All File Changes

v260_preview to v260_preview2 (2011-11-15 to 2011-11-22) v260

• python/lib/ucscgenomics/mkChangeNotes.py
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    fixed a mkChangenotes bug, loose was applied to alpha metaDb, but it shouldn't
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    for printing solo report, the gbdb path was set to release path
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 67, context: html, text, full: html, text
    First pass at generating a DAF. Redmine #5986.
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    Added localization to DAF.
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    Added spike-In and meta-data variable spike-in pools.
• src/hg/encode/encodeDownloadReadme/redirectTemplateIndex.html
  • lines changed 31, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 19, context: html, text, full: html, text
    added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
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    this reverts f329d887708f96c02a837be3c02f479c9ad25e81
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    Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81" This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
  • lines changed 11, context: html, text, full: html, text
    changed to GB standard of doing rhe libraries live where you do thing
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    added switch for beta and prod assembly choices
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    Revert "added switch for beta and prod assembly choices" This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
  • lines changed 8, context: html, text, full: html, text
    updated usage statement, and renamed variables
  • lines changed 9, context: html, text, full: html, text
    removed comment line that is no longer needed
  • lines changed 1, context: html, text, full: html, text
    corrected a mispelling
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    resolving merge
  • lines changed 14, context: html, text, full: html, text
    changed the location of the tagging function for the pipeline submissions
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 10, context: html, text, full: html, text
    added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
  • lines changed 10, context: html, text, full: html, text
    this reverts f329d887708f96c02a837be3c02f479c9ad25e81
  • lines changed 10, context: html, text, full: html, text
    Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81" This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
  • lines changed 10, context: html, text, full: html, text
    changed to GB standard of doing rhe libraries live where you do thing
  • lines changed 1, context: html, text, full: html, text
    added switch for beta and prod assembly choices
  • lines changed 1, context: html, text, full: html, text
    Revert "added switch for beta and prod assembly choices" This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
  • lines changed 1, context: html, text, full: html, text
    removed SafePipe from libraries in unload, it's not being used
  • lines changed 7, context: html, text, full: html, text
    updated usage statement, and renamed variables
  • lines changed 9, context: html, text, full: html, text
    removed comment line that is no longer needed
  • lines changed 1, context: html, text, full: html, text
    corrected a mispelling
  • lines changed 16, context: html, text, full: html, text
    resolving merge
• src/hg/encode/encodeLoad/makefile
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    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeQaInit/encodeQaInit
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    fixed some bugs QA found
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
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    fleshed out an error message
• src/hg/encode/encodeRenameObj/encodeRenameObj.c
  • lines changed 7, context: html, text, full: html, text
    training wheels as requested: now checks that new name starts with composite name
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    add support for multiple files in the fileName meta data field
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    adding support for attic renamed replaced revoked
  • lines changed 8, context: html, text, full: html, text
    fixing newnames list
• src/hg/encode/encodeValidate/config/makefile
  • lines changed 24, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeValidate/config/redirectTemplateIndex.html
  • lines changed 31, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 12, context: html, text, full: html, text
    added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
  • lines changed 1, context: html, text, full: html, text
    removed non-standard package
  • lines changed 12, context: html, text, full: html, text
    this reverts f329d887708f96c02a837be3c02f479c9ad25e81
  • lines changed 12, context: html, text, full: html, text
    Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81" This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
  • lines changed 12, context: html, text, full: html, text
    changed to GB standard of doing rhe libraries live where you do thing
  • lines changed 3, context: html, text, full: html, text
    added switch for beta and prod assembly choices
  • lines changed 3, context: html, text, full: html, text
    Revert "added switch for beta and prod assembly choices" This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
  • lines changed 7, context: html, text, full: html, text
    updated usage statement, and renamed variables
  • lines changed 11, context: html, text, full: html, text
    removed comment line that is no longer needed
  • lines changed 1, context: html, text, full: html, text
    corrected a mispelling
  • lines changed 4, context: html, text, full: html, text
    changed the location of the tagging function for the pipeline submissions
  • lines changed 5, context: html, text, full: html, text
    put a check to get pwd if you run from the firectory itself (for appending submission dir to table name for camand line runs or validate
  • lines changed 5, context: html, text, full: html, text
    Revert "put a check to get pwd if you run from the firectory itself (for appending submission dir to table name for camand line runs or validate" This reverts commit dadaf46d634bad2f66b8391d7567f58de974fc26.
