All File Changes

v244_base to v245_preview (2010-12-07 to 2010-12-14) v245

• src/hg/encode/DAFs/2.0/dukeDnaseSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Updated the validationSettings for OpenChromatin Labs to include nMatch,isSort options.
• src/hg/encode/DAFs/2.0/gisChiaPet.daf
  • lines changed 21, context: html, text, full: html, text
    changed the suffix, added a ddf header
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Removed validateFastq option and use default settings for fastq validation.
• src/hg/encode/DAFs/2.0/haibCnv.daf
  • lines changed 7, context: html, text, full: html, text
    Added information about SNP files
• src/hg/encode/DAFs/2.0/haibMethylArray.daf
  • lines changed 41, context: html, text, full: html, text
    changing Methyl27 or MethylBead to MethylArray
• src/hg/encode/DAFs/2.0/haibMethylBead.daf
  • lines changed 4, context: html, text, full: html, text
    changing the composite name to haibMethylArray
  • lines changed 41, context: html, text, full: html, text
    changing Methyl27 or MethylBead to MethylArray
• src/hg/encode/DAFs/2.0/psuMm9Histone.daf
  • lines changed 20, context: html, text, full: html, text
    Updated the DAF for the PSU Histone track, which was previously inconsistent with the TFBS track.
  • lines changed 1, context: html, text, full: html, text
    Updated version from 1.5 to 1.6
• src/hg/encode/DAFs/2.0/sunyRipSeq.daf
  • lines changed 54, context: html, text, full: html, text
    Changed RnaSeq to RipSeq
• src/hg/encode/DAFs/2.0/sunyRnaSeq.daf
  • lines changed 17, context: html, text, full: html, text
    there is no strand information for the signals
  • lines changed 54, context: html, text, full: html, text
    Changed RnaSeq to RipSeq
• src/hg/encode/DAFs/2.0/sunySwitchgear.daf
  • lines changed 1, context: html, text, full: html, text
    updated the list of metadata
• src/hg/encode/DAFs/2.0/uncFaireSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Updated the validationSettings for OpenChromatin Labs to include nMatch,isSort options.
• src/hg/encode/DAFs/2.0/utAustinChipSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Updated the validationSettings for OpenChromatin Labs to include nMatch,isSort options.
• src/hg/encode/DAFs/2.0/uwDnaseDgf.daf
  • lines changed 4, context: html, text, full: html, text
    Added new variable treatment to UW tracks.
• src/hg/encode/DAFs/2.0/uwDnaseSeq.daf
  • lines changed 4, context: html, text, full: html, text
    Added new variable treatment to UW tracks.
• src/hg/encode/docId/docIdView/docIdView.c
  • lines changed 4, context: html, text, full: html, text
    fixes for #1486 note 11
• src/hg/encode/docId/docIdView/makefile
  • lines changed 3, context: html, text, full: html, text
    fixes for #1486 note 11
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 9, context: html, text, full: html, text
    add hgPal links to sgdGenes
• src/hg/hgGene/wikiTrack.c
  • lines changed 2, context: html, text, full: html, text
    Some missed changes to allow for variome belonging to a subcategory in the wiki
• src/hg/hgTables/makefile
  • lines changed 8, context: html, text, full: html, text
    added install target for greatData
  • lines changed 6, context: html, text, full: html, text
    fixed great conf install to not fail when file own by different user
  • lines changed 4, context: html, text, full: html, text
    remove greatData before installing to prevent user conflicts
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 10, context: html, text, full: html, text
    fix problem that made "Update custom track" button not work in modal dialog
  • lines changed 47, context: html, text, full: html, text
    Added support for 'downloadsOnly' style tracks which will call fileDb APIs to present downloadable files from cgi.
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
  • lines changed 2, context: html, text, full: html, text
    Updated NCBI hot links of hg18 and hg19 to reflect their URL changes.
  • lines changed 2, context: html, text, full: html, text
    Not ready for prime time 'downloadsOnly track type.
  • lines changed 3, context: html, text, full: html, text
    Part of redmine #1333.4 fix. Subtracks were *sometimes* not getting vis from parent on rightClick.
