All File Changes

v263_base to v264_preview (2012-02-14 to 2012-02-21) v264

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 1, context: html, text, full: html, text
    forgot to also remove revoked tables from the change table status set, possibly need to remove attic, but i'll do it if the problem comes up
  • lines changed 17, context: html, text, full: html, text
    changed the reporting of changed tables state to be a critical error
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Updating the DAF
• src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Updated daf to use new type document instead of doc. Redmine #6626.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibMethylWgbs.daf
  • lines changed 38, context: html, text, full: html, text
    Adding a daf for new file
  • lines changed 2, context: html, text, full: html, text
    Correcting the CpG to CpGSites for clarity
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUncBsuProt.daf
  • lines changed 9, context: html, text, full: html, text
    Getting submission 5558 in and adding the structure for a new view
• src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDgf.daf
  • lines changed 4, context: html, text, full: html, text
    Added treatment as a variable. Redmine #3631.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeUwDnase.daf
  • lines changed 4, context: html, text, full: html, text
    Added treatment to list of variables. Redmine #4468.
• src/hg/encode/encodeExp/tests/expected/modifyTest.out.ra
  • lines changed 1, context: html, text, full: html, text
    Allow changing expVars that are not CV defined
• src/hg/encode/encodeExp/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    Allow changing expVars that are not CV defined
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 2, context: html, text, full: html, text
    the threading of the md5sums was causing problems with the database objects not being able to be clones, so i dosconnect fom the database, then reconnect after making the md5sums
  • lines changed 70, context: html, text, full: html, text
    changed the gzip md5sum function to check internally for the contents, but report the external md5sum to the metaDb
• src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
  • lines changed 2, context: html, text, full: html, text
    changed it to show the server and foldername onthe same line
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 10, context: html, text, full: html, text
    changed it to complain and die upon subId setting to reviewing failure
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 6, context: html, text, full: html, text
    Added information about new field platform that is needed for microarray platforms. Redmine #6626.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    We do not allow .doc because they are proprietary, I think that this was meant to mean type document (generic), but it was being interpreted and used to submit Word doc. So I am changing it to pdf. We may need to change it back or come up with something for none pdf documents.
  • lines changed 5, context: html, text, full: html, text
    Changed type doc to spell full document since doc was getting confused with MS doc format. Also changed type pdf back to document that was done in commit: 09a85f5ed26fcf2664db8e887fd1268e7d3627af.
• src/hg/encode/qaAddTrackReferences/makefile
  • lines changed 28, context: html, text, full: html, text
    first draft of qaAddTrackReferences
• src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
  • lines changed 423, context: html, text, full: html, text
    first draft of qaAddTrackReferences
  • lines changed 60, context: html, text, full: html, text
    removed unnecessary lines
  • lines changed 17, context: html, text, full: html, text
    changed how collective name is put in the author list. It's always put at the front now.
• src/hg/encode/qaEncodeTracks2/qaEncodeTracks
  • lines changed 8, context: html, text, full: html, text
    uncomment parser line, and reomved Test \d: from test names
• src/hg/hgGene/hgGeneData/Rat/rn4/links.ra
  • lines changed 7, context: html, text, full: html, text
    try a different select rule to get other organisms blast tabs
• src/hg/hgGene/rgdInfo.c
  • lines changed 1, context: html, text, full: html, text
    genes_rat table is now rgdGene2Raw
• src/hg/hgTables/bigWig.c
  • lines changed 14, context: html, text, full: html, text
    Fixing bug in min/max logic where min/max was just taken from first region.
• src/hg/hgTables/wiggle.c
  • lines changed 4, context: html, text, full: html, text
    make sure we get the right trackDb entry for the current table when we're getting statistics. #7047
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    Changes that Brian made for finding track handlers closest to home, uncovered a dormant bug which had been masked by a dangerous method of swapping parent and child structs. This newly uncovered bug was due to referring to a track type of 'bedFloatScoreWithFdr' when it should have been 'bed5FloatScoreWithFdr'. The result of this uncovered bug is that the TrackCheck robot failed on hg17 and hg18 as described in redmine 6783 note 4. This fix is a candidate for patching.
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    redmine Bug #7026 Gene Reviews hgc page has needless long line of hyphens.
