All File Changes

v238_base to v239_preview (2010-08-17 to 2010-08-24) v239

• src/hg/encode/DAFs/2.0/broadChipSeq.daf
  • lines changed 17, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
  • lines changed 17, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • lines changed 25, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
  • lines changed 1, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
  • lines changed 14, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
  • lines changed 1, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/haibMethylSeq.daf
  • lines changed 16, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
  • lines changed 1, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 22, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
  • lines changed 1, context: html, text, full: html, text
    Updated daf's for the Ren lab to not require Signal, as they are having trouble generating bigWig files.
  • lines changed 1, context: html, text, full: html, text
    Uptaded revision of DAF
• src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
  • lines changed 20, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
  • lines changed 1, context: html, text, full: html, text
    Updated daf's for the Ren lab to not require Signal, as they are having trouble generating bigWig files.
  • lines changed 1, context: html, text, full: html, text
    Uptaded versions, that I forgot in last commit
• src/hg/encode/DAFs/2.0/psuMm95c.daf
  • lines changed 17, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/psuMm9DnaseSeq.daf
  • lines changed 18, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/psuMm9Histone.daf
  • lines changed 20, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
  • lines changed 21, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/stanfordHg19Hist.daf
  • lines changed 18, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
  • lines changed 1, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf
  • lines changed 19, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
  • lines changed 1, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
  • lines changed 23, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
  • lines changed 23, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • lines changed 15, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • lines changed 14, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
• src/hg/encode/DAFs/2.0/uwChipSeq.daf
  • lines changed 47, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
• src/hg/encode/DAFs/2.0/uwDnaseDgf.daf
  • lines changed 30, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
• src/hg/encode/DAFs/2.0/uwDnaseSeq.daf
  • lines changed 18, context: html, text, full: html, text
    Updated Human DAFs for tracks that I own, to include a explanation of the DDF line
• src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf
  • lines changed 17, context: html, text, full: html, text
    Updated all Mouse DAFs to include an explanation of the DDF line
• src/hg/encode/encodeLoad/makefile
  • lines changed 1, context: html, text, full: html, text
    take out flags that were preventing the most recent copy from being installed
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 460, context: html, text, full: html, text
    First draft of adding pi.ra to the cv.ra
  • lines changed 289, context: html, text, full: html, text
    this has the ripChip Antibodies as Antibodies but commented out until we are ready to make the change
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 94, context: html, text, full: html, text
    Comments in Fields.ra
• src/hg/encode/encodeValidate/config/ripAntibody.cv.ra
  • lines changed 1220, context: html, text, full: html, text
    Comments in Fields.ra
• src/hg/encode/hgEncodeSubmit/app/models/project.rb
  • lines changed 1, context: html, text, full: html, text
    making sure the order of the archives in a project is preserved
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
  • lines changed 2, context: html, text, full: html, text
    making sure validate and load links are available in advancedView, basically admins
  • lines changed 1, context: html, text, full: html, text
    oops
  • lines changed 1, context: html, text, full: html, text
    Revert "oops" This reverts commit 3c39fe091da71c3e024ebb6fc0a4dc55cabf6da4.
  • lines changed 2, context: html, text, full: html, text
    Revert "making sure validate and load links are available in advancedView, basically admins" This reverts commit afd44e0061f2a607e027ef321dc54bdcb6d11849. This turns out to need corresponding changes in the controller, and now it seems like not that safe to do anyway.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 1, context: html, text, full: html, text
    fix another bonehead move (left out a '/')
• src/hg/encode/validateCv/makefile
  • lines changed 18, context: html, text, full: html, text
    shell of a program to validate cv.ra and make sure metadata is compliant
• src/hg/encode/validateCv/validateCv.c
  • lines changed 39, context: html, text, full: html, text
    shell of a program to validate cv.ra and make sure metadata is compliant
  • lines changed 15, context: html, text, full: html, text
    add usage message (woooo!)
• src/hg/estOrient/makefile
  • lines changed 2, context: html, text, full: html, text
    watch out for MYSQLIBS to have other stuff there than just library names
• src/hg/hgGene/localization.c
  • lines changed 2, context: html, text, full: html, text
    Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org.
