All File Changes

v268_base to v269_preview (2012-06-05 to 2012-06-12) v269

• python/lib/ucscGb/encode/mkChangeNotes.py
  • lines changed 5, context: html, text, full: html, text
    making output better to read
  • lines changed 4, context: html, text, full: html, text
    changed it so the top header will show all supplemental instead of just enw ones, same behavior as the rest of the categories
• src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrHistoneV2.daf
  • lines changed 61, context: html, text, full: html, text
    resubmission of fastq, bam files which contain errors in previous release
• src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrTfbsV2.daf
  • lines changed 59, context: html, text, full: html, text
    resubmission of fastq, bam files which contain errors in previous release
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    missing a line to strip out whitespace from a command line argument. Dunno how I didn't catch this in testing.
  • lines changed 1, context: html, text, full: html, text
    this line should skip loop iteration, not break out of the subroutine.
• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 175, context: html, text, full: html, text
    moving directory over to new name
  • lines changed 15, context: html, text, full: html, text
    adding a plain text mode
  • lines changed 5, context: html, text, full: html, text
    fixing some issues with plain text mode
  • lines changed 22, context: html, text, full: html, text
    found a python library that does what I did, so didn't need to reinvent this wheel
• src/hg/encode/getTrackReferences/makefile
  • lines changed 27, context: html, text, full: html, text
    moving directory over to new name
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 1, context: html, text, full: html, text
    Fixing stricter gcc warning: string comparison using ==.
• src/hg/encode/qaAddTrackReferences/getTrackReferences
  • lines changed 175, context: html, text, full: html, text
    renaming to getTrackReferences
  • lines changed 175, context: html, text, full: html, text
    moving directory over to new name
• src/hg/encode/qaAddTrackReferences/makefile
  • lines changed 2, context: html, text, full: html, text
    correcting the makefile for name change
  • lines changed 27, context: html, text, full: html, text
    moving directory over to new name
• src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
  • lines changed 1, context: html, text, full: html, text
    incorrect way of failover for the regex is corrected
  • lines changed 37, context: html, text, full: html, text
    reworked how the htmlStr is constructed according to Brooke's request redmine:7236
  • lines changed 175, context: html, text, full: html, text
    renaming to getTrackReferences
• src/hg/hgGene/hgGeneData/C_elegans/links.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/hgGene/hgGeneData/D_melanogaster/dm1/links.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/hgGene/hgGeneData/D_melanogaster/dm2/links.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/links.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/hgGene/hgGeneData/Zebrafish/links.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 2, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/hgGene/hgGeneData/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/hgLogin/hgLogin.c
  • lines changed 57, context: html, text, full: html, text
    Change based on code review feedback (8116) from Brian, plus restrict username length to 32 no longer than 32 characters
  • lines changed 1, context: html, text, full: html, text
    Removed commented out line '//int delay=nSec*1000;'.
• src/hg/hgSession/hgSession.c
  • lines changed 2, context: html, text, full: html, text
    Removed 'Your Account Information' heading when user is not logged in in hgSession.
• src/hg/hgTables/joining.c
  • lines changed 28, context: html, text, full: html, text
    fix fix4009 to suport All Tables
  • lines changed 8, context: html, text, full: html, text
    fixes #8148; trigger join with primary table if regions are in use but no field from primary table is in output or filter-tables
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    put Data version on separate line (see #8032)
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    inversed order of stylesheet/background for themes, added more docs
• src/hg/hgTracks/hgTracks.h
  • lines changed 8, context: html, text, full: html, text
    add another mode for highlighting for Mark and GENCODE
• src/hg/hgTracks/simpleTracks.c
  • lines changed 16, context: html, text, full: html, text
    add another mode for highlighting for Mark and GENCODE
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    change URL for IMAGE database to www.orfeomecollaboration.org
• src/hg/hgc/mgcClick.c
  • lines changed 1, context: html, text, full: html, text
    change URL for IMAGE database to www.orfeomecollaboration.org
• src/hg/hgc/pubs.c
  • lines changed 1, context: html, text, full: html, text
    bad bug in pubs details page screwed up table
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 2, context: html, text, full: html, text
    Tweak wording to be friendlier to mouse pages, by request of QA
• src/hg/htdocs/ENCODE/dataStandards.html
  • lines changed 18, context: html, text, full: html, text
    Add section for Quality Metrics page
  • lines changed 3, context: html, text, full: html, text
    Minor tweaks for usability
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 14, context: html, text, full: html, text
    Revert to prior to addition of Quality Metrics material -- this belongs on Data Standards page, not here
• src/hg/htdocs/ENCODE/qualityMetrics.html
  • lines changed 80, context: html, text, full: html, text
    Reformatting and edits for more usability (e.g. add Contents box with navigation links). Replace spreadsheet with numerous usability changes (after discussion with Mike Pazin, who created it from Anshul's)
  • lines changed 8, context: html, text, full: html, text
    Usability changes
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 2, context: html, text, full: html, text
    Fixed sample data line that was inadvertently outside of TT tag.