  • lines changed 6, context: html, text, full: html, text
    Fix for after midnight release hold bug. This reintroduces lesser problem of finding and selecting both composite and child subtrack at the same time, but solves the major problem of not being able to set composite level visibility
  • lines changed 1, context: html, text, full: html, text
    add the ability to add a release tag(s) to include statements #452
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/hgTracks/imageV2.c
  • lines changed 3, context: html, text, full: html, text
    modify configureBy defaults to cover more snp tracks
• src/hg/hgTracks/imageV2.h
  • lines changed 1, context: html, text, full: html, text
    turn off CONTEXT_MENU for v244 build
  • lines changed 1, context: html, text, full: html, text
    turn CONTEXT_MENU back on for dev tree
• src/hg/hgTracks/simpleTracks.c
  • lines changed 152, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/hgTracks/variation.c
  • lines changed 25, context: html, text, full: html, text
    Fixed type=ld2 form remine #1333.4. Didn't work with ClosestToHome logic which caused rightClick weirdnesses.
• src/hg/hgc/hgc.c
  • lines changed 19, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/hgc/hgc.h
  • lines changed 30, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/hgc/makefile
  • lines changed 2, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/hgc/variomeClick.c
  • lines changed 444, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/hgc/wikiTrack.c
  • lines changed 3, context: html, text, full: html, text
    Some missed changes to allow for variome belonging to a subcategory in the wiki
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 10, context: html, text, full: html, text
    adding UW DNaseI DGF to the ENCODE downloads page
  • lines changed 10, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/htdocs/goldenPath/help/hg18ToHg19LiftOver.html
  • lines changed 2, context: html, text, full: html, text
    added capability for liftOver comments from hg17
  • lines changed 2, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/htdocs/images/17.jpg
  • lines changed 0, context: html, text, full: html, text
    added capability for liftOver comments from hg17
  • lines changed 0, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/htdocs/style/HGStyle.css
  • lines changed 8, context: html, text, full: html, text
    Added styles to support table.sortable.
• src/hg/inc/fileUi.h
  • lines changed 34, context: html, text, full: html, text
    Needed for fileDb APIs which present downloadable files from cgi as table.sortable
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    Added tdbForTrack to replace hTrackDbForTrack. New version allows passing in the list of tdbs, so that the list is not regenerated time and time again.
• src/hg/inc/hui.h
  • lines changed 7, context: html, text, full: html, text
    Split compositeUiSubtracks into hgTrackUi vs hgTable versions. Remade subtrack list using the new 'sortable' table methods. Remade makeTrackHashWithComposites to take in/out for tdbList, enabling few rebuilds of this list.
  • lines changed 1, context: html, text, full: html, text
    Fix makeTrackHash macro for only 2 args
• src/hg/inc/mdb.h
  • lines changed 7, context: html, text, full: html, text
    Added 2 useful APIs
• src/hg/inc/trackDb.h
  • lines changed 5, context: html, text, full: html, text
    add the ability to add a release tag(s) to include statements #452
• src/hg/inc/variome.h
  • lines changed 122, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/inc/wikiTrack.h
  • lines changed 2, context: html, text, full: html, text
    Some missed changes to allow for variome belonging to a subcategory in the wiki
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    don't include hgsdid in getDna call (redmine 1333 #5)
  • lines changed 2, context: html, text, full: html, text
    suppress getDna and selectWholeGene for wigs and bigWigs (see redmine 1333 2 & 3)
  • lines changed 5, context: html, text, full: html, text
    Fixed obscure bug where map area had no COORDS. FF on Linux prevented rightClick occasionally because of this.
• src/hg/js/hui.js
  • lines changed 397, context: html, text, full: html, text
    Moved sort routines from hui.js to utils.js and rewrote them so they are not hgTrackUi subtrack list specific. Use table.sortable to make almost any table sortable
• src/hg/js/utils.js
  • lines changed 604, context: html, text, full: html, text
    Moved sort routines from hui.js to utils.js and rewrote them so they are not hgTrackUi subtrack list specific. Use table.sortable to make almost any table sortable
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    ClosestToHome will now support suffixes that begin with '_'.
  • lines changed 8, context: html, text, full: html, text
    Emergency fix to composite reshaping code. Checked it with code commented out to illustrate the exact change.
  • lines changed 10, context: html, text, full: html, text
    Did I say last time was the fix? No no, this time really.