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    redid how the previous commit handled things, it turns out at that point in the code, validate has chdired into the submit directory
• src/hg/encode/encodeValidate/doc/errors.txt
  • lines changed 21, context: html, text, full: html, text
    making things obsolete
• src/hg/encode/encodeValidate/makefile
  • lines changed 40, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/encodeValidate/newtest/doEncodeValidate.pl
  • lines changed 2409, context: html, text, full: html, text
    removed doEncodeValidate from the testing suite, changed how it worked.
• src/hg/encode/encodeValidate/obsolete/doc/errors.txt
  • lines changed 21, context: html, text, full: html, text
    making things obsolete
• src/hg/encode/encodeValidate/obsolete/tagAlignSanityCheck.pl
  • lines changed 124, context: html, text, full: html, text
    making things obsolete
• src/hg/encode/encodeValidate/tagAlignSanityCheck.pl
  • lines changed 124, context: html, text, full: html, text
    making things obsolete
• src/hg/encode/inc/encodePatchTdb.h
  • lines changed 2, context: html, text, full: html, text
    adding support for attic renamed replaced revoked
• src/hg/encode/lib/encodePatchTdb.c
  • lines changed 3, context: html, text, full: html, text
    adding support for attic renamed replaced revoked
• src/hg/encode/makefile
  • lines changed 3, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/hg/encode/metaCheck/makefile
  • lines changed 1, context: html, text, full: html, text
    adding support for attic renamed replaced revoked
• src/hg/encode/metaCheck/metaCheck.c
  • lines changed 409, context: html, text, full: html, text
    adding support for attic renamed replaced revoked
• src/hg/hgTables/schema.c
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    Since hgTables sometimes displays a schema for a table that is not a track, I had to bring back the earlier code that does not require a tdb. This fixes redmine 5990.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 12, context: html, text, full: html, text
    display code for publications (t2g) track, most of them by larrym
• src/hg/hgTracks/hgTracks.c
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    Adding back in the routine to give subtracks a pointer to their group. This is the more thorough fix for 5992 which was rolled back to do a very simple patch.
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    work on merging gene suggest into position search (#5933); currently only on in larrym's tree
• src/hg/hgTracks/imageV2.c
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    At Angie's request, adding ability to have map items with mouse-over title but no actual link
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    use attributeEncode instead of htmlEncode in title attributes (e.g. allow encoded unicode)
• src/hg/hgTracks/imageV2.h
  • lines changed 3, context: html, text, full: html, text
    At Angie's request, adding ability to have map items with mouse-over title but no actual link
• src/hg/hgTracks/simpleTracks.c
  • lines changed 105, context: html, text, full: html, text
    display code for publications (t2g) track, most of them by larrym
• src/hg/hgTracks/vcfTrack.c
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    Feature #3711 (VCF haplotype-sorting display): Reverting to the originalstyle of drawing the hap-cluster tree (clustering-tool style instead of phylogenetic-ish style). This reverts commit 5770f49f480bbfe5d920ece22f96961954e43116.
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    Feature #3711 (VCF haplotype-sorting display): suggestion from David:draw boundaries of leaf clusters in purple.
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    Feature #3711 (VCF haplotype-sorting display): Added mouseover titles forclusters in left label area. Thanks Tim for adding the capability to make a mouseover title with no link! Also fixed mapBox for center variant: it needs to be created *before* the other variants are drawn and mapped; this is the opposite of drawing (center variant is drawn last so it appears on top). Also added variant name (if not "." placeholder) to variant mouseover.
• src/hg/hgc/hgc.c
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    Add a <BR> if there is no description of an OMIM Gene.
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    display code for publications (t2g) track, most of them by larrym
• src/hg/hgc/t2g.c
  • lines changed 225, context: html, text, full: html, text
    display code for publications (t2g) track, most of them by larrym
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    Fixes for stricter -Wall warnings: use puts instead of printf if there's noformat argument, and use TRUE & FALSE instead of true & false.
• src/hg/htdocs/ENCODE/pubs.html
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    fixed erronous entry as reported by issue 5916
• src/hg/htdocs/goldenPath/credits.html
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    Fixed up the cow credits a bit.
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    Removed comment around microbat link.
