All File Changes

v259_preview to v259_preview2 (2011-10-25 to 2011-11-01) v259

• python/lib/setup.py
  • lines changed 0, context: html, text, full: html, text
    removed execute flag on setup.py. it's now executable
• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 57, context: html, text, full: html, text
    removed executable portion, fixed bug with special mdb
  • lines changed 0, context: html, text, full: html, text
    unsetting exectuable flag for these
  • lines changed 29, context: html, text, full: html, text
    moved a function out for cleanliness
  • lines changed 386, context: html, text, full: html, text
    refactored a bit, removed some random newlines in output
  • lines changed 12, context: html, text, full: html, text
    fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
  • lines changed 8, context: html, text, full: html, text
    cleaned up output a little
  • lines changed 53, context: html, text, full: html, text
    pulled out functions that may be useful outside of mkChangeNotes
  • lines changed 78, context: html, text, full: html, text
    changed output a little, added in some some printing functions, prints out a missing tables list now also
  • lines changed 22, context: html, text, full: html, text
    declared some attributes earlier to bypass a qa check.
  • lines changed 3, context: html, text, full: html, text
    put in date notes file was generated
  • lines changed 7, context: html, text, full: html, text
    using correct path from dropped files
  • lines changed 26, context: html, text, full: html, text
    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• python/lib/ucscgenomics/qa.py
  • lines changed 111, context: html, text, full: html, text
    added some documentation, added in 2 new functions, and corrected some other stuff i noticed
  • lines changed 88, context: html, text, full: html, text
    reworked qa.py and separated out the executable portion into another app in encode
  • lines changed 0, context: html, text, full: html, text
    unsetting exectuable flag for these
  • lines changed 4, context: html, text, full: html, text
    added skipping of comment lines for label check
  • lines changed 1, context: html, text, full: html, text
    added timeout to error message
  • lines changed 1, context: html, text, full: html, text
    upped timeout to 20 seconds
  • lines changed 22, context: html, text, full: html, text
    added smarted filtering error messages
• python/lib/ucscgenomics/track.py
  • lines changed 26, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 16, context: html, text, full: html, text
    added in a property I needed in qaInit
  • lines changed 11, context: html, text, full: html, text
    added in ability to use a custom mdb
  • lines changed 1, context: html, text, full: html, text
    minor bug fix for composite track
  • lines changed 10, context: html, text, full: html, text
    added qa test dir attribute
  • lines changed 22, context: html, text, full: html, text
    style.txt updated, fixed merge conflict
• python/lib/ucscgenomics/ucscUtils.py
  • lines changed 41, context: html, text, full: html, text
    pulled out functions that may be useful outside of mkChangeNotes
• python/programs/mkChangeNotes/mkChangeNotes
  • lines changed 446, context: html, text, full: html, text
    merge conflict resolved
• python/programs/mkGeoPkg/mkGeoPkg
  • lines changed 104, context: html, text, full: html, text
    minor updates to mkGeoPkg
  • lines changed 707, context: html, text, full: html, text
    somehow these got removed when I pulled??? I put them back
• python/programs/qaInit/qaInit.py
  • lines changed 417, context: html, text, full: html, text
    merge conflict resolved
• python/programs/qaUpdateMetadata/qaUpdateMetadata
  • lines changed 82, context: html, text, full: html, text
    merge conflict resolved
• python/programs/trackInfo/trackInfo
  • lines changed 8, context: html, text, full: html, text
    trackInfo now supports the bam/bai comma separated filenames, style guide updated
  • lines changed 182, context: html, text, full: html, text
    somehow these got removed when I pulled??? I put them back
• python/style.txt
  • lines changed 30, context: html, text, full: html, text
    trackInfo now supports the bam/bai comma separated filenames, style guide updated
  • lines changed 36, context: html, text, full: html, text
    style.txt updated, fixed merge conflict
• src/hg/das/das.c
  • lines changed 16, context: html, text, full: html, text
    skip tables which have "tableBrowser off" in trackDb (e.g. decipher; see redmine #5803)
• src/hg/encode/DAFs/3.0/hg19/wgEncodeBroadHistone.daf
  • lines changed 5, context: html, text, full: html, text
    Updated DAF to Version 1.8 to add treatment as a variable and removed peaks as required so that lab can submit controls.