  • lines changed 1, context: html, text, full: html, text
    Added a colon.
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 125, context: html, text, full: html, text
    Removed old instructions in favor of links to current instructions (redmine #2511)
• src/hg/htdocs/admin/mirror.html
  • lines changed 559, context: html, text, full: html, text
    Removed old instructions in favor of links to current instructions (redmine #2511)
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    capitalizing
• src/hg/htdocs/images/Chrysemys_picta_bellii.jpg
  • lines changed 0, context: html, text, full: html, text
    photo in public domain courtesy of: U.S. Fish & Wildlife Service
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    Added new css file.
• src/hg/htdocs/style/userAccounts.css
  • lines changed 117, context: html, text, full: html, text
    Adding css for the new login, signup, etc. screens
  • lines changed 41, context: html, text, full: html, text
    Oops, removed some css at the botton that wasn't supposed to be checked it.
• src/hg/lib/cart.c
  • lines changed 28, context: html, text, full: html, text
    inversed order of stylesheet/background for themes, added more docs
  • lines changed 7, context: html, text, full: html, text
    Revert "Removing out of form input tag."
    This reverts commit 152ec1fcab421d8e4663191e9012fd28434537a3.
    
• src/hg/lib/hgFind.c
  • lines changed 8, context: html, text, full: html, text
    simplify the title line for hgGateway
• src/hg/lib/wikiLink.c
  • lines changed 19, context: html, text, full: html, text
    Change based on code review feedback (8116) from Brian, plus restrict username length to 32 no longer than 32 characters
• src/hg/makeDb/doc/bosTau6.txt
  • lines changed 42, context: html, text, full: html, text
    bosTau6 to bosTau4, 5 and 7 LIFTOVER.
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 10, context: html, text, full: html, text
    Document using new makeGenomeDb.pl to generate description.html.
• src/hg/makeDb/doc/choHof1.txt
  • lines changed 67, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/chrPic1.txt
  • lines changed 31, context: html, text, full: html, text
    add photo and fix search rule for assembly track/gold table
• src/hg/makeDb/doc/danRer3.txt
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release2.notes
  • lines changed 6, context: html, text, full: html, text
    updating notes files
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release3.notes
  • lines changed 0, context: html, text, full: html, text
    First draft of notes file
  • lines changed 2437, context: html, text, full: html, text
    Un-atticed the revoked files so that I caould finally generate a working notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhHistone.release3.notes
  • lines changed 42, context: html, text, full: html, text
    Added 2 experiments that were missing before. Updated release notes and matrix ordering to not include numbers. Redmine #7510
• src/hg/makeDb/doc/eriEur1.txt
  • lines changed 65, context: html, text, full: html, text
    completed with genbank run and loading
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 91, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 29, context: html, text, full: html, text
    fixup search rule for assembly track/gold table
• src/hg/makeDb/doc/melUnd1.txt
  • lines changed 91, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/micMur1.txt
  • lines changed 90, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/oreNil2.txt
  • lines changed 92, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/proCap1.txt
  • lines changed 90, context: html, text, full: html, text
    finished with genbank run
• src/hg/makeDb/doc/pteVam1.txt
  • lines changed 89, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/rn5.txt
  • lines changed 27, context: html, text, full: html, text
    fixup search rule for assembly track/gold table
• src/hg/makeDb/doc/speTri2.txt
  • lines changed 90, context: html, text, full: html, text
    done with genbank run
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
  • lines changed 70, context: html, text, full: html, text
    most everything is done. Time to churn!
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    adding melUnd1 to the daily builds
  • lines changed 1, context: html, text, full: html, text
    Added eriEur1.
  • lines changed 1, context: html, text, full: html, text
    Added choHof1.
  • lines changed 1, context: html, text, full: html, text
    Added gadMor1.
  • lines changed 1, context: html, text, full: html, text
    Added oreNil2.