  • lines changed 9, context: html, text, full: html, text
    Reverting back 2 previous checkins in order to give single clean checkin as push request.
  • lines changed 9, context: html, text, full: html, text
    This is the sime clean fix for Showstopper bug 1071 on 12-13-2010
  • lines changed 9, context: html, text, full: html, text
    Back out all last minute changes to cart as ill adviced at this time
• src/hg/lib/decipherRaw.sql
  • lines changed 1, context: html, text, full: html, text
    Updated DECIPHER raw data table format.
• src/hg/lib/fileUi.c
  • lines changed 491, context: html, text, full: html, text
    Added fileUi.c which supports making downloadable files cgi with table.sortable and eventually filterBoxes
• src/hg/lib/hdb.c
  • lines changed 19, context: html, text, full: html, text
    Added tdbForTrack to replace hTrackDbForTrack. New version allows passing in the list of tdbs, so that the list is not regenerated time and time again.
• src/hg/lib/hgFindSpecCustom.c
  • lines changed 2, context: html, text, full: html, text
    add the ability to add a release tag(s) to include statements #452
• src/hg/lib/hui.c
  • lines changed 252, context: html, text, full: html, text
    Split compositeUiSubtracks into hgTrackUi vs hgTable versions. Remade subtrack list using the new 'sortable' table methods. Remade makeTrackHashWithComposites to take in/out for tdbList, enabling few rebuilds of this list.
• src/hg/lib/itemAttr.sql
  • lines changed 1, context: html, text, full: html, text
    don't require name to be unique (not requred by code)
• src/hg/lib/knownToLocusLink.as
  • lines changed 2, context: html, text, full: html, text
    small change to satisfy pair review comment
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
  • lines changed 1, context: html, text, full: html, text
    Added fileUi.c which supports making downloadable files cgi with table.sortable and eventually filterBoxes
• src/hg/lib/mdb.c
  • lines changed 65, context: html, text, full: html, text
    Added 2 useful APIs
• src/hg/lib/refLink.as
  • lines changed 1, context: html, text, full: html, text
    small change to satisfy pair review comment
• src/hg/lib/trackDbCustom.c
  • lines changed 41, context: html, text, full: html, text
    add the ability to add a release tag(s) to include statements #452
• src/hg/lib/variome.as
  • lines changed 20, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/lib/variome.c
  • lines changed 424, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/lib/variome.sql
  • lines changed 29, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/lib/wikiTrack.c
  • lines changed 6, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 155, context: html, text, full: html, text
    now running genbank
  • lines changed 8, context: html, text, full: html, text
    done with genbank
  • lines changed 33, context: html, text, full: html, text
    initial assembly in the pushQ
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release1.notes
  • lines changed 11, context: html, text, full: html, text
    Removed tables for 5 lab specific experiments, total of 9 tables removed.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release1.notes
  • lines changed 138, context: html, text, full: html, text
    Added release 1 directory of the Mouse SYDH first mouse track.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Update to Track #1656 (GWAS Catalog): reloaded hg18 and hg19gwasCatalog with latest data.
  • lines changed 5, context: html, text, full: html, text
    indicate grp creation for denisova assembly
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    Update to Track #1656 (GWAS Catalog): reloaded hg18 and hg19gwasCatalog with latest data.
  • lines changed 3, context: html, text, full: html, text
    adding instructions that were forgotten by somebody for making knownToGnf1h
  • lines changed 43, context: html, text, full: html, text
    Added instructions for building Rfam, which is used as an intermediary in building UCSC Genes
  • lines changed 4, context: html, text, full: html, text
    Minor file renaming in the Rfam build
  • lines changed 44, context: html, text, full: html, text
    added vistaEnhancers track to hg19
  • lines changed 148, context: html, text, full: html, text
    Re-built UniGene track for hg19 based on Version 228.