• src/hg/hgTables/hgTables.c
  • lines changed 15, context: html, text, full: html, text
    Added support for new trackDb setting 'tableBrowser off' which prevents hgTables from displaying a track (if related tables need to be excluded from All Tables, they go after 'off', space-sep.
• src/hg/hgTables/hgTables.h
  • lines changed 1, context: html, text, full: html, text
    Added support for new trackDb setting 'tableBrowser off' which prevents hgTables from displaying a track (if related tables need to be excluded from All Tables, they go after 'off', space-sep.
• src/hg/hgTables/mainPage.c
  • lines changed 35, context: html, text, full: html, text
    Added support for new trackDb setting 'tableBrowser off' which prevents hgTables from displaying a track (if related tables need to be excluded from All Tables, they go after 'off', space-sep.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 7, context: html, text, full: html, text
    Changes for ajax=1 version of cfg dialog
  • lines changed 14, context: html, text, full: html, text
    Fixed off by one bug seen in ie.
  • lines changed 19, context: html, text, full: html, text
    Find Tracks now has a description only popup
  • lines changed 17, context: html, text, full: html, text
    Got popup box for descrition in findTracks working properly
• src/hg/hgTracks/hgTracks.c
  • lines changed 11, context: html, text, full: html, text
    Fixed table in row bug
  • lines changed 3, context: html, text, full: html, text
    Removed call to trackHash for parentTdb, since composite parent should only be necessary for foundTracks and foundTracks has incomplete trackHash built
  • lines changed 3, context: html, text, full: html, text
    Screwed this up again. Limiting vis from composite parent should only be done by searchTracks, not normal image generation
• src/hg/hgTracks/imageV2.c
  • lines changed 10, context: html, text, full: html, text
    Fixed json to find the composite parent
• src/hg/hgTracks/searchTracks.c
  • lines changed 44, context: html, text, full: html, text
    Adding support for popup cfg even though there is currently some duplicated code
  • lines changed 3, context: html, text, full: html, text
    Screwed this up again. Limiting vis from composite parent should only be done by searchTracks, not normal image generation
  • lines changed 1, context: html, text, full: html, text
    Fixed off by one bug seen in ie.
  • lines changed 19, context: html, text, full: html, text
    Find Tracks now has a description only popup
  • lines changed 1, context: html, text, full: html, text
    Got popup box for descrition in findTracks working properly
• src/hg/hgTracks/simpleTracks.c
  • lines changed 13, context: html, text, full: html, text
    Updated to implement changes suggested by data provider of R-DMR track.
  • lines changed 2, context: html, text, full: html, text
    [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation.
• src/hg/hgc/ccdsClick.c
  • lines changed 87, context: html, text, full: html, text
    add CCDS public notes to the CCDS details page
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Updated to implement changes suggested by data provider of R-DMR track.
  • lines changed 12, context: html, text, full: html, text
    [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 13, context: html, text, full: html, text
    alphabetized the tracks in the regulatation super track
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org.
• src/hg/htdocs/goldenPath/help/hgNearHelp.html
  • lines changed 1, context: html, text, full: html, text
    Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 13, context: html, text, full: html, text
    putting the cat in the news, archiving old stories
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 71, context: html, text, full: html, text
    "Release log update"
  • lines changed 41, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/images/loading.gif
  • lines changed 0, context: html, text, full: html, text
    loading image used when loading tracks (copied from CB)
• src/hg/htdocs/indexNews.html
  • lines changed 55, context: html, text, full: html, text
    putting the cat in the news, archiving old stories
• src/hg/htdocs/style/jquery-ui.css
  • lines changed 2, context: html, text, full: html, text
    Make the cfg popup a bit more recognizable
  • lines changed 3, context: html, text, full: html, text
    Find Tracks now has a description only popup
  • lines changed 3, context: html, text, full: html, text
    Got popup box for descrition in findTracks working properly
• src/hg/inc/ccdsNotes.h
  • lines changed 66, context: html, text, full: html, text
    added support for importing CCDS public notes into a table
• src/hg/inc/genePred.h
  • lines changed 5, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/hg/inc/sgdAbundance.h
  • lines changed 1, context: html, text, full: html, text
    Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org.