• src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
  • lines changed 17, context: html, text, full: html, text
    1. Add crosshair hover effect on matrix. Break out functions for readability (thanks to Teresa for code review).
  • lines changed 36, context: html, text, full: html, text
    Layout fixes, especially for IE. Dynamically size row and column headers. Use jQuery cell rotate on headers to achieve vertical text (required for IE, doesn't harm others). Cleanup css with shortcuts.
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 1, context: html, text, full: html, text
    Layout fixes, especially for IE. Dynamically size row and column headers. Use jQuery cell rotate on headers to achieve vertical text (required for IE, doesn't harm others). Cleanup css with shortcuts.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    Added section for UW Repli-seq (redmine #4577)
• src/hg/htdocs/ENCODE/experiment_guidelines.html
  • lines changed 2, context: html, text, full: html, text
    Quarterly ENCODE portal update (redmine #6870)
• src/hg/htdocs/ENCODE/platform_characterization.html
  • lines changed 18, context: html, text, full: html, text
    Quarterly ENCODE portal update (redmine #6870)
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 2, context: html, text, full: html, text
    Quarterly ENCODE portal update (redmine #6870)
  • lines changed 2, context: html, text, full: html, text
    Re-inserted 'ENCODE Project Consortium' into authors list (redmine #6870)
  • lines changed 1, context: html, text, full: html, text
    Added period to end of author list
  • lines changed 1, context: html, text, full: html, text
    Updated date
• src/hg/htdocs/ENCODE/terms.html
  • lines changed 16, context: html, text, full: html, text
    Quarterly ENCODE portal update (redmine #6870)
  • lines changed 2, context: html, text, full: html, text
    Made link open in new window
  • lines changed 3, context: html, text, full: html, text
    Re-inserted 'ENCODE Project Consortium' into authors list (redmine #6870)
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 6, context: html, text, full: html, text
    updated group track line text to provide more useful information; per redmine #6958
• src/hg/htdocs/robots.rr.txt
  • lines changed 16, context: html, text, full: html, text
    Jorge edited the RR version to disallow msnbot, and to clean up the cgi-bin entries (collapse down into one).
• src/hg/js/encodeDataMatrix.js
  • lines changed 159, context: html, text, full: html, text
    1. Add crosshair hover effect on matrix. Break out functions for readability (thanks to Teresa for code review).
  • lines changed 39, context: html, text, full: html, text
    Layout fixes, especially for IE. Dynamically size row and column headers. Use jQuery cell rotate on headers to achieve vertical text (required for IE, doesn't harm others). Cleanup css with shortcuts.
  • lines changed 9, context: html, text, full: html, text
    Cripple for IE (floating header, crosshair effect)
• src/hg/js/hui.js
  • lines changed 7, context: html, text, full: html, text
    Further tighten the screws on matrix checkboxes. ABC checkboxes will go to the cart but XY CBs should not. Since ABC CBs will get marked 'changed', then class accounting must exclude 'changed' class. This and last subCfg.js checkin are for redmine 7015
• src/hg/js/jquery.rotateTableCellContent.js
  • lines changed 32, context: html, text, full: html, text
    Layout fixes, especially for IE. Dynamically size row and column headers. Use jQuery cell rotate on headers to achieve vertical text (required for IE, doesn't harm others). Cleanup css with shortcuts.
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    clean up for use with htdocs-<user> (thanks larrym)
• src/hg/js/subCfg.js
  • lines changed 3, context: html, text, full: html, text
    Matrix checkboxes were being marked with changed class which screws up class accounting in hui.js.
  • lines changed 2, context: html, text, full: html, text
    Further tighten the screws on matrix checkboxes. ABC checkboxes will go to the cart but XY CBs should not. Since ABC CBs will get marked 'changed', then class accounting must exclude 'changed' class. This and last subCfg.js checkin are for redmine 7015
• src/hg/lib/encode/encodeExp.c
  • lines changed 7, context: html, text, full: html, text
    Allow changing expVars that are not CV defined
• src/hg/lib/kgXrefPrevious.sql
  • lines changed 22, context: html, text, full: html, text
    to supply a description for rn4 table kgXrefPrevious
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShortRnaSeq.release2.notes
  • lines changed 304, context: html, text, full: html, text
    New release notes adding the protocol docs
  • lines changed 308, context: html, text, full: html, text
    A better notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release2.notes
  • lines changed 135, context: html, text, full: html, text
    updated notes again
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUmassDekker5C.release1.notes
  • lines changed 115, context: html, text, full: html, text
    Added release1 notes for track. Redmine #225.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release3.notes
  • lines changed 30, context: html, text, full: html, text
    corrected notes, last time was premature
• src/hg/makeDb/doc/sarHar1.txt
  • lines changed 515, context: html, text, full: html, text
    Finished mask, genbank, cpgIsland. blat server tasks
• src/hg/makeDb/hgLoadWiggle/hgWiggle.c
  • lines changed 5, context: html, text, full: html, text
    add warning about 0-relative output vs. 1-relative output
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Add 44 databases to tRNAsDbs list in all.joiner
  • lines changed 1, context: html, text, full: html, text
    Added a check for kgXrefOld5 to the knownGeneOld5 identifier.