• src/hg/htdocs/goldenPath/help/bam.html
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    Doc #5964 (document some trackDb variables): added BAM-specificsettings showNames and noColorTag to trackDb/README. noColorTag is internal-use-only, and I'm considering dropping it and just not offering the bamColorTag UI option if the bamColorTag setting is not present. So I added only showNames to goldenPath/help/bam.html.
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    One more place to mention showNames in bam.html.
• src/hg/htdocs/goldenPath/newsarch.html
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    Added UMD cow announcement, archived some news items, fixed some typos etc.
• src/hg/htdocs/goldenPath/pubs.html
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    Added pub for David.
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    Added NAR DB pubs.
• src/hg/htdocs/images/phylo/gorGor3_11way.png
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    phylo tree for Gorilla 11-way primate alignment
• src/hg/htdocs/indexNews.html
  • lines changed 112, context: html, text, full: html, text
    Added UMD cow announcement, archived some news items, fixed some typos etc.
• src/hg/htdocs/style/HGStyle.css
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    Added '.descTbl th' to declaration so table header rows pick up the style too.
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    add styles for new position input design (#5933)
• src/hg/inc/hgBam.h
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    hgBam.h should include samAlignment.h regardless of USE_BAM, in order toavoid compilation error when USE_BAM is not defined.
• src/hg/js/hgGateway.js
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    work on #3484; corner-case where user hits enter w/o selecting item from list
• src/hg/js/hgTracks.js
  • lines changed 33, context: html, text, full: html, text
    work on #3484; corner-case where user hits enter w/o selecting item from list. Some experimental code for #5933 (only turned on in larrym's tree)
  • lines changed 4, context: html, text, full: html, text
    At Angie's request, adding ability to have map items with mouse-over title but no actual link
  • lines changed 4, context: html, text, full: html, text
    copy coordinates in location input when user clicks on static copy of position
  • lines changed 1, context: html, text, full: html, text
    use removeAttr to fix a jQuery 1.7 problem
• src/hg/js/utils.js
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    One-line change for an eleventh our bug: trackSearch [+][-] buttons not working. This may be a patch request.
  • lines changed 10, context: html, text, full: html, text
    add preloadImg
  • lines changed 45, context: html, text, full: html, text
    Fixed bug occurring on ddcl mdbVals that are beneath an added or removed line.
• src/hg/lib/cosmicRaw.sql
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    Added cosmic_mutation_id as an index key.
• src/hg/lib/hgFind.c
  • lines changed 12, context: html, text, full: html, text
    allow refLink searches to work when accessions have version numbers (ignore the accession version number) RedMine issue 6040
• src/hg/lib/hui.c
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    Vanessa requested a wording change in redmine 6082.
• src/hg/makeDb/doc/anoCar2.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/calJac3.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 2, context: html, text, full: html, text
    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes
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    updated notes
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechTfbs.release1.notes
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    fixed notes after a mkChange bugfix
• src/hg/makeDb/doc/fr3.txt
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    initial genome build with repeat masker, simple repeats, and gaps fixed up
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    windowMasker and blat server now running
• src/hg/makeDb/doc/gorGor3.txt
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    running synNet maf split for 11-way alignment
• src/hg/makeDb/doc/loxAfr3.txt
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    redmine track #5959 pairwise alignment : loxAfr3 <-> monDom5
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    Set chainNet priority and matrix values for loxAfr3 vs. monDom5.
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 3, context: html, text, full: html, text
    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/micMur1.txt
  • lines changed 3, context: html, text, full: html, text
    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/monDom5.txt
  • lines changed 67, context: html, text, full: html, text
    redmine track #5959 pairwise alignment : loxAfr3 <-> monDom5
  • lines changed 7, context: html, text, full: html, text
    Set chainNet priority and matrix values for loxAfr3 vs. monDom5.