• src/hg/js/ajax.js
  • lines changed 33, context: html, text, full: html, text
    Fixed off by one bug seen in ie.
• src/hg/js/hgTracks.js
  • lines changed 74, context: html, text, full: html, text
    Changed the rightClick menu and prepared the ground for common hgTrackUi popup for findTracks
  • lines changed 28, context: html, text, full: html, text
    Fixed off by one bug seen in ie.
  • lines changed 22, context: html, text, full: html, text
    Find Tracks now has a description only popup
  • lines changed 4, context: html, text, full: html, text
    Something strange happened to last checkin. Also changed popup title.
  • lines changed 33, context: html, text, full: html, text
    add showLoadingImage
  • lines changed 9, context: html, text, full: html, text
    Got popup box for descrition in findTracks working properly
• src/hg/js/jquery.tablednd.js
  • lines changed 16, context: html, text, full: html, text
    Added some protection for strange interactions between DnD and contextMenu
• src/hg/lib/ccdsNotes.as
  • lines changed 7, context: html, text, full: html, text
    added support for importing CCDS public notes into a table
• src/hg/lib/ccdsNotes.c
  • lines changed 148, context: html, text, full: html, text
    added support for importing CCDS public notes into a table
  • lines changed 1, context: html, text, full: html, text
    fixed bugs in ccdsNotes load
• src/hg/lib/ccdsNotes.sql
  • lines changed 13, context: html, text, full: html, text
    added support for importing CCDS public notes into a table
• src/hg/lib/decipherRaw.sql
  • lines changed 3, context: html, text, full: html, text
    Updated decipherRaw.sql
• src/hg/lib/genePred.c
  • lines changed 136, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/hg/lib/hui.c
  • lines changed 6, context: html, text, full: html, text
    Changes for ajax=1 version of cfg dialog
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    added support for importing CCDS public notes into a table
• src/hg/lib/sgdAbundance.as
  • lines changed 1, context: html, text, full: html, text
    Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org.
• src/hg/lib/sgdAbundance.sql
  • lines changed 1, context: html, text, full: html, text
    Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org.
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    In overrideField, ignore release tag because it has already been processed and removed from overTd->settingsHash. Now we can have release-specific overrides.
• src/hg/makeDb/doc/blastTab.txt
  • lines changed 320, context: html, text, full: html, text
    rebuilding all blast tabs on account of new Ensembl v59 genes
  • lines changed 4, context: html, text, full: html, text
    add not about scripts to run everything
  • lines changed 85, context: html, text, full: html, text
    updated with ce6 sacCer2 and dm3 recipBest
  • lines changed 40, context: html, text, full: html, text
    adding danRer6 recip best
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 66, context: html, text, full: html, text
    phastCons 13-way DONE
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaSeq.release1.notes.txt
  • lines changed 88, context: html, text, full: html, text
    The release notes
• src/hg/makeDb/doc/felCat3.txt
  • lines changed 14, context: html, text, full: html, text
    felCat3 liftOver to felCat4
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 14, context: html, text, full: html, text
    re-did Human Proteins.
  • lines changed 13, context: html, text, full: html, text
    liftOver to felCat3
• src/hg/makeDb/doc/hg19.txt
  • lines changed 486, context: html, text, full: html, text
    documenting patch2 update procedure
  • lines changed 1, context: html, text, full: html, text
    DONE Sestan Brain
  • lines changed 32, context: html, text, full: html, text
    [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation.
• src/hg/makeDb/genbank/etc/genbank.tbls
  • lines changed 1, context: html, text, full: html, text
    added support for importing CCDS public notes into a table
• src/hg/makeDb/genbank/src/ccds/ccdsMkTables.c
  • lines changed 162, context: html, text, full: html, text
    added support for importing CCDS public notes into a table
  • lines changed 2, context: html, text, full: html, text
    fixed bugs in ccdsNotes load
• src/hg/makeDb/genbank/src/dbload/gbDbLoadStep
  • lines changed 1, context: html, text, full: html, text
    added support for importing CCDS public notes into a table
• src/hg/makeDb/trackDb/README
  • lines changed 3, context: html, text, full: html, text
    Added support for new trackDb setting 'tableBrowser off' which prevents hgTables from displaying a track (if related tables need to be excluded from All Tables, they go after 'off', space-sep.