  • lines changed 4, context: html, text, full: html, text
    Revising the rules connecting the tRNAs track with the kgXref table, given the wise advice of Goddess Brooke
  • lines changed 5, context: html, text, full: html, text
    Add sarHar1 to all.joiner
  • lines changed 5, context: html, text, full: html, text
    adding identifier rn4KgPrevious as rn4 knownGene becomes knownGenePrevious
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 16, context: html, text, full: html, text
    added in provisional views for haib Bisulfite
  • lines changed 19, context: html, text, full: html, text
    Adding the terms for the WGBS track
  • lines changed 2, context: html, text, full: html, text
    for the merge
  • lines changed 16, context: html, text, full: html, text
    removing temporary provisional views
  • lines changed 2, context: html, text, full: html, text
    Correcting the CpG to CpGSites for clarity
  • lines changed 1, context: html, text, full: html, text
    changing tag to conform to norm
  • lines changed 9, context: html, text, full: html, text
    Fixes for some typos in the CV
  • lines changed 16, context: html, text, full: html, text
    Adding missing references to RefSeq for some antibodies
  • lines changed 30, context: html, text, full: html, text
    Minor CV edits
  • lines changed 95, context: html, text, full: html, text
    added in antibody target to the decsription field (Willy)
  • lines changed 1, context: html, text, full: html, text
    Fix capitalization inconsistency in datatype label
  • lines changed 7, context: html, text, full: html, text
    Adding and fixing terms for the Proteogenomics group
  • lines changed 74, context: html, text, full: html, text
    Fixes found during code review. Redmine #6966.
  • lines changed 2, context: html, text, full: html, text
    Fixed labeling for eGFP-JunB and eGFP-JunD.
  • lines changed 20, context: html, text, full: html, text
    Added labels for Mouse tissues that have trucated terms. Also fixed some provisional labels and moved a comment to the end of a stanza.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 709, context: html, text, full: html, text
    Moved over approved changes from beta/cv.ra to public/cv.ra. Redmine #6966.
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/dog/canFam3/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/dog/canFam3/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.html
  • lines changed 7, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 4, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDNAseSuper.html
  • lines changed 5, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDnaMethylSuper.html
  • lines changed 4, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.html
  • lines changed 7, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 3, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeExonArraySuper.html
  • lines changed 5, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHistoneSuper.html
  • lines changed 5, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html
  • lines changed 6, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 3, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • lines changed 7, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 3, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRnaSeqSuper.html
  • lines changed 4, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRnaSubcellLocSuper.html
  • lines changed 5, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeTfBindingSuper.html
  • lines changed 5, context: html, text, full: html, text
    Made links to genome.ucsc.edu and hgwdev.cse.ucsc.edu into relative links (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 687, context: html, text, full: html, text
    correcting for the gzip bug error in mkFilesList
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 276, context: html, text, full: html, text
    Adding the V2 files for the bedRnaElements files that had . in the score
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 2159, context: html, text, full: html, text
    Adding protocols and fixing the trackDb to have new defualts and to have filterComposite
  • lines changed 699, context: html, text, full: html, text
    Removing release 3 protocols, adding one more release 1
  • lines changed 10, context: html, text, full: html, text
    Adding a missing md5sum
  • lines changed 145, context: html, text, full: html, text
    more internal gzip bug fixes
  • lines changed 101, context: html, text, full: html, text
    Adding missing readType and origAssembly
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibBisulfate.ra
  • lines changed 115, context: html, text, full: html, text
    added in provisional views for haib Bisulfite
  • lines changed 157, context: html, text, full: html, text
    more fake stanzas
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 21, context: html, text, full: html, text
    expIds and accessions for rna seq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 9, context: html, text, full: html, text
    some merge problem needs this
  • lines changed 9, context: html, text, full: html, text
    more lab found errors
  • lines changed 21, context: html, text, full: html, text