• src/hg/makeDb/doc/nomLeu1.txt
  • lines changed 18, context: html, text, full: html, text
    Sort rmsk tables by chromStart (redmine Bug #5557)
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    Document blat server assignment for gibbon nonLeu1
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    Document how to set gibbon/trackDb.chainNet.ra
• src/hg/makeDb/doc/otoGar1.txt
  • lines changed 3, context: html, text, full: html, text
    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/panTro3.txt
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/papHam1.txt
  • lines changed 193, context: html, text, full: html, text
    catch up some ancient instructions for Baboon
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    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/ponAbe2.txt
  • lines changed 2, context: html, text, full: html, text
    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/rheMac2.txt
  • lines changed 3, context: html, text, full: html, text
    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/tarSyr1.txt
  • lines changed 3, context: html, text, full: html, text
    add link to WGS Traces information for these assemblies
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
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    Removing the commands to build the knownToCdsSnp and knownToGnf1h tables. knownToGnf1h is obsolete, superceded by knownToGnfAtlas2. knownToCdsSnp never really worked out, and decisions were made to drop it (see git #20, comment #49)
• src/hg/makeDb/genbank/etc/genbank.conf
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    no refseq natives for gorGor3
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    adding definitions for fr3 Fugu
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    Added gorGor3 and nomLeu1
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    Removing some dependencies to tables pepMwAa and pepPi, which are/were specific to the Proteome Browser
  • lines changed 5, context: html, text, full: html, text
    eliminate felCat3 from identifier ensemblTranscriptId checks
• src/hg/makeDb/trackDb/README
  • lines changed 4, context: html, text, full: html, text
    Doc #5964 (document some trackDb variables): added BAM-specificsettings showNames and noColorTag to trackDb/README. noColorTag is internal-use-only, and I'm considering dropping it and just not offering the bamColorTag UI option if the bamColorTag setting is not present. So I added only showNames to goldenPath/help/bam.html.
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Added override section for gorGor3. Added shortLabel tag to gorGor1 override section.
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    Added matrix line to gorGor3 override section so chain/net description page matches results of getMatrixLines.csh
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 57, context: html, text, full: html, text
    Edited this file for readability and added some info.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Fixing cell line protocol
  • lines changed 241, context: html, text, full: html, text
    Added Mouse and Human tags for Antibody validation documents to clearly indicate when an antibody has been validated for Mouse or Human. Redmine #1012.
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    Fixed spacing issues in validation files list.
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    added cell line stanzas to cv
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    Adding Differentiation Protocol Treatments, Removing Myocyte Diff Protocols
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 311, context: html, text, full: html, text
    Copying alpha cv to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Fixing a broken link
  • lines changed 237, context: html, text, full: html, text
    Moved over Labels from beta/cv.ra only. Two labels that were modified to not include semicolon are: 1. ELAVL1 (SC-5261) which is ELAVL1 (SC-5261; 07-1735 is recommended replacement for AB5831) beta/cv.ra 2. T7Tag (AB3790) which is T7Tag (AB3790; Nov_69522) in beta/cv.ra Need to discuss with Jeff about those labels, but these should suffice for now.
• src/hg/makeDb/trackDb/elephant/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Set chainNet priority and matrix values for loxAfr3 vs. monDom5.
• src/hg/makeDb/trackDb/fugu/fr3/description.html
  • lines changed 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/fugu/fr3/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/fugu/fr3/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
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    proper searching for gold table
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
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    Changed the URL to NCBI to a simpler, yet still-correct one. Fixed an html formatting error.
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gap.html
  • lines changed 16, context: html, text, full: html, text
    Rearranged first sentence. Added links to NCBI, WashU and Baylor.
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gold.html
  • lines changed 20, context: html, text, full: html, text
    Rearranged first sentence. Added links to NCBI, WashU and Baylor. Made other minor formatting changes.
• src/hg/makeDb/trackDb/gibbon/nomLeu1/trackDb.ra
  • lines changed 32, context: html, text, full: html, text
    remove all_mrna and all_est and fixup gold search
• src/hg/makeDb/trackDb/gibbon/trackDb.chainNet.ra
  • lines changed 8, context: html, text, full: html, text
    overrides for hg19 and gorGor3
  • lines changed 8, context: html, text, full: html, text
    Set the priority and matrix value based on chainNet.pl and findScore.pl results.
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    Removed blank line from the top of the file
• src/hg/makeDb/trackDb/gibbon/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    overrides for hg19 and gorGor3
• src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
  • lines changed 4, context: html, text, full: html, text
    add a two item name between region display example
  • lines changed 4, context: html, text, full: html, text
    indicate NM version number searches ignore the version extension
  • lines changed 1, context: html, text, full: html, text
    Changed the URL to NCBI to a simpler, yet still-correct one
• src/hg/makeDb/trackDb/gorilla/gorGor3/gap.html
  • lines changed 10, context: html, text, full: html, text
    Changed the structure of the first sentence and included links to the Wellcome Trust Sanger Institute. Made various formatting corrections.