  • lines changed 20, context: html, text, full: html, text
    Added hg19 lifted GAD view make instructions; GAD view and fishClones trackDb updates
  • lines changed 36, context: html, text, full: html, text
    doing evofold track for hg19
  • lines changed 16, context: html, text, full: html, text
    targetScanS track for hg19
  • lines changed 47, context: html, text, full: html, text
    added Neandertal contigs bam
  • lines changed 20, context: html, text, full: html, text
    trying to clean up git garbage
  • lines changed 47, context: html, text, full: html, text
    adding neandertal bam contigs
  • lines changed 39, context: html, text, full: html, text
    Lift instructions for FISH clones added before a git pull
• src/hg/makeDb/doc/mm9.txt
  • lines changed 19, context: html, text, full: html, text
    adding targetScanS to mm9
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 37, context: html, text, full: html, text
    Added commands for incorporating data from the tRNAs and Rfam repositories
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added danRer7.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 15, context: html, text, full: html, text
    adding danRer7 definition
  • lines changed 1, context: html, text, full: html, text
    better specification of danRer7.11.ooc file location
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added danRer7.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 8, context: html, text, full: html, text
    add the ability to add a release tag(s) to include statements #452
• src/hg/makeDb/trackDb/affyExonTissues.html
  • lines changed 1, context: html, text, full: html, text
    Fixed/updated link to Affy Mouse Exon 1.0 ST array product page
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 4, context: html, text, full: html, text
    added TGFb treatment
  • lines changed 7, context: html, text, full: html, text
    testing an email address encoded by encodeEmail.pl
  • lines changed 6, context: html, text, full: html, text
    another test of encoded addresses
  • lines changed 1, context: html, text, full: html, text
    Giving up on the idea of encoded email addresses
  • lines changed 1, context: html, text, full: html, text
    Giving up on encoded email addresses:
  • lines changed 27, context: html, text, full: html, text
    For all Lonza cell types, replaced the specific order URL with a URL to Lonza'shome page. The reason: they changed their online catalog recently, making all specific order URLs invalid. There's no reason to assume that they won't do so again. I believe that maintaining specific order URLs is more trouble than it's worth, given that the users can enter the catalog number in the online catalog themselves.
  • lines changed 3, context: html, text, full: html, text
    Updating the ordering information for HRCE, by request of Rajinder Kaul from UW
  • lines changed 7, context: html, text, full: html, text
    added dataType SwitchGear
  • lines changed 2, context: html, text, full: html, text
    added dataType SwitchGear
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 1563, context: html, text, full: html, text
    Moving a load of changes to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 1563, context: html, text, full: html, text
    releasing cv.ra changes:
• src/hg/makeDb/trackDb/human/affyGnf1h.html
  • lines changed 18, context: html, text, full: html, text
    Corrected citation format, moved to References section, cleaned up page (sorry, should have done that in a separate edit
• src/hg/makeDb/trackDb/human/denisova.html
  • lines changed 52, context: html, text, full: html, text
    updated denisova documentation
  • lines changed 2, context: html, text, full: html, text
    fix bwa reference
• src/hg/makeDb/trackDb/human/evofold.html
  • lines changed 2, context: html, text, full: html, text
    doing evofold track for hg19
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 61, context: html, text, full: html, text
    in response to #630, removed metadata from trackDb for MethylSeq tracks, discovered that H9ES had the same metadata as H9ESb, so wasn't in the the metaDb ra file, added it, delete "treatment=none" since it was always that, added view=Regions for a bunch where that was not set. Still confused about where the alignments are for the H9 data.
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 906, context: html, text, full: html, text
    staging metaDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 1650); staging trackDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 811)
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 906, context: html, text, full: html, text
    releasing metaDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 1650); staging trackDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 811)
• src/hg/makeDb/trackDb/human/hg18/microattrLoci.html
  • lines changed 14, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/makeDb/trackDb/human/hg18/rdmr.html
  • lines changed 25, context: html, text, full: html, text
    Corrected some grammar and line length per code review
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 19, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
  • lines changed 9, context: html, text, full: html, text
    add a bunch of release alpha's to stanzas whose parent were release alpha
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 172, context: html, text, full: html, text
    removed the metadata lines for tracks with metaDb entries
  • lines changed 79, context: html, text, full: html, text
    removed more metadata project lines
  • lines changed 1, context: html, text, full: html, text
    releasing metaDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 1650); staging trackDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 811)
  • lines changed 29, context: html, text, full: html, text
    in response to #630, removed metadata from trackDb for MethylSeq tracks, discovered that H9ES had the same metadata as H9ESb, so wasn't in the the metaDb ra file, added it, delete "treatment=none" since it was always that, added view=Regions for a bunch where that was not set. Still confused about where the alignments are for the H9 data.