  • lines changed 1, context: html, text, full: html, text
    Added micMur1.
  • lines changed 1, context: html, text, full: html, text
    Added speTri2.
  • lines changed 1, context: html, text, full: html, text
    Added pteVam1.
  • lines changed 1, context: html, text, full: html, text
    Added proCap1.
  • lines changed 1, context: html, text, full: html, text
    Added ochPri2.
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 31, context: html, text, full: html, text
    add script to copy to euronode. This is run from the genbank user's crontab on euronode
• src/hg/makeDb/genbank/etc/euronode-dbload
  • lines changed 23, context: html, text, full: html, text
    euronode dbload script, and genbank crontab on euronode
• src/hg/makeDb/genbank/etc/euronode.crontab
  • lines changed 26, context: html, text, full: html, text
    euronode dbload script, and genbank crontab on euronode
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    add ooc file for tenrec/echTel1
  • lines changed 2, context: html, text, full: html, text
    turn off genbank.mrna.native.load and genbank.mrna.xeno.load for vicPac1
• src/hg/makeDb/genbank/etc/hgnfs1-copy
  • lines changed 1, context: html, text, full: html, text
    changed genbank-10 to hgwdev cuz genbank-10 no longer exists
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 4, context: html, text, full: html, text
    Added bosTau7, chrPic1, galGal4 and rn5 (redmine #251, #6044, #6718, #7269)
  • lines changed 1, context: html, text, full: html, text
    added new canFam3 assembly
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    adding melUnd1 to the daily builds
  • lines changed 1, context: html, text, full: html, text
    Added eriEur1.
  • lines changed 1, context: html, text, full: html, text
    Added choHof1.
  • lines changed 1, context: html, text, full: html, text
    Added gadMor1.
  • lines changed 1, context: html, text, full: html, text
    Added oreNil2.
  • lines changed 1, context: html, text, full: html, text
    Added micMur1.
  • lines changed 1, context: html, text, full: html, text
    Added speTri2.
  • lines changed 1, context: html, text, full: html, text
    Added pteVam1.
  • lines changed 1, context: html, text, full: html, text
    Added proCap1.
  • lines changed 1, context: html, text, full: html, text
    Added ochPri2.
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 4, context: html, text, full: html, text
    Added bosTau7, chrPic1, galGal4 and rn5 (redmine #251, #6044, #6718, #7269)
• src/hg/makeDb/genbank/src/dbload/gbMDParse.c
  • lines changed 2, context: html, text, full: html, text
    parse mdiff records where the numbers start with ">"
• src/hg/makeDb/trackDb/apis/apiMel2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/makeDb/trackDb/chicken/galGal4/description.html
  • lines changed 116, context: html, text, full: html, text
    new auto-generated with new variables
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Made changes to alter the default genome location and default track settings for chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
  • lines changed 6, context: html, text, full: html, text
    add search rule for gold table
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
  • lines changed 117, context: html, text, full: html, text
    New descrition.html generated automatically by new makeGenomeDb.pl.
• src/hg/makeDb/trackDb/cow/bosTau7/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    Set the serach term for gold and ctgPos2 tables.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 33, context: html, text, full: html, text
    Adding epithelium comments to CV
  • lines changed 6, context: html, text, full: html, text
    Updated descriptions for some views, provided by transcriptome group.