• src/hg/makeDb/trackDb/gorilla/gorGor3/gold.html
  • lines changed 3, context: html, text, full: html, text
    Moved a period from inside to outside a hyperlink. Removed an unnecessary period. Italicized the species name.
  • lines changed 1, context: html, text, full: html, text
    Removed an unnecessary period
  • lines changed 1, context: html, text, full: html, text
    Changed the URL to NCBI to a simpler, yet still-correct one
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra
  • lines changed 40, context: html, text, full: html, text
    adding chainNet overrides and proper search for gold track
  • lines changed 2, context: html, text, full: html, text
    Added matrix line to calJac3 override section so chain/net description page matches results of getMatrixLines.csh
• src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    adding proper search rule for gold table
  • lines changed 7, context: html, text, full: html, text
    adding chainNet overrides and proper search for gold track
• src/hg/makeDb/trackDb/human/hg19/agilentCgh.html
  • lines changed 117, context: html, text, full: html, text
    Did some major cleanup to html table: simplified code greatly, got rid of depricated attributes and used css, lowercased tags, and fixed issue with alternating colored rows where two of the same color were together. Colors are still really ugly, but we can fix that later. ;-)
  • lines changed 5, context: html, text, full: html, text
    Correct two links that were out of date and hit redirects on Agilent's website.
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra
  • lines changed 2, context: html, text, full: html, text
    fixup URL for alternate sequence
• src/hg/makeDb/trackDb/human/hg19/lincRNAs.html
  • lines changed 2, context: html, text, full: html, text
    Remove the last sentnece 'From which all the raw data can be downloaded'
  • lines changed 32, context: html, text, full: html, text
    Hard wrapped text to 100 chars. Reformatted and lower-cased tags.
  • lines changed 16, context: html, text, full: html, text
    Corrected grammar for redundant wording, redundant workding. Split main paragraph into two for better readability. Corrected citation format and links.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 74, context: html, text, full: html, text
    Added origAssembly
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 1, context: html, text, full: html, text
    removed a random # sign
  • lines changed 19, context: html, text, full: html, text
    added md5sums to V2 entries
  • lines changed 63, context: html, text, full: html, text
    Added GEO Accession numbers for track. Redmine #2783.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 3, context: html, text, full: html, text
    fixing rename problem when encodeRenameObj accepted an incorrect target name without the full composite prefix
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 185, context: html, text, full: html, text
    Adding the Caltech submitted files for the HAIB track.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 20, context: html, text, full: html, text
    just finishing up an encode rename for Matt
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 7, context: html, text, full: html, text
    revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 6, context: html, text, full: html, text
    revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 1, context: html, text, full: html, text
    added bai for skmc
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 98, context: html, text, full: html, text
    Adding dccAccession only
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 5, context: html, text, full: html, text
    revoked monocytes cd14 on uw dnase for beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
  • lines changed 1, context: html, text, full: html, text
    restaging UW Histone metaDb with Matts changes, redmine # 4459
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwHistone.ra
  • lines changed 11267, context: html, text, full: html, text
    Releasing UW Histone, redmine# 4459
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changed to match the config page
  • lines changed 28, context: html, text, full: html, text
    Changed 'bosTau4' to 'bosTau6' in placental mammal section. Added oviAri1 to placental mammal section.
  • lines changed 43, context: html, text, full: html, text
    Changed 'xenTro2' to 'xenTro3' in vertebrate section. Added melGal1 to vertebrate section.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Adding the Chromatin supertrack and moving three tracks into it
  • lines changed 2, context: html, text, full: html, text
    Releasing UW Histone, redmine# 4459
• src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
  • lines changed 132, context: html, text, full: html, text
    New Super track description for chromatin interaction
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
  • lines changed 5, context: html, text, full: html, text
    Changing the track description according to ticket #5901, letting this small fix leak to public.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
  • lines changed 2, context: html, text, full: html, text
    changed according to ticket 5901 (removed 'but not annotated...')