  • lines changed 66, context: html, text, full: html, text
    remove some commented out stuff, and the Chai track which is kaput
  • lines changed 413, context: html, text, full: html, text
    restore metadata lines that I deleted, add release alpha version of wgEncodeHudsonalphaMethylSeq
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeRikenRawSignal.ra
  • lines changed 436, context: html, text, full: html, text
    these are outdated
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeYaleRnaSeq.new.ra
  • lines changed 6, context: html, text, full: html, text
    removed the metadata lines for tracks with metaDb entries
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • lines changed 4, context: html, text, full: html, text
    adding note to release notes section of HAIB TFBS hg18 regarding the updates released yesterday (#660 and #1155)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 361, context: html, text, full: html, text
    staging metaDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 1650); staging trackDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 811)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 435, context: html, text, full: html, text
    releasing metaDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 1650); staging trackDb changes made to wgEncodeHudsonAlphaChipSeq (Redmine #660, 1155, 811)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 328, context: html, text, full: html, text
    new composite
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.alpha.ra
  • lines changed 721, context: html, text, full: html, text
    these are outdated
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.beta.ra
  • lines changed 699, context: html, text, full: html, text
    these are outdated
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
  • lines changed 4, context: html, text, full: html, text
    changed the NHEK status to Tier3
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 215, context: html, text, full: html, text
    Two missing controls were submitted
  • lines changed 50, context: html, text, full: html, text
    Noticed 49 fileIndexes missing from the mdb
  • lines changed 2, context: html, text, full: html, text
    Fix typo
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 1996, context: html, text, full: html, text
    added Duke Affy composite
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 10, context: html, text, full: html, text
    Removed tables for 5 lab specific experiments, total of 9 tables removed.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 90, context: html, text, full: html, text
    Added submission 1968 to track.
  • lines changed 644, context: html, text, full: html, text
    Revoked 13 experiments see Redmine issue #55
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 3673, context: html, text, full: html, text
    Added 13 new submissions to trackDb and metaDb.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 805, context: html, text, full: html, text
    Added 7 submissions to track and display.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 55, context: html, text, full: html, text
    added the metadata for new Suny submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
  • lines changed 35, context: html, text, full: html, text
    added the metadata for new Suny submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 3742, context: html, text, full: html, text
    Added 205 Uniform signal tracks generated by Anshul and AWG. replaced about 36 existing signals with updated signals and meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging Caltech RNA-Seq on hgwbeta, redmine #35
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethylRrbs.ra
  • lines changed 10, context: html, text, full: html, text
    staging changes Venkat made to Methyl RRBS metaData on beta because we are removing 9 tables from the track
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 49, context: html, text, full: html, text
    staging addition of fastq metadata on beta
  • lines changed 49, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing to release UW DNaseI DGF to the Rr
  • lines changed 1, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 1247, context: html, text, full: html, text
    preparing to release UW DNaseI DGF to the Rr
  • lines changed 1247, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/makeDb/trackDb/human/hg19/targetScanS.html
  • lines changed 57, context: html, text, full: html, text
    targetScanS track for hg19
  • lines changed 57, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    back out an include of a file that hasn't been checked in
  • lines changed 1, context: html, text, full: html, text
    Removed stray "release alpha" from snp131 -- thanks to Brooke fornoticing that some options were missing!
  • lines changed 11, context: html, text, full: html, text
    hg19's snp131 override does need release alpha for visibility hide.Adding a release beta,public stanza without the vis change, like I should have back in August.
  • lines changed 4, context: html, text, full: html, text
    added vistaEnhancers track to hg19
  • lines changed 8, context: html, text, full: html, text
    Lifted GAD view track for hg19.
  • lines changed 1, context: html, text, full: html, text
    Added hg19 lifted GAD view make instructions; GAD view and fishClones trackDb updates
  • lines changed 1, context: html, text, full: html, text
    added origAssembly to lifted track
  • lines changed 5, context: html, text, full: html, text
    doing evofold track for hg19
  • lines changed 12, context: html, text, full: html, text
    targetScanS track for hg19
  • lines changed 12, context: html, text, full: html, text
    trying to clean up git garbage
  • lines changed 16, context: html, text, full: html, text
    Added stuff to trackDb before git pull
  • lines changed 4, context: html, text, full: html, text
    adding overrides for ntHumChimpCodingDiff and ntSssTop5p
  • lines changed 1, context: html, text, full: html, text
    added hg17-ball to evofold track
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Replaced methyl27 include with wgEncodeHaibMethylArray as files have changed.
