All File Changes

v239_base to v240_preview (2010-08-31 to 2010-09-07) v240

• src/hg/cartDump/cartDump.c
  • lines changed 33, context: html, text, full: html, text
    After changing cartDump to encode vars and vals, I decided to make it all ajaxy
  • lines changed 2, context: html, text, full: html, text
    Errors not seen until genome-test build
  • lines changed 5, context: html, text, full: html, text
    Added a reset the cart button which seems appropriate.
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • lines changed 1, context: html, text, full: html, text
    inputType has been replaced by controlId and labExpId was added
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Updated Antibody validation document naming and links.
  • lines changed 19, context: html, text, full: html, text
    Added a provisional cell type entry for PBDE
  • lines changed 240, context: html, text, full: html, text
    added targets for all antibodies, commented on any that were not in metaDb
  • lines changed 167, context: html, text, full: html, text
    added grants to the cv.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed cv.ra with tag's with no term and a ? in front of term
  • lines changed 4, context: html, text, full: html, text
    added urls for ripAntibodies
  • lines changed 1, context: html, text, full: html, text
    fixed a # typo
  • lines changed 18, context: html, text, full: html, text
    Fixed typo's in ra structure and variable names
  • lines changed 14, context: html, text, full: html, text
    Added Antibody for NF-E2, using different term and tag name. Utilizing targert as well.
  • lines changed 6, context: html, text, full: html, text
    Added Genome Analyzer II, which is the precursor to IIe and IIx.
• src/hg/encode/mkEncodeFrameset/makefile
  • lines changed 2, context: html, text, full: html, text
    need to remove destination before moving to destination
• src/hg/encode/paraMd5sum/paraMd5sum
  • lines changed 1, context: html, text, full: html, text
    added return 10 to post clean up code on error
• src/hg/hgTables/filterFields.c
  • lines changed 1, context: html, text, full: html, text
    Redmine #717: obey tableBrowser off setting in 'selected fields from primary and related tables' page (thanks Brooke) and table schema 'Connected Tables and Joining Fields'.
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    Redmine #717: Plugging one more leak that needs to check accessControlDenied.
• src/hg/hgTables/hgTables.h
  • lines changed 4, context: html, text, full: html, text
    Redmine #717: obey tableBrowser off setting in 'selected fields from primary and related tables' page (thanks Brooke) and table schema 'Connected Tables and Joining Fields'.
• src/hg/hgTables/mainPage.c
  • lines changed 37, context: html, text, full: html, text
    Redmine #717: obey tableBrowser off setting in 'selected fields from primary and related tables' page (thanks Brooke) and table schema 'Connected Tables and Joining Fields'.
• src/hg/hgTables/schema.c
  • lines changed 2, context: html, text, full: html, text
    Redmine #717: obey tableBrowser off setting in 'selected fields from primary and related tables' page (thanks Brooke) and table schema 'Connected Tables and Joining Fields'.
• src/hg/hgTracks/bamTrack.c
  • lines changed 4, context: html, text, full: html, text
    Fix to addBamPaired for code that detects unpaired items for gray mode -- Brian found that it was missing most of them, doh!
• src/hg/hgTracks/cds.c
  • lines changed 8, context: html, text, full: html, text
    Performance fix for drawScaledBoxSampleWithText: fixed unnecessary O(N^2) loop condition -- now it will iterate no more than (winEnd-winStart), at base zoom.
  • lines changed 4, context: html, text, full: html, text
    Geez, got my min and max swapped in f808c044.
• src/hg/hgTracks/hgTracks.c
  • lines changed 26, context: html, text, full: html, text
    Larry found this bug where the image file was being built with much empty space at bottom when doing flatTracks and subTrack level vis
• src/hg/hgTracks/imageV2.c
  • lines changed 82, context: html, text, full: html, text
    Movved 2 functions out of searchTracks.