    renaming some files before they are released
  • lines changed 9, context: html, text, full: html, text
    reverted a metaDB change, becuase hte objects already went out in release 1
  • lines changed 191, context: html, text, full: html, text
    renamed objects to now have antibody vendor id
  • lines changed 183, context: html, text, full: html, text
    added in FoxM1 experiment
  • lines changed 17, context: html, text, full: html, text
    added in md5sums
  • lines changed 37, context: html, text, full: html, text
    expIds for haib
  • lines changed 1076, context: html, text, full: html, text
    more internal gzip bug fixes
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 113, context: html, text, full: html, text
    md5sums for open chrom dnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
  • lines changed 139, context: html, text, full: html, text
    Added md5sum's, expId's and DCCaccession numbers. Redmine #225.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 24, context: html, text, full: html, text
    Getting submission 5558 in and adding the structure for a new view
  • lines changed 20, context: html, text, full: html, text
    Trying to add bigBeds, but having issues. Checking it in for others to work on
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 98, context: html, text, full: html, text
    correcting for the gzip bug error in mkFilesList
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 271, context: html, text, full: html, text
    expIds and other mdb fixes
  • lines changed 3, context: html, text, full: html, text
    more metadata corrections
  • lines changed 627, context: html, text, full: html, text
    fixed internal gzip md5sum
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
  • lines changed 353, context: html, text, full: html, text
    Replaced the Freeze date from 'post ENCODE Jan 2011 Freeze' to 'ENCODE Mar 2012 Freeze'. Redmine #4577, #6581.
  • lines changed 23, context: html, text, full: html, text
    Fixed issues found in Redmine #4577 20. Updated pixcel heigh to default to 64 to make viewing data more reasonable 21. Removed sex for BGO2ES cell line as it is stated in the cv.ra
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 409, context: html, text, full: html, text
    more internal gzip bug fixes
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 8939, context: html, text, full: html, text
    Staging CSHL Sm RNA-seq (Release 2) on beta (redmine #1634)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
  • lines changed 4032, context: html, text, full: html, text
    Staging UW Histone (Release 3) on beta (redmine #6324)
  • lines changed 271, context: html, text, full: html, text
    Matt made changes to the metadata (redmine #6324)
  • lines changed 627, context: html, text, full: html, text
    Matt made some changes to the metadata (redmine #6324)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwRepliSeq.ra
  • lines changed 353, context: html, text, full: html, text
    Venkat edited the freeze data (redmine #4577)
  • lines changed 23, context: html, text, full: html, text
    Venkat removed 'sex' from BG02ES cell line metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Releasing UW Repli-seq to RR (redmine #4577)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwHistone.ra
  • lines changed 3998, context: html, text, full: html, text
    Releasing UW Histone (Release 3) to RR (redmine #6324)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwRepliSeq.ra
  • lines changed 7933, context: html, text, full: html, text
    Venkat removed 'sex' from BG02ES cell line metadata
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Releasing UW Repli-seq to RR (redmine #4577)
  • lines changed 2, context: html, text, full: html, text
    added in the rest of the bisulfate test track
  • lines changed 1, context: html, text, full: html, text
    forgot alpha tag
  • lines changed 2, context: html, text, full: html, text
    Staging UW Histone (Release 3) on beta (redmine #6324)
  • lines changed 2, context: html, text, full: html, text
    Staging CSHL Sm RNA-seq (Release 2) on beta (redmine #1634)
  • lines changed 2, context: html, text, full: html, text
    Releasing UW Histone (Release 3) to RR (redmine #6324)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
  • lines changed 3, context: html, text, full: html, text
    Added some information and removed 2 sentences from the 5C description section. Redmine #2606.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 4, context: html, text, full: html, text
    Changing links to be relative
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 205, context: html, text, full: html, text
    Adding the V2 files for the bedRnaElements files that had . in the score
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html
  • lines changed 138, context: html, text, full: html, text
    This file was replaced a long time ago with .release2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html
  • lines changed 4, context: html, text, full: html, text
    Changing links to be relative
  • lines changed 2, context: html, text, full: html, text
    Some html changes for Jacob, cleaning up some metaData to be consistent.
