, text
    clean up long labels
  • lines changed 1, context: html, text, full: html, text
    clean up long labels
  • lines changed 57, context: html, text, full: html, text
    updatenew cell type, age, histone modification with new submission
  • lines changed 88, context: html, text, full: html, text
    Added in missing treatment in the subGroup line that was forgotten in commit 98353eb7fbf5b2f0c5a2e3ee07c7e4f680181206.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
  • lines changed 407, context: html, text, full: html, text
    Added 15 experiments to track. Redmine #4468.
• src/hg/makeDb/trackDb/rat/rn4/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/rat/rn4/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/rat/rn4/rgdGene2.html
  • lines changed 25, context: html, text, full: html, text
    adding closing p tags as well as making the line length shorter. In general, standardizing it for easier reading. No actual words changed.
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    adding html codes for quotes and removing quotes around a _blank. Per code review #7137
• src/hg/makeDb/trackDb/rhesus/rheMac2/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/makeDb/trackDb/rhesus/rheMac2/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Staging all of the other assemblies to have metaDb dirs instead of metaDb in the files
• src/hg/utils/omim/buildOmimTracks.csh
  • lines changed 54, context: html, text, full: html, text
    more changes to otto-mate the OMIM load (#6943)
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    more OMIM otto tasks. #6943
• src/hg/utils/omim/checkOmim.sh
  • lines changed 1, context: html, text, full: html, text
    more changes to make OMIM update otto-matic (#6943)
  • lines changed 5, context: html, text, full: html, text
    more changes to otto-mate the OMIM load (#6943)
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    more OMIM otto tasks. #6943
• src/hg/utils/omim/doOmimAv/doOmimAv.c
  • lines changed 1, context: html, text, full: html, text
    more changes to otto-mate the OMIM load (#6943)
• src/hg/utils/omim/doOmimAv/makefile
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    more changes to make OMIM update otto-matic (#6943)
• src/hg/utils/omim/doOmimGene2/doOmimGene2.c
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    more changes to otto-mate the OMIM load (#6943)
• src/hg/utils/omim/doOmimGene2/makefile
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    more changes to make OMIM update otto-matic (#6943)
• src/hg/utils/omim/doOmimGeneSymbols/doOmimGeneSymbols.c
  • lines changed 1, context: html, text, full: html, text
    more changes to otto-mate the OMIM load (#6943)
• src/hg/utils/omim/doOmimGeneSymbols/makefile
  • lines changed 35, context: html, text, full: html, text
    more changes to make OMIM update otto-matic (#6943)
• src/hg/utils/omim/doOmimLocation/doOmimLocation.c
  • lines changed 1, context: html, text, full: html, text
    more changes to otto-mate the OMIM load (#6943)
• src/hg/utils/omim/doOmimLocation/makefile
  • lines changed 35, context: html, text, full: html, text
    more changes to make OMIM update otto-matic (#6943)
• src/hg/utils/omim/makefile
  • lines changed 21, context: html, text, full: html, text
    more OMIM otto tasks. #6943
• src/hg/utils/omim/omim.tables
  • lines changed 9, context: html, text, full: html, text
    more OMIM otto tasks. #6943
• src/hg/utils/omim/omimWrapper.sh
  • lines changed 6, context: html, text, full: html, text
    more OMIM otto tasks. #6943
• src/hg/utils/omim/validateOmim.sh
  • lines changed 29, context: html, text, full: html, text
    more OMIM otto tasks. #6943
• src/lib/htmshell.c
  • lines changed 1, context: html, text, full: html, text
    "Error(s)" => "Warning/Error(s)" (#6842)
• src/utils/qa/weeklybld/buildEnv.csh
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    v264 final build

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