  • lines changed 1, context: html, text, full: html, text
    Add isSubtrack into json tdb settings
  • lines changed 2, context: html, text, full: html, text
    support configureByPopup trackDb setting (currently experimental)
  • lines changed 1, context: html, text, full: html, text
    add onmouseover and onmouseout event handlers for map area items
• src/hg/hgTracks/imageV2.h
  • lines changed 7, context: html, text, full: html, text
    Movved 2 functions out of searchTracks.
• src/hg/hgTracks/oneTrack.c
  • lines changed 1, context: html, text, full: html, text
    update hChromSize call to use database
• src/hg/hgTracks/searchTracks.c
  • lines changed 60, context: html, text, full: html, text
    Movved 2 functions out of searchTracks.
  • lines changed 1, context: html, text, full: html, text
    Oops. Duplicated end of script.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    Toggle track vis was going to hide when subtrack vis overrode composite vis=hide.
• src/hg/hgc/ccdsClick.c
  • lines changed 5, context: html, text, full: html, text
    check for existance of ccdsNotes table before using it. Also fix some possible unnecessary connects
• src/hg/hgc/hgc.c
  • lines changed 28, context: html, text, full: html, text
    a couple of changes to Gencode track
  • lines changed 52, context: html, text, full: html, text
    first pass at a handler for the altSequence hg19Patch2 PSL track
  • lines changed 6, context: html, text, full: html, text
    disable the debug printouts
  • lines changed 9, context: html, text, full: html, text
    print out level if we have a class table with a level field
  • lines changed 6, context: html, text, full: html, text
    do the spacing correctly when there is more than one transcript for an id. I think this only happens on the PAR regions.
• src/hg/htdocs/ENCODE/otherTerms.html
  • lines changed 57, context: html, text, full: html, text
    removing rip target proteins and antibody sections because they've been incorporated into antibody
• src/hg/htdocs/FAQ/index.html
  • lines changed 2, context: html, text, full: html, text
    adding search boxes and deleting 'updated on <date>'
• src/hg/htdocs/goldenPath/help/hgNearHelp.html
  • lines changed 13, context: html, text, full: html, text
    adding search boxes and deleting 'updated on <date>'
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 12, context: html, text, full: html, text
    adding search boxes and deleting 'updated on <date>'
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 14, context: html, text, full: html, text
    adding search boxes and deleting 'updated on <date>'
• src/hg/htdocs/staff.html
  • lines changed 75, context: html, text, full: html, text
    Made several updates to info.
• src/hg/inc/cart.h
  • lines changed 3, context: html, text, full: html, text
    After changing cartDump to encode vars and vals, I decided to make it all ajaxy
• src/hg/inc/gencodeGeneClass.h
  • lines changed 31, context: html, text, full: html, text
    update to reflect reality, apparently these haven't been used for a while
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    adding PSL configuration for multi-views
• src/hg/inc/jksql.h
  • lines changed 9, context: html, text, full: html, text
    export existing sqlEscape function in .h file
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    adding PSL configuration for multi-views
• src/hg/js/ajax.js
  • lines changed 30, context: html, text, full: html, text
    Made getAllVars understand subtrack vis. Redid cfg popup OK with subtrack vis understanding in mind
  • lines changed 24, context: html, text, full: html, text
    Change popup cfg to recognize only changed vars for update to cart and page update
  • lines changed 5, context: html, text, full: html, text
    Added two useful functions for overriding forms with ajax
• src/hg/js/hgTracks.js
  • lines changed 30, context: html, text, full: html, text
    restore mapIsUpdateable == false logic for safari
  • lines changed 27, context: html, text, full: html, text
    move showLoadingImage/hideLoadingImage to utils.js
  • lines changed 33, context: html, text, full: html, text
    Make rightClick work for all of image, not just map items
  • lines changed 13, context: html, text, full: html, text
    keep local state in sync if user changed visibility in hgTrackUi dialog
  • lines changed 6, context: html, text, full: html, text
    Tracks with children should not be rightClick configured with a popup
  • lines changed 81, context: html, text, full: html, text
    Made getAllVars understand subtrack vis. Redid cfg popup OK with subtrack vis understanding in mind
  • lines changed 15, context: html, text, full: html, text
    Change popup cfg to recognize only changed vars for update to cart and page update
  • lines changed 2, context: html, text, full: html, text
    Larry noticed my bug. Thanks. Now localVisibility should again be kept up to date
  • lines changed 7, context: html, text, full: html, text
    support configureByPopup trackDb setting (currently experimental)
  • lines changed 21, context: html, text, full: html, text
    add currentMapItem logic; fixes problem where right-click wasn't getting all the details for map items under IE
• src/hg/js/hui.js
  • lines changed 29, context: html, text, full: html, text
    Change popup cfg to recognize only changed vars for update to cart and page update
• src/hg/js/jquery.tablednd.js
  • lines changed 1, context: html, text, full: html, text
    MSIE thinks its button 1 but other browsers think its button 0. These children should learn to play nice.