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 1, context: html, text, full: html, text
    Adding the Chromatin supertrack and moving three tracks into it
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 1, context: html, text, full: html, text
    fixing rename problem when encodeRenameObj accepted an incorrect target name without the full composite prefix
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra
  • lines changed 7, context: html, text, full: html, text
    Adding the Chromatin supertrack and moving three tracks into it
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed mistake in label for MCF7 and SH-SY5Y GATA3 experiments. The Label for the matrix and subGroup didn't match meta-data.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed mistake in label for MCF7 and SH-SY5Y GATA3 experiments. The Label for the matrix and subGroup didn't match meta-data.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
  • lines changed 4, context: html, text, full: html, text
    Removing redundant note
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
  • lines changed 2, context: html, text, full: html, text
    Adding the Chromatin supertrack and moving three tracks into it
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.new.ra
  • lines changed 12, context: html, text, full: html, text
    Adding the Chromatin supertrack and moving three tracks into it
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 36, context: html, text, full: html, text
    revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 21, context: html, text, full: html, text
    revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 21, context: html, text, full: html, text
    revoked monocytes cd14 on uw dnase for beta
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
  • lines changed 18, context: html, text, full: html, text
    Releasing UW Histone, redmine# 4459
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    correct ordering issue
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 2491, context: html, text, full: html, text
    Releasing UW Histone, redmine# 4459
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
  • lines changed 1, context: html, text, full: html, text
    fixed some pre-QA stuff
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 2, context: html, text, full: html, text
    fixed some pre-QA stuff
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Added override section for gorGor3. Added shortLabel tag to gorGor1 override section.
  • lines changed 1, context: html, text, full: html, text
    Added matrix line to gorGor3 override section so chain/net description page matches results of getMatrixLines.csh
  • lines changed 6, context: html, text, full: html, text
    Set correct priority and matrix of gibbon nomLeu1 in hg19.
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding fr3 fugu to the build
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Added override section for gorGor3. Added shortLabel tag to gorGor2 override section.
  • lines changed 1, context: html, text, full: html, text
    Added matrix line to gorGor3 override section so chain/net description page matches results of getMatrixLines.csh
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 1441, context: html, text, full: html, text
    Added 6 submissions to track. Redmine # 111.
  • lines changed 961, context: html, text, full: html, text
    Added 4 submissions to track. Redmine #111.
  • lines changed 241, context: html, text, full: html, text
    Added new submission for track. Redmine #111.
  • lines changed 241, context: html, text, full: html, text
    Added another submissions to track. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 817, context: html, text, full: html, text
    Added 3 new submissions for track. Redmine #110.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging caltech tfbs mm9, redmine# 4154
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechTfbs.ra
  • lines changed 3758, context: html, text, full: html, text
    staging caltech tfbs mm9, redmine# 4154
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    staging caltech tfbs mm9, redmine# 4154
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html
  • lines changed 6, context: html, text, full: html, text
    Fixed errors found in Redmine #4154, that were the same inRedmine #4155 1. Changed header size from h2 -> h3 for "Maps of Occupancy by Transcription Factors" 2. Update "Information on antibodies used is available via the hyperlinks in the "Select subtracks" menu." -> "Information on antibodies used is available via the metadata for each sub-track." 3. Added spaces between units and scalars and added period for: "Reads of 32bp, 36bp or 50bp length were generated" 4. Added comma after Thus in "Thus we will be...." 5. Fixed sentence "was used to map reads to the male of female version of the mouse genome" to read "... male or female ... "
  • lines changed 2, context: html, text, full: html, text
    Fixed the issues found in Redmine #4154 which are relevant to Redmine #4155 1. Added period after Signal View description 2. Updated Sentences about information on Antibodies to read: "Information on the antibodies used is available via the metadata (click the down arrow in the subtrack list) for each subtrack"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html
  • lines changed 6, context: html, text, full: html, text
    Fixed errors found in Redmine #4154, that were the same inRedmine #4155 1. Changed header size from h2 -> h3 for "Maps of Occupancy by Transcription Factors" 2. Update "Information on antibodies used is available via the hyperlinks in the "Select subtracks" menu." -> "Information on antibodies used is available via the metadata for each sub-track." 3. Added spaces between units and scalars and added period for: "Reads of 32bp, 36bp or 50bp length were generated" 4. Added comma after Thus in "Thus we will be...." 5. Fixed sentence "was used to map reads to the male of female version of the mouse genome" to read "... male or female ... "
  • lines changed 2, context: html, text, full: html, text
    Fixed the issues found in Redmine #4154 which are relevant to Redmine #4155 1. Added period after Signal View description 2. Updated Sentences about information on Antibodies to read: "Information on the antibodies used is available via the metadata (click the down arrow in the subtrack list) for each subtrack"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 110, context: html, text, full: html, text
    Added 6 submissions to track. Redmine # 111.