  • lines changed 2, context: html, text, full: html, text
    Updated DAF to be correct composite which is Broad Histone.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeUwRepliSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Updated DAF say downloadOnly for Alignment files.
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 1, context: html, text, full: html, text
    merge conflict resolved
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 550, context: html, text, full: html, text
    made directory work with rename
  • lines changed 1, context: html, text, full: html, text
    changed program name in usage
• src/hg/encode/encodeQaInit/makefile
  • lines changed 27, context: html, text, full: html, text
    renamed directory qaInit > encodeQaInit
  • lines changed 1, context: html, text, full: html, text
    made directory work with rename
• src/hg/encode/encodeQaInit/qaInit
  • lines changed 550, context: html, text, full: html, text
    renamed directory qaInit > encodeQaInit
  • lines changed 550, context: html, text, full: html, text
    made directory work with rename
• src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease
  • lines changed 96, context: html, text, full: html, text
    first draft (still in perl, but it doesn't need library functions, so porting is not a priority) for qa's program to insert a row into the L queue
• src/hg/encode/encodeQaSqlRelease/makefile
  • lines changed 27, context: html, text, full: html, text
    first draft (still in perl, but it doesn't need library functions, so porting is not a priority) for qa's program to insert a row into the L queue
• src/hg/encode/encodeReport/atticReport.sh
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    This is not a package that we have installed
  • lines changed 1, context: html, text, full: html, text
    I do not think this line should have been commented out
  • lines changed 2, context: html, text, full: html, text
    corrected erroneously commented out line
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 2, context: html, text, full: html, text
    Swapped tissue and lineage in cell table.
• src/hg/encode/mkChangeNotes/makefile
  • lines changed 27, context: html, text, full: html, text
    fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
• src/hg/encode/mkChangeNotes/mkChangeNotes
  • lines changed 7, context: html, text, full: html, text
    added in the ability to custom define a composite mdb
• src/hg/encode/mkChangeNotes/tests/CurrentMkChangeNotes.py
  • lines changed 126, context: html, text, full: html, text
    new testing structure for mkChangeNotes, still needs full function testing
  • lines changed 411, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
  • lines changed 13, context: html, text, full: html, text
    fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
  • lines changed 8, context: html, text, full: html, text
    updating test
  • lines changed 53, context: html, text, full: html, text
    pulled out functions that may be useful outside of mkChangeNotes
  • lines changed 123, context: html, text, full: html, text
    updated test to reflect newer version of mkChangenotes
• src/hg/encode/mkChangeNotes/tests/mkChangeTest
  • lines changed 83, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/mkChangeTest.py
  • lines changed 36, context: html, text, full: html, text
    new testing structure for mkChangeNotes, still needs full function testing
  • lines changed 72, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/release1test/wgEncodeTest.ra
  • lines changed 73, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/release2test/wgEncodeTest.ra
  • lines changed 143, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/release3test/wgEncodeTest.ra
  • lines changed 145, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/release4test/wgEncodeTest.ra
  • lines changed 173, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkChangeNotes/tests/testRunner
  • lines changed 61, context: html, text, full: html, text
    fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
• src/hg/encode/mkGeoPkg/mkGeoPkg
  • lines changed 707, context: html, text, full: html, text
    style.txt updated, fixed merge conflict
• src/hg/encode/qaEncodeTracks2/qaEncodeTracks
  • lines changed 67, context: html, text, full: html, text
    reworked qa.py and separated out the executable portion into another app in encode
  • lines changed 14, context: html, text, full: html, text