  • lines changed 14, context: html, text, full: html, text
    http://redmine.soe.ucsc.edu/issues/1634#note-111, A bunch of html
  • lines changed 9, context: html, text, full: html, text
    Adding references
  • lines changed 3, context: html, text, full: html, text
    Changed the release policy
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Some html changes for Jacob, cleaning up some metaData to be consistent.
  • lines changed 53, context: html, text, full: html, text
    Adding protocols and fixing the trackDb to have new defualts and to have filterComposite
  • lines changed 204, context: html, text, full: html, text
    Changing the tags back to starting with 1 and 2 because a and b did not work as expected
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
  • lines changed 19, context: html, text, full: html, text
    capitlizing bulleted sentences with a period at the end per Steve's code review; also decided to remove periods from other bulleted lists that weren't full sentences, redmine 6971
  • lines changed 3, context: html, text, full: html, text
    adding target=_blank to biotype links since they are external per Steve's code review, redmine 6971
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.html
  • lines changed 125, context: html, text, full: html, text
    added in the rest of the bisulfate test track
  • lines changed 74, context: html, text, full: html, text
    flo's version of haib bisulfate
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibBisulfate.ra
  • lines changed 84, context: html, text, full: html, text
    added in the rest of the bisulfate test track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
  • lines changed 41, context: html, text, full: html, text
    pre=qa fixes and reformed references
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    changed view limit according to lab
  • lines changed 47, context: html, text, full: html, text
    changed short labels according to lab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 8, context: html, text, full: html, text
    renaming some files before they are released
  • lines changed 64, context: html, text, full: html, text
    renamed objects to now have antibody vendor id
  • lines changed 45, context: html, text, full: html, text
    added in FoxM1 experiment
  • lines changed 1, context: html, text, full: html, text
    changed filter to all for treatment
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 7, context: html, text, full: html, text
    Made relative links to hgdownload (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, the reference to jquery was already included and the second reference caused problems. Removed this reference (redmine #6930)
  • lines changed 2, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
  • lines changed 8, context: html, text, full: html, text
    Made relative links to hgdownload (redmine #6526)
  • lines changed 1, context: html, text, full: html, text
    Per Tim, the reference to jquery was already included and the second reference caused problems. Removed this reference (redmine #6930)
  • lines changed 3, context: html, text, full: html, text
    Per Tim, removed all jquery.js references and all head tags from non-supertracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html
  • lines changed 103, context: html, text, full: html, text
    Updated track description. Redmine #225.
  • lines changed 16, context: html, text, full: html, text
    Fixes track description errors found in Redmine #225 1) Made new sentence after phrase and added comma "however users..." 2) Removed comma in phrase ", by using the built in" 3) Changed "built in" -> "built-in" 4) Removed comma in phrase "strength, with" 5) Changed sentence "Sequencing files are provided in fastQ format" -> "Sequencing files provided in fastQ format" 6) Removed acrynym in 2nd pharagraph and added in first of Methods "transcription start site (TSS)" 7) Changed "transcription start (TSS)" -> "TSS" in 2nd pharagraph of methods 8) Removed "(Tm)" 9) Added comma after Currently in phrase "Currently data" 10) Added Oxford comma in phrase " and H1 human embryonic" 11) Placed html tage for special character in 1st reference 12) Changed "using 5C" -> "using the 5C" 13) Changed "These tracks show" -> "This track shows" 14) Changed "Does not function in a linear fashion" -> "Does not function linearly" 15) Changed "To dramatically increase the 3C throughput, the 5C method was developed" -> "The 5C method was developed to dramatically increase 3C throughput" 16) Changed "The major advantage of LMA is that it can be performed at a very high level of multiplexing using" -> "LMA is advantageous due to a much higher level of multiplexing by using" 17) Changed "correspond precisely" -> "precisely correspond"
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
  • lines changed 5, context: html, text, full: html, text
    Updated long labels and removed extra visibility setting. Redmine #225.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra
  • lines changed 47, context: html, text, full: html, text
    Getting submission 5558 in and adding the structure for a new view
  • lines changed 14, context: html, text, full: html, text
    Trying to add bigBeds, but having issues. Checking it in for others to work on
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html
  • lines changed 1, context: html, text, full: html, text
    fixed tense
  • lines changed 17, context: html, text, full: html, text
    fixed html and order of cells in list
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
  • lines changed 42, context: html, text, full: html, text
    I have no idea how that one got commented out
  • lines changed 1, context: html, text, full: html, text
    fixed html and order of cells in list
  • lines changed 2, context: html, text, full: html, text
    fixed alphabetization
  • lines changed 1, context: html, text, full: html, text
    this time for real on alphabetize
  • lines changed 1, context: html, text, full: html, text
    fixed capitalization
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed issues found in Redmine #4577 20. Updated pixcel heigh to default to 64 to make viewing data more reasonable 21. Removed sex for BGO2ES cell line as it is stated in the cv.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.html
  • lines changed 3, context: html, text, full: html, text
    pre-qa fixes
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding canFam3 to the build
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Removed Strain as an expVar since it is not being varried on. Redmine #5986.