  • lines changed 1, context: html, text, full: html, text
    new composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 89, context: html, text, full: html, text
    Broad finally provided their methods update.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
  • lines changed 248, context: html, text, full: html, text
    Broad submitted 2 missing controls.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html
  • lines changed 70, context: html, text, full: html, text
    corrected typos, encoded emails, and rearranged the config description to reflect the configration order, redmine issue #35
  • lines changed 70, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 155, context: html, text, full: html, text
    Added release tags back into track to fix track visibile in supertrack configuration page on RR.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 1011, context: html, text, full: html, text
    added Duke Affy composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 19, context: html, text, full: html, text
    htmlize
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 4, context: html, text, full: html, text
    add release alpha tags to view stanzas where the parent is release alpha
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 759, context: html, text, full: html, text
    changing Methyl27 or MethylBead to MethylArray
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylArray.html
  • lines changed 122, context: html, text, full: html, text
    changing Methyl27 or MethylBead to MethylArray
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylArray.ra
  • lines changed 759, context: html, text, full: html, text
    changing Methyl27 or MethylBead to MethylArray
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 22, context: html, text, full: html, text
    Updated short labels to follow track label guide and provided description in the Track Configuration Page.
  • lines changed 2, context: html, text, full: html, text
    Updated comments in trackDb and fixed errors in description page.
  • lines changed 2, context: html, text, full: html, text
    Fixed li tag problem to be enclosed by ul tag.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo of /ul with /li which is correct.
  • lines changed 9, context: html, text, full: html, text
    removing some info from the description because I don't think it is necessary
  • lines changed 34, context: html, text, full: html, text
    Removed Lab specific information from labels and track description.
  • lines changed 34, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 1, context: html, text, full: html, text
    Updated Composite long label to follow track label conventions.
  • lines changed 142, context: html, text, full: html, text
    Updated long labels to follow track label guide.
  • lines changed 131, context: html, text, full: html, text
    Updated short labels to follow track label guide and provided description in the Track Configuration Page.
  • lines changed 2, context: html, text, full: html, text
    Updated comments in trackDb and fixed errors in description page.
  • lines changed 88, context: html, text, full: html, text
    Commented out duplicte cell lines obtained by multiple lines. Choose the Yale Cell combination that had the largest file size when adding two replicates. Also updated the track matrix to be between Cell line and Treatment.
  • lines changed 13, context: html, text, full: html, text
    Updated ordering of Tier 1 cells to be alphabetical. Ordered Tier 1 and 2 cells to force them to be ahead of Tier 3 cells which are ordered alphabetically.
  • lines changed 248, context: html, text, full: html, text
    Removed Lab specific information from labels and track description.
  • lines changed 261, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 26, context: html, text, full: html, text
    Added submission 1968 to track.
  • lines changed 140, context: html, text, full: html, text
    Revoked 13 experiments see Redmine issue #55
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 17, context: html, text, full: html, text
    Updated the default Signals and view's limits of Signals. Turned default track visibility as full.
  • lines changed 678, context: html, text, full: html, text
    Added 13 new submissions to trackDb and metaDb.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 191, context: html, text, full: html, text
    Added 7 submissions to track and display.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 1, context: html, text, full: html, text
    add release alpha tags to view stanzas where the parent is release alpha
  • lines changed 55, context: html, text, full: html, text
    new composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
  • lines changed 23, context: html, text, full: html, text
    new composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 2192, context: html, text, full: html, text
    Added 205 Uniform signal tracks generated by Anshul and AWG. replaced about 36 existing signals with updated signals and meta-data.
  • lines changed 53, context: html, text, full: html, text
    Updated display conventions for track. Need to update default tracks that are shown.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
  • lines changed 1, context: html, text, full: html, text
    Removed errant </h2> tag
  • lines changed 1, context: html, text, full: html, text
    clarifying NOTE
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 2, context: html, text, full: html, text
    Updated the Composite Long and Short Labels to correspond with track label standards.