    added in delimiters for human readibility in script output
  • lines changed 9, context: html, text, full: html, text
    put in better delimiters
• src/hg/encode/qaInit/makefile
  • lines changed 27, context: html, text, full: html, text
    fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
  • lines changed 27, context: html, text, full: html, text
    renamed directory qaInit > encodeQaInit
• src/hg/encode/qaInit/qaInit
  • lines changed 60, context: html, text, full: html, text
    added in qa checks from ported qaEncodeTracks
  • lines changed 17, context: html, text, full: html, text
    bug fixes and added in ability to use custom mdb names
  • lines changed 3, context: html, text, full: html, text
    added in switch to take errors in local mkChangeNotes data into account
  • lines changed 1, context: html, text, full: html, text
    updated usage
  • lines changed 2, context: html, text, full: html, text
    Changing the error message and made it not fatal
  • lines changed 45, context: html, text, full: html, text
    last draft before reviewing for qaInit, added test mode, print out list of subIds
  • lines changed 23, context: html, text, full: html, text
    changed what initdate means, added function to keep it rolling along everytime init is run
  • lines changed 550, context: html, text, full: html, text
    renamed directory qaInit > encodeQaInit
• src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
  • lines changed 2, context: html, text, full: html, text
    Updated description
• src/hg/encode/trackInfo/trackInfo
  • lines changed 182, context: html, text, full: html, text
    style.txt updated, fixed merge conflict
• src/hg/hgApi/hgApi.c
  • lines changed 1, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 21, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 5, context: html, text, full: html, text
    merge conflict resolved
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 3, context: html, text, full: html, text
    note that a routine consumes one of its arguments. om nom nom. #5754
  • lines changed 1, context: html, text, full: html, text
    added a little snippet of HTML per Greg
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 44, context: html, text, full: html, text
    Long overdue checkboxes added to superTrack config page.
  • lines changed 2, context: html, text, full: html, text
    Minor fix for turning off SUPERS_WITH_CHECKBOXES
  • lines changed 2, context: html, text, full: html, text
    Fixed bug where rightClick popup cfg sometimes had wrong visibility
  • lines changed 1, context: html, text, full: html, text
    Add limited support for bigBeds to have scoreFilter controls.
• src/hg/hgTracks/config.c
  • lines changed 9, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 6, context: html, text, full: html, text
    Long overdue checkboxes added to superTrack config page.
• src/hg/hgTracks/cytoBandTrack.c
  • lines changed 7, context: html, text, full: html, text
    merge conflict resolved
• src/hg/hgTracks/hgTracks.c
  • lines changed 54, context: html, text, full: html, text
    merge conflict resolved
• src/hg/hgTracks/imageV2.c
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
• src/hg/hgTracks/rmskTrack.c
  • lines changed 9, context: html, text, full: html, text
    MLQ #5795 (question mark in repeats table): user asked about the ?'s thatappear at the end of some repClass and repFamily names in rmsk. I asked Robert Hubley and he said they are just an indication that a new repeat is suspected to be in some class but hasn't been confirmed yet. He suggested ignoring the ?. I looked at rmskTrack.c and found that the ? at end was causing such items to default to the Other category. This change strips a trailing ? from the class name that we look up in the hash (but leaves it in the ro.repClass field because that's used for the mouseover title). Now if repClass is "DNA?" the item will still be drawn in the DNA row.
• src/hg/hgTracks/searchTracks.c
  • lines changed 7, context: html, text, full: html, text
    merge conflict resolved
• src/hg/hgTracks/vcfTrack.c
  • lines changed 102, context: html, text, full: html, text
    merge conflict resolved
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    Create lincRNAs supertrack
  • lines changed 1, context: html, text, full: html, text
    Rename track lincRNAsIsoforms to lincRNAsTranscripts
  • lines changed 2, context: html, text, full: html, text
    Changed punctuation in two places to match commit 39c3f339e5b.