• src/hg/js/utils.js
  • lines changed 27, context: html, text, full: html, text
    move showLoadingImage/hideLoadingImage to utils.js
  • lines changed 39, context: html, text, full: html, text
    add getAllVars and objectToQueryString
  • lines changed 10, context: html, text, full: html, text
    Made getAllVars understand subtrack vis. Redid cfg popup OK with subtrack vis understanding in mind
  • lines changed 19, context: html, text, full: html, text
    Change popup cfg to recognize only changed vars for update to cart and page update
  • lines changed 12, context: html, text, full: html, text
    Added two useful functions for overriding forms with ajax
  • lines changed 40, context: html, text, full: html, text
    Encapulated waitMaskSetup and waitMaskClear to use them with ajaxWait code. Also made sure that waitmask has a timeout.
• src/hg/lib/cart.c
  • lines changed 27, context: html, text, full: html, text
    After changing cartDump to encode vars and vals, I decided to make it all ajaxy
  • lines changed 3, context: html, text, full: html, text
    Counter adds an extra touch
• src/hg/lib/gencodeGeneClass.as
  • lines changed 6, context: html, text, full: html, text
    update to reflect reality, apparently these haven't been used for a while
• src/hg/lib/gencodeGeneClass.c
  • lines changed 104, context: html, text, full: html, text
    update to reflect reality, apparently these haven't been used for a while
• src/hg/lib/gencodeGeneClass.sql
  • lines changed 6, context: html, text, full: html, text
    update to reflect reality, apparently these haven't been used for a while
• src/hg/lib/hui.c
  • lines changed 57, context: html, text, full: html, text
    adding PSL configuration for multi-views
  • lines changed 58, context: html, text, full: html, text
    consolidate the baseColor drop down box code to a single instance
  • lines changed 4, context: html, text, full: html, text
    Disable 'view table schema' link when setting 'tableBrowser off' is present.
• src/hg/lib/rgdGene2Xref.sql
  • lines changed 9, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/lib/rgdGeneCds.sql
  • lines changed 6, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/lib/rgdGeneRaw0.sql
  • lines changed 2, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    adding PSL configuration for multi-views
• src/hg/makeDb/doc/dm3.txt
  • lines changed 45, context: html, text, full: html, text
    More liftOver'd BDTNP data.
• src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt
  • lines changed 32, context: html, text, full: html, text
    more doc
  • lines changed 9, context: html, text, full: html, text
    reload classes table with hgLoadSqlTab to get around some munging
• src/hg/makeDb/doc/hg18.txt
  • lines changed 3, context: html, text, full: html, text
    GWAS catalog data update.
  • lines changed 221, context: html, text, full: html, text
    finishing off the hg18 and hg19 ContigDiff tracks
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    GWAS catalog data update.
  • lines changed 13, context: html, text, full: html, text
    Barely started gathering data for fosEndPairs. checking in so I can switch branches.