  • lines changed 42, context: html, text, full: html, text
    Fixed biochain links, H1-hESC order link and ZNF263 order link.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 338, context: html, text, full: html, text
    Updating beta CV
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 48, context: html, text, full: html, text
    auto-generated minimal gateway page
• src/hg/makeDb/trackDb/drosophila/dp1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 39, context: html, text, full: html, text
    Updating dateUnrestricted
  • lines changed 37, context: html, text, full: html, text
    updating dateUnrestricted
  • lines changed 4, context: html, text, full: html, text
    Renaming a file to V2
  • lines changed 53, context: html, text, full: html, text
    Removing two stanzas
  • lines changed 3, context: html, text, full: html, text
    Un-atticed the revoked files so that I caould finally generate a working notes file
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 202, context: html, text, full: html, text
    md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 293, context: html, text, full: html, text
    Added 2 experiments that were missing before. Updated release notes and matrix ordering to not include numbers. Redmine #7510
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 105, context: html, text, full: html, text
    adding in missing controls
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhHistone.ra
  • lines changed 1239, context: html, text, full: html, text
    staging SYDH Histone (Release3) on beta, redmine# 7510
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 3926, context: html, text, full: html, text
    Staging Uw DNaseI HS (Release 5) on beta, redmine #6807
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging Uw DNaseI HS (Release 5) on beta, redmine #6807
  • lines changed 2, context: html, text, full: html, text
    starting release 3 for us affy exon redmine:6777
  • lines changed 1, context: html, text, full: html, text
    correcting spelling error
  • lines changed 1, context: html, text, full: html, text
    forgot to change this over to release 5
  • lines changed 2, context: html, text, full: html, text
    staging SYDH Histone (Release3) on beta, redmine# 7510
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 28, context: html, text, full: html, text
    accidently over wrote Katrina's version with a bad checkin, reverting.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 2, context: html, text, full: html, text
    Fixed some grammar issues on the description page for CSHL Long, redmine# 5698
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 1, context: html, text, full: html, text
    lowered maxWindow to 100k bases, 1 million was getting memory errors
  • lines changed 5, context: html, text, full: html, text
    Cahnging defaults
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 682, context: html, text, full: html, text
    Trying to group the exp 1090 and 1740 so we can track what happened
  • lines changed 137, context: html, text, full: html, text
    Short labels
  • lines changed 2, context: html, text, full: html, text
    Renaming a file to V2
  • lines changed 522, context: html, text, full: html, text
    Adding protocols to short label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 74, context: html, text, full: html, text
    fixing haib methyl array's tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.release3.ra
  • lines changed 188, context: html, text, full: html, text
    Changing the tags and promoting the TIER 2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 30, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
  • lines changed 5, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 1048, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 141, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.ra
  • lines changed 1847, context: html, text, full: html, text
    starting new release trackDbs for uw hsitone and open chrom dnase
  • lines changed 204, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
  • lines changed 76, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
  • lines changed 17, context: html, text, full: html, text
    correcting the tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.ra
  • lines changed 468, context: html, text, full: html, text
    correcting tags on riken cage for cricket
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.html
  • lines changed 1, context: html, text, full: html, text
    Added 2 experiments that were missing before. Updated release notes and matrix ordering to not include numbers. Redmine #7510
  • lines changed 2, context: html, text, full: html, text
    Fixed errant space in Peggy Farnham email address. Redmine #7510.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra
  • lines changed 88, context: html, text, full: html, text
    Added 2 experiments that were missing before. Updated release notes and matrix ordering to not include numbers. Redmine #7510
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra
  • lines changed 63, context: html, text, full: html, text
    Changing the tags on Uchicago
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra
  • lines changed 1474, context: html, text, full: html, text
    starting release 3 for us affy exon redmine:6777
  • lines changed 159, context: html, text, full: html, text
    correcting tags for uwAffyEcon release 3
  • lines changed 164, context: html, text, full: html, text
    there was a tag error due to metadata in the cell subgroup, corrected now
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.ra
  • lines changed 193, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.html
  • lines changed 14, context: html, text, full: html, text
    removed message that no longer applies
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.ra
  • lines changed 1, context: html, text, full: html, text
    changing viewlimits to 1:10 for Raw
  • lines changed 2, context: html, text, full: html, text
    changing the scorefilter to mathc the range of the data:
  • lines changed 625, context: html, text, full: html, text
    correcting the cell tier tags in UwDnase release 5
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
  • lines changed 6293, context: html, text, full: html, text
    removing patch, changes will go out in release5
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release5.ra
  • lines changed 6299, context: html, text, full: html, text
    starting new release trackDbs for uw hsitone and open chrom dnase
  • lines changed 724, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release4.ra
  • lines changed 373, context: html, text, full: html, text
    correcting my tracks on alpha tags
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 2, context: html, text, full: html, text
    turning on summary and frames
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 27, context: html, text, full: html, text
    Added in missing file and meta-data for Signal Rep2 of MEL. Redmine #829.