• src/hg/htdocs/ENCODE/dataMatrix/chipMatrix.css
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
  • lines changed 41, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 39, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
  • lines changed 2, context: html, text, full: html, text
    1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
• src/hg/htdocs/ENCODE/dataMatrix/dataSummary.css
  • lines changed 50, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 12, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 8, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 1, context: html, text, full: html, text
    Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
  • lines changed 25, context: html, text, full: html, text
    1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
  • lines changed 1, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixMouse.html
  • lines changed 7, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 8, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 1, context: html, text, full: html, text
    Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
  • lines changed 20, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
  • lines changed 2, context: html, text, full: html, text
    1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
  • lines changed 1, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixMouse.html
  • lines changed 7, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 8, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
  • lines changed 7, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 11, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
  • lines changed 2, context: html, text, full: html, text
    1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
  • lines changed 1, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryMouse.html
  • lines changed 7, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 11, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/ENCODE/experiment_guidelines.html
  • lines changed 2, context: html, text, full: html, text
    Relating to ticket 5523
• src/hg/htdocs/ENCODE/platform_characterization.html
  • lines changed 19, context: html, text, full: html, text
    related to redmine ticket 5523
  • lines changed 2, context: html, text, full: html, text
    Relating to ticket 5523
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 310, context: html, text, full: html, text
    updated pubs
  • lines changed 38, context: html, text, full: html, text
    readded seperator lines, moved an entry around
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    This is related to ticket 5526 adding the publications
  • lines changed 109, context: html, text, full: html, text
    converted to new encode format, updated old html tags, and fixed a character that need to be in ascii format, redmine# 5526
  • lines changed 88, context: html, text, full: html, text
    The first 2 sections of this are ordered.
  • lines changed 754, context: html, text, full: html, text
    Large amounts of citations were added and sorted.
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 47, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 2, context: html, text, full: html, text
    Commented out reference to the VCF format page which is not yet active on the RR
  • lines changed 7, context: html, text, full: html, text
    Changing wording on score handling
  • lines changed 4, context: html, text, full: html, text
    Changing is to includes
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 5, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 46, context: html, text, full: html, text
    merge conflict resolved
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    Put org name in italics.
• src/hg/htdocs/staff.html
  • lines changed 23, context: html, text, full: html, text
    added Steve, Matt, Gary
• src/hg/htdocs/style/encodeProject.css
  • lines changed 62, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 3, context: html, text, full: html, text
    Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
  • lines changed 26, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
  • lines changed 9, context: html, text, full: html, text
    1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
  • lines changed 6, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/inc/jsHelper.h
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/inc/vcfUi.h
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/js/ajax.js
  • lines changed 35, context: html, text, full: html, text
    merge conflict resolved
• src/hg/js/encodeChipMatrix.js
  • lines changed 19, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 32, context: html, text, full: html, text
    Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
  • lines changed 4, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
  • lines changed 93, context: html, text, full: html, text
    1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
  • lines changed 32, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/js/encodeDataMatrix.js
  • lines changed 39, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 37, context: html, text, full: html, text
    Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
  • lines changed 111, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
  • lines changed 11, context: html, text, full: html, text
    1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
  • lines changed 35, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/js/encodeDataSummary.js
  • lines changed 30, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 43, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
  • lines changed 9, context: html, text, full: html, text
    1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
  • lines changed 55, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/js/encodeProject.js
  • lines changed 14, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 27, context: html, text, full: html, text
    1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
  • lines changed 23, context: html, text, full: html, text
    Add filtering by assembly
• src/hg/js/hgCustom.js
  • lines changed 7, context: html, text, full: html, text
    merge conflict resolved
• src/hg/js/hgTracks.js
  • lines changed 1956, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 5, context: html, text, full: html, text
    replace some instances of $(#...) with document.getElementById to deal with possible metacharacter in track names
• src/hg/js/hui.js
  • lines changed 93, context: html, text, full: html, text
    Long overdue checkboxes added to superTrack config page.