  • lines changed 4, context: html, text, full: html, text
    Fix snp131Clinical's missing-func item, which is still in snp131.bed.
  • lines changed 6, context: html, text, full: html, text
    finishing off the hg18 and hg19 ContigDiff tracks
• src/hg/makeDb/doc/hg19Patch2.txt
  • lines changed 103, context: html, text, full: html, text
    added blat server and lastz to hg19
  • lines changed 140, context: html, text, full: html, text
    add the business to construct the altSequence chains and nets and PSL track
• src/hg/makeDb/doc/mm9.txt
  • lines changed 5, context: html, text, full: html, text
    Add comment for redmine issue 480
• src/hg/makeDb/genbank/doc/to-do.txt
  • lines changed 3, context: html, text, full: html, text
    added note on bogus cDNA to private doc
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    do not need ccds genes for hg19Patch2
  • lines changed 17, context: html, text, full: html, text
    Added ce9 C. elegans WS120
• src/hg/makeDb/trackDb/README
  • lines changed 3, context: html, text, full: html, text
    comment about deprecated type wig to type bigWig types
  • lines changed 3, context: html, text, full: html, text
    configureByPopup related changes
• src/hg/makeDb/trackDb/drosophila/bdtnpChipper.html
  • lines changed 15, context: html, text, full: html, text
    Added brief mention of new subtracks and the new reference for them.
• src/hg/makeDb/trackDb/drosophila/bdtnpChipperOld.html
  • lines changed 189, context: html, text, full: html, text
    Adding html override for bdtnpChipper until release of new data.
• src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html
  • lines changed 57, context: html, text, full: html, text
    Description by Mark Biggin w/minor formatting/wording tweaks.
  • lines changed 7, context: html, text, full: html, text
    Small tweaks based on Results section of manuscript.
• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Adding html override for bdtnpChipper until release of new data.
• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Adding html override for bdtnpChipper until release of new data.
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Use complete gene names for all factor labels, not just the latter half of them -- don't know why I didn't before.
• src/hg/makeDb/trackDb/human/agilentCgh.notPublic.html
  • lines changed 123, context: html, text, full: html, text
    Made new Agilent HTML for release alpha
• src/hg/makeDb/trackDb/human/agilentProbes.html
  • lines changed 131, context: html, text, full: html, text
    Changes to Agilent tracks, Aug 2010: tables in description pages, mapping directly to hg19 vs lift, two more arrays for both mouse and rat, corrections to mouse and rat AMADIDs.
  • lines changed 13, context: html, text, full: html, text
    Subtrack listing at top of description page redundant.
  • lines changed 118, context: html, text, full: html, text
    Old Agilent description that should be public during QA
• src/hg/makeDb/trackDb/human/altSeqComposite.html
  • lines changed 17, context: html, text, full: html, text
    loading the hg19Patch2 sequences as psl tracks
• src/hg/makeDb/trackDb/human/darned.html
  • lines changed 32, context: html, text, full: html, text
    making it more readable. adding more structure to the page
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 13, context: html, text, full: html, text
    adding data use restrictions per nigel carter
• src/hg/makeDb/trackDb/human/dgv.html
  • lines changed 6, context: html, text, full: html, text
    fixed broken end-font tag that only showed up in IE
• src/hg/makeDb/trackDb/human/hg18/agilentProbes.html
  • lines changed 150, context: html, text, full: html, text
    Changes to Agilent tracks, Aug 2010: tables in description pages, mapping directly to hg19 vs lift, two more arrays for both mouse and rat, corrections to mouse and rat AMADIDs.