• src/hg/makeDb/trackDb/human/hg18/rdmr.html
  • lines changed 26, context: html, text, full: html, text
    Updated to implement changes suggested by data provider of R-DMR track.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 129, context: html, text, full: html, text
    NumtS tracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeReg.html
  • lines changed 5, context: html, text, full: html, text
    one of the labs was missing credis and so I changed credits per Kate's request
• src/hg/makeDb/trackDb/human/hg19/altSequence.html
  • lines changed 16, context: html, text, full: html, text
    changing haplotypeLocations track to altSequence
• src/hg/makeDb/trackDb/human/hg19/haplotypeLocations.html
  • lines changed 7, context: html, text, full: html, text
    changing haplotypeLocations track to altSequence
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 105, context: html, text, full: html, text
    update subId to hg19 submission id
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
  • lines changed 5, context: html, text, full: html, text
    add a few missing variables
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 7, context: html, text, full: html, text
    change the filenames to be *.bigWig
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 6, context: html, text, full: html, text
    creating new makefiles and folders for switching hg19 Mapability track to using metaDb
  • lines changed 1, context: html, text, full: html, text
    staging metaDb for GIS PET DNA on hgwbeta
  • lines changed 1, context: html, text, full: html, text
    enabling metadata on Gencode Genes V4 to complete staging on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencode.ra
  • lines changed 95, context: html, text, full: html, text
    enabling metadata on Gencode Genes V4 to complete staging on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisDnaPet.ra
  • lines changed 121, context: html, text, full: html, text
    staging metaDb for GIS PET DNA on hgwbeta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeMapability.ra
  • lines changed 85, context: html, text, full: html, text
    creating new makefiles and folders for switching hg19 Mapability track to using metaDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 6, context: html, text, full: html, text
    creating new makefiles and folders for switching hg19 Mapability track to using metaDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeMapability.ra
  • lines changed 85, context: html, text, full: html, text
    creating new makefiles and folders for switching hg19 Mapability track to using metaDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    more chromosomes available for haplotypeLocations track
  • lines changed 4, context: html, text, full: html, text
    override dataVersion
  • lines changed 22, context: html, text, full: html, text
    adding patch2Chain and patch2Psl tracks
  • lines changed 8, context: html, text, full: html, text
    [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation.
  • lines changed 5, context: html, text, full: html, text
    changing haplotypeLocations track to altSequence
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 6, context: html, text, full: html, text
    remove metadata from Mapabililty composite
  • lines changed 1, context: html, text, full: html, text
    Start the GIS RNA PET track
  • lines changed 144, context: html, text, full: html, text
    get wgEncodeGencode into it's own include file
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibTfbs.ra
  • lines changed 55, context: html, text, full: html, text
    Added data from subId=1848.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 28, context: html, text, full: html, text
    Changed short labels to match DNA PET and added settings for bam files
  • lines changed 5, context: html, text, full: html, text
    Changed short labels to add sh for short
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.ra
  • lines changed 142, context: html, text, full: html, text
    get wgEncodeGencode into it's own include file
  • lines changed 1, context: html, text, full: html, text
    fix up label for the 2way
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html
  • lines changed 2, context: html, text, full: html, text
    changed the cell protocols link reflect the new directory structure and made a grammar change
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 483, context: html, text, full: html, text
    Start the GIS RNA PET track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.html
  • lines changed 3, context: html, text, full: html, text
    Edit the track description according to POH and change some labels to be consistent
  • lines changed 2, context: html, text, full: html, text
    changed the cell protocols link reflect the new directory structure and made a grammar change
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
  • lines changed 15, context: html, text, full: html, text
    Edit the track description according to POH and change some labels to be consistent
• src/hg/makeDb/trackDb/human/snp131Clinical.html
  • lines changed 261, context: html, text, full: html, text
    [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation.