• src/hg/js/jquery.floatheader-min.js
  • lines changed 143, context: html, text, full: html, text
    Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
• src/hg/js/jquery.floatheader.js
  • lines changed 282, context: html, text, full: html, text
    Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 1, context: html, text, full: html, text
    Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
  • lines changed 2, context: html, text, full: html, text
    Merge branch 'master' into matrix
  • lines changed 2, context: html, text, full: html, text
    Merge branch 'matrix'
• src/hg/lib/fileUi.c
  • lines changed 37, context: html, text, full: html, text
    No functional change. Just better commenting and some name changing as requested by Brian in code review.
  • lines changed 1, context: html, text, full: html, text
    Oops. Not a long int.
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    To resolve Redmine # 1118, repeating domain links. The issue is that when a protein has multiple instances of the same domain, the known gene details page shows multiple (redundant) links to the domain entry. Resolved this by replacing a 'select' statement with a 'select distinct'
• src/hg/lib/hui.c
  • lines changed 12, context: html, text, full: html, text
    Add limited support for bigBeds to have scoreFilter controls.
• src/hg/lib/jsHelper.c
  • lines changed 34, context: html, text, full: html, text
    merge conflict resolved
• src/hg/lib/search.c
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/lib/trackDbCustom.c
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    Add limited support for bigBeds to have scoreFilter controls.
• src/hg/lib/vcfUi.c
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    merge conflict resolved
• src/hg/lib/web.c
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    remove obsolete TOO_TIMID_FOR_CURRENT_HTML_STANDARDS code (code cleanup to get ready for jabico related menu redesign)
  • lines changed 3, context: html, text, full: html, text
    This should be a safe change to js and css links in the CGI ouutput. It will eliminate problems with htmlCheck linkChecker.
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    add NEW_MENUS code to experiment with using jabico derived menus (see redmine #5245)
• src/hg/makeDb/doc/bosTau4.txt
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    merge conflict resolved
• src/hg/makeDb/doc/bosTau6.txt
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    merge conflict resolved
• src/hg/makeDb/doc/calJac3.txt
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    finishing up the lastz runs to gorGor3
• src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release1.notes
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    notes location for encodeTest
• src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release2.notes
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    notes location for encodeTest
• src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release3.notes
  • lines changed 119, context: html, text, full: html, text
    notes location for encodeTest
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 1503, context: html, text, full: html, text
    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeMapability.release3.notes
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    merge conflict resolved
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    Newer version of mkChangeNotes generated this one. However, it is hand edited to compensate for minor discrepency
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
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    Fixing the long labels and removing the preamble from the notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
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    merge conflict resolved
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release2.notes
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    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechHist.release1.notes
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    merge conflict resolved
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    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechTfbs.release1.notes
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    merge conflict resolved
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    added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
• src/hg/makeDb/doc/gorGor3.txt
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    done with Chimp and Orangutan lastz
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    finishing up the lastz runs to gorGor3
• src/hg/makeDb/doc/hg18.txt
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    merge conflict resolved
• src/hg/makeDb/doc/hg19.txt
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    merge conflict resolved
• src/hg/makeDb/doc/melGal1.txt
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    merge conflict resolved
• src/hg/makeDb/doc/nomLeu1.txt
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    merge conflict resolved
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    finishing up the lastz runs to gorGor3
• src/hg/makeDb/doc/panTro3.txt
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    finishing up the lastz runs to gorGor3
• src/hg/makeDb/doc/ponAbe2.txt
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    finished with lastz gorGor3 to rheMac2 and ponAbe2
• src/hg/makeDb/doc/rheMac2.txt
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    finished with lastz gorGor3 to rheMac2 and ponAbe2
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
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    merge conflict resolved
• src/hg/makeDb/genbank/etc/align.dbs
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    Added macEug2 - Wallaby
• src/hg/makeDb/genbank/etc/genbank.conf
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    merge conflict resolved
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    Added melGal1, myoLuc2 and xenTro3
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    Added macEug2 - Wallaby
• src/hg/makeDb/genbank/etc/rr.dbs
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    Added bosTau6, melGal1, myoLuc2 and xenTro3
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
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    Initial set up for expression data of lincRNAs
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    Group lincRNAs microarray data
• src/hg/makeDb/hgKgGetText/hgKgGetText.c
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    merge conflict resolved
• src/hg/makeDb/schema/all.joiner
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    merge conflict resolved
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    Track #34 (dbVar/ISCA): added isca% to tablesIgnored $hg.