• src/hg/makeDb/trackDb/human/hg18/hg18ContigDiff.html
  • lines changed 31, context: html, text, full: html, text
    changing track name
  • lines changed 16, context: html, text, full: html, text
    add table of color and score to indicate category of change
• src/hg/makeDb/trackDb/human/hg18/hg19ContigDiff.html
  • lines changed 31, context: html, text, full: html, text
    changing track name
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metaDb for SUNY RBP on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeSunyalbanyRnaGeneChip.ra
  • lines changed 141, context: html, text, full: html, text
    staging metaDb for SUNY RBP on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    making it so SUNY RBP on rr uses metaDb for its metadata
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeSunyalbanyRnaGeneChip.ra
  • lines changed 141, context: html, text, full: html, text
    making it so SUNY RBP on rr uses metaDb for its metadata
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    configureByPopup related changes
  • lines changed 6, context: html, text, full: html, text
    hg18ContigDiff changing track name and becomes itemRgb
• src/hg/makeDb/trackDb/human/hg19/agilentProbes.html
  • lines changed 158, context: html, text, full: html, text
    Changes to Agilent tracks, Aug 2010: tables in description pages, mapping directly to hg19 vs lift, two more arrays for both mouse and rat, corrections to mouse and rat AMADIDs.
• src/hg/makeDb/trackDb/human/hg19/hg18ContigDiff.html
  • lines changed 31, context: html, text, full: html, text
    changing track name
• src/hg/makeDb/trackDb/human/hg19/hg19ContigDiff.html
  • lines changed 31, context: html, text, full: html, text
    changing track name
  • lines changed 16, context: html, text, full: html, text
    add table of color and score to indicate category of change
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 801, context: html, text, full: html, text
    Added 6 new submissions for SYDH TFBS track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 554, context: html, text, full: html, text
    Removed duplcate UwHistone track. Update metaData for UW to remove rank, as this is duplicated information as replicate
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 57, context: html, text, full: html, text
    loading the hg19Patch2 sequences as psl tracks
  • lines changed 23, context: html, text, full: html, text
    make the altSeqComposite be a view in the middle composite
  • lines changed 8, context: html, text, full: html, text
    attempting to baseColor altSeq
  • lines changed 14, context: html, text, full: html, text
    adding base coloring options to altSequence
  • lines changed 66, context: html, text, full: html, text
    adding chain net tracks to the altSeqComposite
  • lines changed 2, context: html, text, full: html, text
    no need for the URL to the otherDb
  • lines changed 22, context: html, text, full: html, text
    removing experiments testChainHg19Patch2 and patch2Psl
  • lines changed 6, context: html, text, full: html, text
    hg19ContigDiff changing track name and becomes itemRgb
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 4, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibRrbs.ra
  • lines changed 574, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeHaibTfbs.ra
  • lines changed 2596, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhHistone.ra
  • lines changed 301, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhTfbs.ra
  • lines changed 764, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDNAseSuper.html
  • lines changed 41, context: html, text, full: html, text
    rewrote the Display Conventions and Credits sections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDnaMethylSuper.html
  • lines changed 23, context: html, text, full: html, text
    rewrote the Display Conventions and Credits sections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeExonArraySuper.html
  • lines changed 25, context: html, text, full: html, text
    rewrote the Display Conventions and Credits sections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • lines changed 2, context: html, text, full: html, text
    some changes that Katrina requested, version 4 instead of release 4, and taking V4 out of the short table
  • lines changed 3, context: html, text, full: html, text
    edits to Level descriptions
  • lines changed 4, context: html, text, full: html, text
    modified the second sentence of the Release Notes section in accordance with Mark's re-write
  • lines changed 1, context: html, text, full: html, text
    change 2way_consensus_pseudogene to 2way_pseudogene
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.ra
  • lines changed 1, context: html, text, full: html, text
    some changes that Katrina requested, version 4 instead of release 4, and taking V4 out of the short table
  • lines changed 2, context: html, text, full: html, text
    change 2way_consensus_pseudogene to 2way_pseudogene
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.html
  • lines changed 23, context: html, text, full: html, text
    added more documentation, removed unnecessary dashes, and changed colour to American English
  • lines changed 2, context: html, text, full: html, text
    added info about alignability
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRrbs.ra
  • lines changed 574, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 2596, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHistoneSuper.html
  • lines changed 61, context: html, text, full: html, text
    rewrote the Display Conventions and Credits sections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRnaSeqSuper.html
  • lines changed 44, context: html, text, full: html, text
    rewrote the Display Conventions and Credits sections
  • lines changed 10, context: html, text, full: html, text
    made some edits
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRnaSubcellLocSuper.html
  • lines changed 19, context: html, text, full: html, text
    rewrote the Display Conventions and Credits sections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 301, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 764, context: html, text, full: html, text
    Updated Encode tracDb names to be only the composite name.ra instead of including prefix trackDb
  • lines changed 122, context: html, text, full: html, text
    Added 6 new submissions for SYDH TFBS track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
  • lines changed 21, context: html, text, full: html, text
    rewrote the Display Conventions and Credits sections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwChIPSeq.ra
  • lines changed 2613, context: html, text, full: html, text
    Removed duplcate UwHistone track. Update metaData for UW to remove rank, as this is duplicated information as replicate
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 1011, context: html, text, full: html, text
    Removed reference to rank, No rank in metaData only replicate information. Changed rank to replicate.