• src/hg/makeDb/trackDb/human/snp131NonClinical.html
  • lines changed 265, context: html, text, full: html, text
    [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Added support for new trackDb setting 'tableBrowser off' which prevents hgTables from displaying a track (if related tables need to be excluded from All Tables, they go after 'off', space-sep.
  • lines changed 61, context: html, text, full: html, text
    [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Added metaData for Uw Dnase-Seq submissions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 3372, context: html, text, full: html, text
    Added metaData for Uw Dnase-Seq submissions
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Added prelimary loaded data for UW Dnase data (Mouse)
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncodeUwDnase.ra
  • lines changed 1016, context: html, text, full: html, text
    Added prelimary loaded data for UW Dnase data (Mouse)
  • lines changed 23, context: html, text, full: html, text
    Updated Description page with blank document. Add default tracks to be viewd ( Brain tissue, Mel, ES and B Cell)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
  • lines changed 40, context: html, text, full: html, text
    Updated Description page with blank document. Add default tracks to be viewd ( Brain tissue, Mel, ES and B Cell)
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    indicated lifted from Ensembl Sscrofa9 for ensGene
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    indicate lifting ensGene from EF 2
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Added support for new trackDb setting 'tableBrowser off' which prevents hgTables from displaying a track (if related tables need to be excluded from All Tables, they go after 'off', space-sep.
  • lines changed 2, context: html, text, full: html, text
    [Genome Browser - Feature #559] Mary-Claire King's wish list: split hg19.snp131 into two tracks, one with only the SNPs marked as clinically associated by dbSNP, and the other with everything else. At Jim's request, making the clinical SNPs hidden by default, and the non-clinical visible by default to give a picture of typical human variation.
• src/hg/near/hgNear/hgNearData/S_cerevisiae/sgdAbundance.html
  • lines changed 3, context: html, text, full: html, text
    Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org.
• src/hg/near/hgNear/hgNearData/S_cerevisiae/sgdLocalization.html
  • lines changed 1, context: html, text, full: html, text
    Changed broken link yeastgfp.ucsf.edu to working link yeastgfp.yeastgenome.org.
• src/hg/overlapSelect/makefile
  • lines changed 3, context: html, text, full: html, text
    MYSQLLIBS should be on the L += line, not the MYLIBS line
• src/hg/pslCDnaFilter/makefile
  • lines changed 2, context: html, text, full: html, text
    MYSQLLIBS should be on the L += line, not the MYLIBS line
• src/hg/pslDiff/makefile
  • lines changed 2, context: html, text, full: html, text
    MYSQLLIBS should be on the L += line, not the MYLIBS line
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 15, context: html, text, full: html, text
    change code that was allocating a 13mb array on the stack to use a scratch area instead
  • lines changed 1, context: html, text, full: html, text
    oops, meant to use needLargeMem to avoid the memsettomg tp -
• src/utils/gtfToGenePred/gtfToGenePred.c
  • lines changed 6, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/utils/gtfToGenePred/tests/expected/dups.out
  • lines changed 1, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/utils/gtfToGenePred/tests/expected/ensembl.gp
  • lines changed 2, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/utils/gtfToGenePred/tests/expected/geneNameAsName2.gp
  • lines changed 2, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/utils/gtfToGenePred/tests/expected/splitStop.gp
  • lines changed 2, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/utils/gtfToGenePred/tests/input/splitStop.gtf
  • lines changed 34, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/utils/gtfToGenePred/tests/makefile
  • lines changed 18, context: html, text, full: html, text
    fix bug where insertions between multiple bases of stop codon generated incorrect frame. Provide explicit control over use of gene_id or gene_name for name2 column
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v239 preview
• src/utils/qa/weeklybld/buildZip.csh
  • lines changed 4, context: html, text, full: html, text
    Revert "fixing zip paths" This reverts commit 6b74a7dc215a8af4fe906c5101cf1b70cd65877e. Hiram requested we keep the old kent/prefix on the zip paths.
• src/utils/qa/weeklybld/makeZip.csh
  • lines changed 1, context: html, text, full: html, text
    keeping the kent/ prefix in zip paths as requested by Hiram

• lines changed: 11839
• files changed: 194