• src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
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    fixup sgpGene searchTable rule to match these scaffold names
• src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
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    fixup checkHgFindSpec errors
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
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    Temporarily commented out 'pseudogene mRNA' sample query from gateway page
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
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    merge conflict resolved
  • lines changed 17, context: html, text, full: html, text
    Adding TCF4 details to clear up ambiguity with TCF7L2
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    Adding more TCF-4 detail to description
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    Adding more TCF7L2 detail to description
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    Adding CD14 stanza for tier 2 cells from second draw
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    Code Review changes
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    A was trying to change the antibodies to have the target description, see ticket #1017, I ended up having a very difficult merge conflict surrounding the doner IDs. I think Jeff needs to look at this
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    Adding CD14, Removing redundant redundancies, CaPiToLiZaTiOn stuff
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    CaPiToLiZaTiOn and more redundant redundanciesremoved
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    A few finishing touches
• src/hg/makeDb/trackDb/cv/beta/cv.ra
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    Code Review changes
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    New CV from alpha
• src/hg/makeDb/trackDb/cv/public/cv.ra
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    pushing reviewed cv.ra changes to public
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    copying over fixes from code review Jeff made in beta/cv.ra
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    fixup nscanGene checkHgFindSpec
• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
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    fixup ensGene and flyBase gene search rules to match the new patterns
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
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    fixup ensGene and flyBase gene search rules to match the new patterns
• src/hg/makeDb/trackDb/fugu/fr1/trackDb.ra
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    update ensGene search rules to work with the Ensembl naming pattern here
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/makefile
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest1.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest2.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest3.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest4.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/makefile
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest1.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest2.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest3.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest4.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/makefile
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest.ra
  • lines changed 145, context: html, text, full: html, text
    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest1.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest2.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest3.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest4.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease1/wgEncodeTest.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease2/wgEncodeTest.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease3/wgEncodeTest.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease4/wgEncodeTest.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/trackDb.wgEncode.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest.html
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest1.html
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest1.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest2.html
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest2.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest3.html
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest3.ra
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    putting in structure for the new encodeTest database
• src/hg/makeDb/trackDb/human/geneReviews.html
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    Edit html based on feedback from Lauren
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 24, context: html, text, full: html, text
    Meta-data for depercated file was left in by accident. Redmine 4558.
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCaltechRnaSeq.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeChromatinMap.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCaltechRnaSeq.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeChromatinMap.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.html
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/cosmic.html
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    Made all the listed URLs into actual links from the text. Corrected a couple target+ attributes. Added some css obfuscation to the listed email address.
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    Created a hard wrap to 100 characters. Added missing <p> and </p> tags. Set html tags to lower case.
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    Added missing </li> tags. Cleaned up citations.
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    Cleaned up one non-standard character.