  • lines changed 65, context: html, text, full: html, text
    update expId
  • lines changed 33, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 1, context: html, text, full: html, text
    add treatment in the top stanza
  • lines changed 277, context: html, text, full: html, text
    hmmm, I think it is the update after the addition of treatment, should have done the commit right away
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 50, context: html, text, full: html, text
    moving mapability over to it's own ra for moving to encode
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeMapability.ra
  • lines changed 50, context: html, text, full: html, text
    moving mapability over to it's own ra for moving to encode
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 184, context: html, text, full: html, text
    cleaned up labels
  • lines changed 6, context: html, text, full: html, text
    remove sort by sex, set default display subtracks
  • lines changed 4, context: html, text, full: html, text
    remove Unknown from long label of MEL subtracks
  • lines changed 1, context: html, text, full: html, text
    added html entry on top stanza
  • lines changed 22, context: html, text, full: html, text
    add Cel and Str to cellType, strain names starts with numbers
  • lines changed 19, context: html, text, full: html, text
    setting default display for different views
  • lines changed 2, context: html, text, full: html, text
    set initial default display of different views
• src/hg/makeDb/trackDb/orfeomeMrna.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to ORFeome Collaboration site (redmine #11)
• src/hg/makeDb/trackDb/rat/rn5/description.html
  • lines changed 47, context: html, text, full: html, text
    new minimalist gateway page and adding chainNet override for Mm10
• src/hg/makeDb/trackDb/rat/rn5/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    new minimalist gateway page and adding chainNet override for Mm10
  • lines changed 1, context: html, text, full: html, text
    Made changes to alter the default genome location and default track settings for chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    new minimalist gateway page and adding chainNet override for Mm10
  • lines changed 5, context: html, text, full: html, text
    Made changes to alter the default genome location and default track settings for chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
  • lines changed 6, context: html, text, full: html, text
    adding search rule for assembly track/gold table
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/makeDb/trackDb/tenrec/echTel1/description.html
  • lines changed 21, context: html, text, full: html, text
    remove description to get a new one
  • lines changed 62, context: html, text, full: html, text
    new minimal description page
• src/hg/makeDb/trackDb/tenrec/echTel1/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Made changes to alter the default genome location and default track settings for chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/tenrec/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    need searchMethod prefix to get the option of .#s
• src/hg/makeDb/trackDb/turtle/chrPic1/description.html
  • lines changed 119, context: html, text, full: html, text
    auto-constructed gateway page
• src/hg/makeDb/trackDb/turtle/chrPic1/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Made changes to alter the default genome location and default track settings for chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/turtle/chrPic1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Made changes to alter the default genome location and default track settings for chrPic1 (redmine #6718), echTel1 (redmine #7671), galGal4 (redmine #251) and rn5 (redmine #7269)
• src/hg/makeDb/trackDb/turtle/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    add search rule for gold table
  • lines changed 3, context: html, text, full: html, text
    correct searching prefix for gold frag names
• src/hg/near/hgNear/hgNearData/Rat/rn4/columnDb.ra
  • lines changed 2, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/near/hgNear/hgNearData/columnDb.ra
  • lines changed 2, context: html, text, full: html, text
    Replaced old link to Genbank with new link (redmine #11)
• src/hg/utils/automation/configFiles/README
  • lines changed 6, context: html, text, full: html, text
    starting this directory, first one in is rn5 from 2012-06-06
• src/hg/utils/automation/configFiles/bosTau7.config.ra
  • lines changed 23, context: html, text, full: html, text
    Initial makeDbGenome bosTau7 config.ra file.
  • lines changed 1, context: html, text, full: html, text
    New descrition.html generated automatically by new makeGenomeDb.pl.
• src/hg/utils/automation/configFiles/canFam3.config.ra
  • lines changed 22, context: html, text, full: html, text
    copy from 2012-06-11 to make gateway page
• src/hg/utils/automation/configFiles/chrPic1.config.ra
  • lines changed 24, context: html, text, full: html, text
    file used on 2012-06-07 to construct gateway page
• src/hg/utils/automation/configFiles/echTel1.config.ra
  • lines changed 22, context: html, text, full: html, text
    very old assembly, very new config file constructed 2012-06-06
• src/hg/utils/automation/configFiles/galGal4.config.ra
  • lines changed 23, context: html, text, full: html, text
    completed file with extra new fields 2012-06-06
• src/hg/utils/automation/configFiles/rn5.config.ra
  • lines changed 22, context: html, text, full: html, text
    starting this directory, first one in is rn5 from 2012-06-06
• src/hg/utils/automation/configFiles/sarHar1.config.ra
  • lines changed 22, context: html, text, full: html, text
    Use new description.html format for sarHar1.
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 152, context: html, text, full: html, text
    implementing the new and improved minimal gateway html page
  • lines changed 9, context: html, text, full: html, text
    add a forceDescription to avoid problems when already exists
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v269 preview1

• lines changed: 35670
• files changed: 215