  • lines changed 337, context: html, text, full: html, text
    Updated the track configuration to display replicate information, which was forgotten last time
  • lines changed 2, context: html, text, full: html, text
    Updated typo's when trying to display replicate
  • lines changed 1, context: html, text, full: html, text
    Misspelled Replicate
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
  • lines changed 795, context: html, text, full: html, text
    Removed duplcate UwHistone track. Update metaData for UW to remove rank, as this is duplicated information as replicate
  • lines changed 3, context: html, text, full: html, text
    Updated the track configuration to display replicate information, which was forgotten last time
• src/hg/makeDb/trackDb/human/hg19Patch2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    loading the hg19Patch2 sequences as psl tracks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    Changes to Agilent tracks, Aug 2010: tables in description pages, mapping directly to hg19 vs lift, two more arrays for both mouse and rat, corrections to mouse and rat AMADIDs.
  • lines changed 18, context: html, text, full: html, text
    Updated dgv track entry in prep for track release.
  • lines changed 85, context: html, text, full: html, text
    Changes to trackDb that for release separation of the Agilent track (even though apparently the Agilent trackDb is already on the RR. The next push to the RR should have the pre-QA version at least).
• src/hg/makeDb/trackDb/mouse/agilentCgh.html
  • lines changed 72, context: html, text, full: html, text
    Changes to Agilent tracks, Aug 2010: tables in description pages, mapping directly to hg19 vs lift, two more arrays for both mouse and rat, corrections to mouse and rat AMADIDs.
  • lines changed 10, context: html, text, full: html, text
    Subtrack listing at top of description page redundant.
  • lines changed 61, context: html, text, full: html, text
    Made a little mess after forgetting the release alpha/beta policy. Rolled the HTML back two commits, added a .notPublic.html for the alpha release trackDbs.
• src/hg/makeDb/trackDb/mouse/agilentCgh.notPublic.html
  • lines changed 90, context: html, text, full: html, text
    Made a little mess after forgetting the release alpha/beta policy. Rolled the HTML back two commits, added a .notPublic.html for the alpha release trackDbs.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Updated the trackDb names used in the include statment for Encode tracks
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncodeSydhHist.ra
  • lines changed 145, context: html, text, full: html, text
    Updated the naming schema for trackDb for Encode tracks to not include prefix trackDb for composites
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncodeSydhTfbs.ra
  • lines changed 571, context: html, text, full: html, text
    Updated the naming schema for trackDb for Encode tracks to not include prefix trackDb for composites
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncodeUwDnase.ra
  • lines changed 1018, context: html, text, full: html, text
    Updated the naming schema for trackDb for Encode tracks to not include prefix trackDb for composites
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
  • lines changed 145, context: html, text, full: html, text
    Updated the naming schema for trackDb for Encode tracks to not include prefix trackDb for composites
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
  • lines changed 571, context: html, text, full: html, text
    Updated the naming schema for trackDb for Encode tracks to not include prefix trackDb for composites
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 1018, context: html, text, full: html, text
    Updated the naming schema for trackDb for Encode tracks to not include prefix trackDb for composites
  • lines changed 1, context: html, text, full: html, text
    Removed the term rank and used replicate
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    Changes to Agilent tracks, Aug 2010: tables in description pages, mapping directly to hg19 vs lift, two more arrays for both mouse and rat, corrections to mouse and rat AMADIDs.