• src/hg/makeDb/trackDb/human/hg19/lincRNAs.ra
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    Create lincRNAs supertrack
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    finished lincRNAs with shadesOfSea color
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    Rename track lincRNAsIsoforms to lincRNAsTranscripts
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    Changed many lables names for lincRNAs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
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    merge conflict resolved
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    Added metadata file for Uw Repli-seq track to makefile.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
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    Add 46 submission for track's second release. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
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    Removing duplicate objects
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    Wrong subIDs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
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    Related to ticket 5577, removing some obsolete objects and changing a table name
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
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    merge conflict resolved
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    Related to ticket 5577, removing some obsolete objects and changing a table name
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
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    removed 12 objects - Willy via Cricket
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
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    merge conflict resolved
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    added in geo accessions - Willy
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    Removing to incoorect geoNumbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
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    There was a duplicate object in here
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
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    Fixing the attic errors
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
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    merge conflict resolved
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    Fixes Redmine #69 1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3 2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
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    Adding new experiments
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    Removing geoAccessions from the trackDB display and adding expIds
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    Adding md5sums and changing hgFileUi columns
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    Removing treatment=None to be consistent with previous entires
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
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    added in SKMC control
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
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    Added meta-data and initial display of peaks and Valley's as bed 9 files. Redmine 4577.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
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    fixed control metadata terms
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    added treatment = None for items that needed it
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    added in None for treatment field in controlId
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    added in SKMC control
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencode.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeMapability.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
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    merge conflict resolved
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    moving metadata changes to beta: added missing origAssembly, dccAccessions, expId
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
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    merge conflict resolved
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    moving metatdata to public in preparation for release, redmine #69
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    adding '\' separator because make public wasn't working
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlLongRnaSeq.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencode.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaPet.ra
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    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeMapability.ra
  • lines changed 104, context: html, text, full: html, text
    releasing mapability track, redmine #3138
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhTfbs.ra
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    moving metatdata to public in preparation for release, redmine #69
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 4672, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    Initial set up for expression data of lincRNAs
  • lines changed 62, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 1, context: html, text, full: html, text
    Add lincRNAs.html for track description
  • lines changed 12, context: html, text, full: html, text
    Covert the lincRNAs custom track to native UCSC GB track
  • lines changed 1, context: html, text, full: html, text
    anoCar2 to dino alignment
  • lines changed 1, context: html, text, full: html, text
    initital work to use composite tracks for lincRNAs.
  • lines changed 15, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 2, context: html, text, full: html, text
    fixing up search rules
  • lines changed 24, context: html, text, full: html, text
    finished lincRNAs with shadesOfSea color
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 6, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 3, context: html, text, full: html, text
    Preliminary comitting the Replication Seq Timing data. Redmine #4577.
  • lines changed 2, context: html, text, full: html, text
    releasing mapability track, redmine #3138
  • lines changed 3, context: html, text, full: html, text
    Staging a new release 3 for this composite.
  • lines changed 4, context: html, text, full: html, text
    added new release for HaibGenotype composite
  • lines changed 2, context: html, text, full: html, text
    adding new release for CshlLong
  • lines changed 5, context: html, text, full: html, text
    Merge branch 'master' into UwReliSeq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 1088, context: html, text, full: html, text
    Add 46 submission for track's second release. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.html
  • lines changed 174, context: html, text, full: html, text
    adding new release for CshlLong
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.ra
  • lines changed 4635, context: html, text, full: html, text
    adding new release for CshlLong
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.html
  • lines changed 1, context: html, text, full: html, text