  • lines changed 477, context: html, text, full: html, text
    Addeded expIds and accessions for track. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 57, context: html, text, full: html, text
    Loaded updated versions of the bam files that were colliding. Updated objStatus on V1 of data. Redmine #5393, note #2. #4931.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 141, context: html, text, full: html, text
    Loaded updated versions of the bam files that were colliding. Updated objStatus on V1 of data. Redmine #5394, note #2. #4931.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 7, context: html, text, full: html, text
    Replaced experiment wgEncodeEM001962 with new version using a Std control. Redmine #5397.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    Removed MS-DOS CRLF line terminators.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    Changed hard link to supplementary from hgdownload to hgdownload-test and from hg19 to mm9. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
  • lines changed 31, context: html, text, full: html, text
    Set default tissues on to be Genital FatPat, Heart, Kidney, Ovary, Spleen and Testis. Redmine #5986.
  • lines changed 3, context: html, text, full: html, text
    Fixed dimensions to have cellType on X-axis. Removed age from sortOrder and fileSortOrder. Correct replicate label in fileSortOrder to be just Replicate since we only have UCSC Replicate in metaDb and not UCSC Replicate. Redmine ##5986.
  • lines changed 243, context: html, text, full: html, text
    Updated long and short labels to follow naming conventions. Used conventions from Human track. Redmine #5986.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.ra
  • lines changed 14, context: html, text, full: html, text
    Replaced experiment wgEncodeEM001962 with new version using a Std control. Redmine #5397.
• src/hg/makeDb/trackDb/rat/rn4/knownGenePrevious.html
  • lines changed 107, context: html, text, full: html, text
    making html for the new Old Genes track. it is essentially a copy of knownGene.html with a few edits. http://redmine.soe.ucsc.edu/issues/29
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    turn current known gene track in a previous known gene track
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    Add ctgPos2 (Scaffold) to rheMac3
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Adding the bigDataUrl for bigBed bam and bigWig
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 29, context: html, text, full: html, text
    changes to trackDb, adding new stanzas
• src/hg/near/hgNear/hgNearData/Rat/rn4/columnDb.ra
  • lines changed 10, context: html, text, full: html, text
    eliminate codingSnps definition here, not needed for Rat
• src/hg/near/hgNear/hgNearData/Rat/rn4/orderDb.ra
  • lines changed 2, context: html, text, full: html, text
    add type abc table and column definitions to get alpha sort to work
  • lines changed 1, context: html, text, full: html, text
    order table to use is rgdGene2ToSymbol instead of rgdGene2ToUniProt
• src/hg/utils/automation/HgDb.pm
  • lines changed 2, context: html, text, full: html, text
    correcting some errors
  • lines changed 1, context: html, text, full: html, text
    removed line that was left from debugging
  • lines changed 38, context: html, text, full: html, text
    fixup/refactor code into processConfFile
  • lines changed 1, context: html, text, full: html, text
    remove un-neeeded use
• src/hg/utils/hubPublicCheck/hubPublicCheck.c
  • lines changed 1, context: html, text, full: html, text
    fix typo, use longLabel, not shortLabel
• src/product/scripts/kentSrcUpdate.sh
  • lines changed 1, context: html, text, full: html, text
    do not print out the error on the compile of gbWarn.c
• src/product/scripts/updateHtml.sh
  • lines changed 9, context: html, text, full: html, text
    proper exit on errors and avoid visiGene broken symLink
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v264 preview1
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
  • lines changed 1, context: html, text, full: html, text
    Fixed an erroneous check in this robot script.

• lines changed: 40737
• files changed: 226