  • lines changed 28, context: html, text, full: html, text
    Made release alpha and release beta,public versions of Agilent trackDb stanzas
  • lines changed 7, context: html, text, full: html, text
    Made a little mess after forgetting the release alpha/beta policy. Rolled the HTML back two commits, added a .notPublic.html for the alpha release trackDbs.
• src/hg/makeDb/trackDb/rat/agilentCgh.html
  • lines changed 73, context: html, text, full: html, text
    Changes to Agilent tracks, Aug 2010: tables in description pages, mapping directly to hg19 vs lift, two more arrays for both mouse and rat, corrections to mouse and rat AMADIDs.
  • lines changed 10, context: html, text, full: html, text
    Subtrack listing at top of description page redundant.
  • lines changed 63, context: html, text, full: html, text
    Made a little mess after forgetting the release alpha/beta policy. Rolled the HTML back two commits, added a .notPublic.html for the alpha release trackDbs.
• src/hg/makeDb/trackDb/rat/agilentCgh.notPublic.html
  • lines changed 90, context: html, text, full: html, text
    Made a little mess after forgetting the release alpha/beta policy. Rolled the HTML back two commits, added a .notPublic.html for the alpha release trackDbs.
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    Changes to Agilent tracks, Aug 2010: tables in description pages, mapping directly to hg19 vs lift, two more arrays for both mouse and rat, corrections to mouse and rat AMADIDs.
  • lines changed 28, context: html, text, full: html, text
    Made release alpha and release beta,public versions of Agilent trackDb stanzas
  • lines changed 7, context: html, text, full: html, text
    Made a little mess after forgetting the release alpha/beta policy. Rolled the HTML back two commits, added a .notPublic.html for the alpha release trackDbs.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    add configureByPopup
  • lines changed 1, context: html, text, full: html, text
    add 2way_pseudogene
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    Added hgApi to the cgis built
• src/hg/oneShot/doRgdGene2/doRgdGene2.c
  • lines changed 71, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/oneShot/doRgdGene2/makefile
  • lines changed 38, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/oneShot/doRgdGene2Xref/doRgdGene2Xref.c
  • lines changed 201, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/oneShot/doRgdGene2Xref/makefile
  • lines changed 38, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/oneShot/getRgdGeneCds/getRgdGeneCds.c
  • lines changed 69, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/oneShot/getRgdGeneCds/makefile
  • lines changed 38, context: html, text, full: html, text
    Created several one shot programs and .sql files for the RGD Genes build pipeline
• src/hg/pslMap/makefile
  • lines changed 1, context: html, text, full: html, text
    fixed broken rule, not sure why this was even working
• src/hg/utils/motifFinder/motifFinder.c
  • lines changed 18, context: html, text, full: html, text
    support uniformBackground
• src/inc/cheapcgi.h
  • lines changed 4, context: html, text, full: html, text
    Moved cgiDropDownnWithTextValsAndExtra from searchTracks
• src/lib/cheapcgi.c
  • lines changed 27, context: html, text, full: html, text
    Moved cgiDropDownnWithTextValsAndExtra from searchTracks
  • lines changed 1, context: html, text, full: html, text
    Insignificant change in spacing of an input box
• src/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    added back in compile of gtfToGenePred, which was removed for no obvious reasons
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v240 preview

• lines changed: 23858
• files changed: 215