  • lines changed 1, context: html, text, full: html, text
    Updated default view of Peaks from Dense to Peak.
  • lines changed 48, context: html, text, full: html, text
    Updated the subTrack Long Labels to match Track label standards.
  • lines changed 12, context: html, text, full: html, text
    Updated Short label abbreviations: Changed Raw Signal Shortlabels to not include anything except Cell.
  • lines changed 14, context: html, text, full: html, text
    Updated comments in trackDb about configuration.
  • lines changed 5, context: html, text, full: html, text
    Updated comments in trackDb pages.
  • lines changed 35, context: html, text, full: html, text
    Added short label abbreviations for Hot Spots and Raw Signal as Hspt and Raw respectivley. Updated forced ordering within browser of K562 and HepG2 to be first and second respectivley regardless of alphabeticall reordering within browser.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 5, context: html, text, full: html, text
    Removed indents and replaced with bullet points.
  • lines changed 1, context: html, text, full: html, text
    changed a broken link, redmine issue #66
  • lines changed 9, context: html, text, full: html, text
    Fixed problems that robot detected in html format.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 8, context: html, text, full: html, text
    Update Composite Long to follow track label standard.
  • lines changed 6, context: html, text, full: html, text
    Updated comments
  • lines changed 338, context: html, text, full: html, text
    Updated Long Labels to follow track label conventions
  • lines changed 255, context: html, text, full: html, text
    Updated Short Labels with appropirate abbreviations.
  • lines changed 15, context: html, text, full: html, text
    Updated comments in trackDb pages.
  • lines changed 130, context: html, text, full: html, text
    Added Short Label for Hot Spots: Hspt. Also updated default tracks on to be Replicate 1 only for All Tier 1 cell and HepG2, 1 tier 2.
  • lines changed 130, context: html, text, full: html, text
    trying to clean up git garbage
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
  • lines changed 17, context: html, text, full: html, text
    Added release notes to fufill Redmine issue #1465
  • lines changed 1, context: html, text, full: html, text
    Inserted reference to wrong number of Bad Bams, had 5 instead of 4.
  • lines changed 1, context: html, text, full: html, text
    Added missing ( around Peaks.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 378, context: html, text, full: html, text
    Updated Track Long label and reverted track short labels back to normal convention, reversing truncation rules used earlier. Updated Short labels for Views to be consistent with DNaseI and DGF tracks.
  • lines changed 423, context: html, text, full: html, text
    Updated Long Labels to follow track labeling conventions.
  • lines changed 2, context: html, text, full: html, text
    Fixed long label to include by, typo last time.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 20, context: html, text, full: html, text
    Added missing input for HCFaa and HBMEC.
  • lines changed 226, context: html, text, full: html, text
    Updated track long label according to track label conventions. Fixed shortlabels to not use abbreviation of cells and factors. Update shortlabel view to match other UW track.
  • lines changed 243, context: html, text, full: html, text
    Updated View long labels to match track labeling conventions.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    add release alpha tags to view stanzas where the parent is release alpha
• src/hg/makeDb/trackDb/human/stsMap.html
  • lines changed 1, context: html, text, full: html, text
    removed link to Stanford TNG as center has closed, per Standford Genetics Dept.
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    add a bunch of release alpha's to stanzas whose parent were release alpha
• src/hg/makeDb/trackDb/human/trackDb.denisova.ra
  • lines changed 15, context: html, text, full: html, text
    adding denisova sequence to the display
  • lines changed 31, context: html, text, full: html, text
    updated denisova documentation
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • lines changed 16, context: html, text, full: html, text
    add a bunch of release alpha's to stanzas whose parent were release alpha
• src/hg/makeDb/trackDb/human/vistaEnhancers.html
  • lines changed 1, context: html, text, full: html, text
    Made quotes into html code quotes ... &quot;
• src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    add release tags
• src/hg/makeDb/trackDb/lamprey/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    add release tags
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Removed reference fleCatV17e, according to Redmine issue 1609.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Made new composite for PSU Histone data, added meta-data file for new composite also. 5 total submission were loaded are displayed.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 601, context: html, text, full: html, text
    Made new composite for PSU Histone data, added meta-data file for new composite also. 5 total submission were loaded are displayed.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 151, context: html, text, full: html, text
    Added Mel CTCF experiment to track.