  • lines changed 72, context: html, text, full: html, text
    Added 4 submissions to track. Redmine #111.
  • lines changed 18, context: html, text, full: html, text
    Added new submission for track. Redmine #111.
  • lines changed 18, context: html, text, full: html, text
    Added another submissions to track. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 55, context: html, text, full: html, text
    Added 3 new submissions for track. Redmine #110.
• src/hg/makeDb/trackDb/mrna.html
  • lines changed 2, context: html, text, full: html, text
    Changed capitalization of journal article title to match actual journal article. Journal article URL was being redirected. Replaced the URL with the new target.
• src/hg/makeDb/trackDb/nestedRepeats.html
  • lines changed 5, context: html, text, full: html, text
    Corrected 'RepBase' to 'Repbase Update'. Link to Repbase Update was being redirected, so replaced the URL with the new target. Corrected capitalization of journal article title.
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Set chainNet priority and matrix values for loxAfr3 vs. monDom5.
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    set priorities for gorGor3 chain net tracks
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    set priorities for gorGor3 chain net tracks
• src/hg/makeDb/trackDb/rmsk.html
  • lines changed 5, context: html, text, full: html, text
    Corrected 'RepBase' to 'Repbase Update'. Link to Repbase Update was being redirected, so replaced the URL with the new target. Corrected capitalization of journal article title.
• src/hg/makeDb/trackDb/t2g.html
  • lines changed 41, context: html, text, full: html, text
    t2g track desc update
  • lines changed 2, context: html, text, full: html, text
    t2g description changes
  • lines changed 9, context: html, text, full: html, text
    t2g track desc corrections
  • lines changed 7, context: html, text, full: html, text
    t2g track desc corrections
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    removed t2g track from trackDb (name clash with sandbox)
  • lines changed 32, context: html, text, full: html, text
    setting t2g to hide in trackDb
  • lines changed 2, context: html, text, full: html, text
    second try to commit trackDb
  • lines changed 2, context: html, text, full: html, text
    fixed missing release tags in trackDb
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 8, context: html, text, full: html, text
    clarify language issues and formatting
• src/hg/makeDb/trackDb/xenTro/xenTro3/description.html
  • lines changed 2, context: html, text, full: html, text
    Removed '.7' from gateway page sample query
• src/hg/makeDb/trackDb/xenoMrna.html
  • lines changed 2, context: html, text, full: html, text
    Changed capitalization of journal article title to match actual journal article. Journal article URL was being redirected. Replaced the URL with the new target.
• src/hg/makeDb/trackDb/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Adjusted capitalization of journal article title to match actual journal article
  • lines changed 1, context: html, text, full: html, text
    Journal article URL was being redirected. Replaced URL with the new target.
• src/hg/utils/automation/Encode.pm
  • lines changed 13, context: html, text, full: html, text
    added switch for beta and prod assembly choices
  • lines changed 13, context: html, text, full: html, text
    Revert "added switch for beta and prod assembly choices" This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
  • lines changed 6, context: html, text, full: html, text
    updated usage statement, and renamed variables
  • lines changed 15, context: html, text, full: html, text
    resolving merge
  • lines changed 4, context: html, text, full: html, text
    fixed a bug
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 16, context: html, text, full: html, text
    load a sorted fa.out file to satisify the QA ordered table check
  • lines changed 1, context: html, text, full: html, text
    one line too much in the head to sorted operation
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 37, context: html, text, full: html, text
    eliminate teh obsolete all_mrna and all_est entries in the initial trackDb.ra file
• src/hg/utils/automation/makefile
  • lines changed 22, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/inc/common.mk
  • lines changed 10, context: html, text, full: html, text
    reworked the makefiles to allow for a split pipeline
• src/inc/htmshell.h
  • lines changed 3, context: html, text, full: html, text
    add htmlTextReplaceTagsWithChar
• src/lib/htmshell.c
  • lines changed 27, context: html, text, full: html, text
    add htmlTextReplaceTagsWithChar
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v260 preview2

• lines changed: 29850
• files changed: 267