• src/hg/makeDb/trackDb/mouse/mm9/rest.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link for Stanton Group
• src/hg/makeDb/trackDb/mouse/mm9/targetScanS.html
  • lines changed 57, context: html, text, full: html, text
    adding targetScanS to mm9
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    adding targetScanS to mm9
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Made new composite for PSU Histone data, added meta-data file for new composite also. 5 total submission were loaded are displayed.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 155, context: html, text, full: html, text
    Made new composite for PSU Histone data, added meta-data file for new composite also. 5 total submission were loaded are displayed.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 22, context: html, text, full: html, text
    Added Mel CTCF experiment to track.
  • lines changed 2, context: html, text, full: html, text
    Updated track labels, short and long.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 3, context: html, text, full: html, text
    add release tags to view stanzas
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    add release alpha tag
• src/hg/makeDb/trackDb/recombRate.html
  • lines changed 3, context: html, text, full: html, text
    added TARGET = _BLANK per Mary
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Addition of wiki track and supporting tracks for microattribution reviews (part of the variome project)
• src/hg/makeDb/trackDb/tetraodon/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    add release tag
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 8, context: html, text, full: html, text
    add a bunch of release alpha's to stanzas whose parent were release alpha
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    add release tags
• src/hg/near/hgMapToGene/hgMapToGene.c
  • lines changed 25, context: html, text, full: html, text
    Updating the ordering information for HRCE, by request of Rajinder Kaul from UW
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 9, context: html, text, full: html, text
    removing pk from the kluster hubs
  • lines changed 1, context: html, text, full: html, text
    broken check-in
• src/hg/utils/automation/doHgNearBlastp.pl
  • lines changed 2, context: html, text, full: html, text
    removing pk from the kluster hubs
• src/hg/utils/refreshNamedSessionCustomTracks/beta.trashCleanMonitor.sh
  • lines changed 79, context: html, text, full: html, text
    cron scripts running on hgnfs1 as of 08 Dec 2010
• src/hg/utils/refreshNamedSessionCustomTracks/beta.trashCleaner.csh
  • lines changed 267, context: html, text, full: html, text
    cron scripts running on hgnfs1 as of 08 Dec 2010
• src/hg/utils/refreshNamedSessionCustomTracks/rr.trashCleanMonitor.sh
  • lines changed 77, context: html, text, full: html, text
    cron scripts running on hgnfs1 as of 08 Dec 2010
• src/hg/utils/refreshNamedSessionCustomTracks/rr.trashCleaner.csh
  • lines changed 286, context: html, text, full: html, text
    cron scripts running on hgnfs1 as of 08 Dec 2010
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 4, context: html, text, full: html, text
    Moved filterOnRelease into tdbsForDbPath, calling it just after weload stanzas from .ra file(s) at each level, instead of calling it after tdbsForDbPath. The reason for filtering earlier is that stanzas for incompatible releases are hard not to trip on somewhere in the complex logic of merging records. The specific case that was failing, mentioned in MLQ #1963: snp131 has no release specified in the top-level trackDb.ra, but in human/hg19/trackDb.ra, it has two overrides, one for release alpha and the other for beta,public. The beta,public one was processed before the alpha one. Since the top-level had no release, it didn't clash with beta,public, so the records were merged, leaving a singe beta,public record. When we encountered the alpha record, it was incompatible with the merged top-level+beta,public record so it was not merged and had only override params, not top-level. Since it was missing the type param, it failed the doRecordChecks test. Filtering out the record for other releases allowed no-release and alpha to merge properly.
  • lines changed 51, context: html, text, full: html, text
    add the ability to add a release tag(s) to include statements #452
• src/product/scripts/browserEnvironment.txt
  • lines changed 2, context: html, text, full: html, text
    add KNETFILE_HOOKS information
• src/utils/qa/alertBqueue.csh
  • lines changed 4, context: html, text, full: html, text
    changed management copy from donna to ann
  • lines changed 1, context: html, text, full: html, text
    added donna back to recipient list
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v245 preview

• lines changed: 39576
• files changed: 292