    Staging a new release 3 for this composite.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 8, context: html, text, full: html, text
    removed duplicate lines, I am not sure how this worked with this trackless stanza before, but those lines were redundant
  • lines changed 1, context: html, text, full: html, text
    Added back track line for track wgEncodeGisRnaPetNhekNucleusPapAlnRep.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.html
  • lines changed 82, context: html, text, full: html, text
    added new release for HaibGenotype composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.ra
  • lines changed 735, context: html, text, full: html, text
    added new release for HaibGenotype composite
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
  • lines changed 6, context: html, text, full: html, text
    Cleaning up labels and such
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 70, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 196, context: html, text, full: html, text
    Cleaning up labels and such
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
  • lines changed 107, context: html, text, full: html, text
    releasing mapability track, redmine #3138
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 1, context: html, text, full: html, text
    changed released date for mapability track, redmine# 3138
• src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.ra
  • lines changed 100, context: html, text, full: html, text
    releasing mapability track, redmine #3138
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 6, context: html, text, full: html, text
    removing visibility lines from multiWig container stanzas because they don't control the visibility and just add confusion. The visibility of the container tracks is controlled by the the superTrack line which has the visibility of the container at the end of the line, e.g. the multiWig stanza would have a line like: superTrack wgEncodeReg hide, redmine 5713, note 4
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 138, context: html, text, full: html, text
    Fixing the long labels and removing the preamble from the notes file
  • lines changed 7, context: html, text, full: html, text
    Shortening long labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 9, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 70, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 593, context: html, text, full: html, text
    Fixed errors found in Redmine #69 1. Updated the longLabels to be consnsitent with the terminology ChIP-seq instead of ChIP-Seq. 2. Removed nextItem button 3. Fixed so that all MCF10A-Er-Src stated control Standard as does its meta-data 4. Updated the track wgEncodeSydhTfbsGm12878Znf274StdSig to use the standard color for GM12878 cell line "153,38,0"
  • lines changed 1, context: html, text, full: html, text
    Fixes Redmine #69 1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3 2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 65, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 595, context: html, text, full: html, text
    Fixed errors found in Redmine #69 1. Updated the longLabels to be consnsitent with the terminology ChIP-seq instead of ChIP-Seq. 2. Removed nextItem button 3. Fixed so that all MCF10A-Er-Src stated control Standard as does its meta-data 4. Updated the track wgEncodeSydhTfbsGm12878Znf274StdSig to use the standard color for GM12878 cell line "153,38,0"
  • lines changed 1, context: html, text, full: html, text
    Fixes Redmine #69 1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3 2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.html
  • lines changed 147, context: html, text, full: html, text
    Making the super track correct and adding the base of a track description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.ra
  • lines changed 2, context: html, text, full: html, text
    Making the super track correct and adding the base of a track description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html
  • lines changed 1, context: html, text, full: html, text
    Adding new experiments
  • lines changed 10, context: html, text, full: html, text
    Adding a reference
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra
  • lines changed 232, context: html, text, full: html, text
    Adding new experiments
  • lines changed 135, context: html, text, full: html, text
    Removing geoAccessions from the trackDB display and adding expIds
  • lines changed 1, context: html, text, full: html, text
    Adding md5sums and changing hgFileUi columns
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 32, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 493, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 4, context: html, text, full: html, text
    Updated tags for CD20 cell line to not include +, as configuration can only handle alphanumeric tags.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 916, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 8, context: html, text, full: html, text
    Fixing the no speacial characters in the tags rule
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 8, context: html, text, full: html, text
    added in SKMC control
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
  • lines changed 1198, context: html, text, full: html, text
    Preliminary comitting the Replication Seq Timing data. Redmine #4577.
  • lines changed 219, context: html, text, full: html, text
    Added meta-data and initial display of peaks and Valley's as bed 9 files. Redmine 4577.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 9, context: html, text, full: html, text
    added in SKMC control
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 135, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 5, context: html, text, full: html, text
    Fixed a reference, fixed some grammar/punctuation. Redmine #5752.
• src/hg/makeDb/trackDb/human/iscaRetrospectiveComposite.html
  • lines changed 123, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 75, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/lizard/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 28, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 127, context: html, text, full: html, text
    Updated expId's and dccAccession for 2 tracks. Redmine #4155 and #4154.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 122, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 247, context: html, text, full: html, text
    Updated expId's and dccAccession for 2 tracks. Redmine #4155 and #4154.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 2431, context: html, text, full: html, text
    Added 10 submission, three of which were previously submitted 3041,3042,3043. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 817, context: html, text, full: html, text
    Added 3 submissions for track. Redmine #110.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html
  • lines changed 6, context: html, text, full: html, text
    Fixes issues in Redmine #4155 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra
  • lines changed 93, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 4, context: html, text, full: html, text
    Fixes issues in Redmine #4155 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html
  • lines changed 6, context: html, text, full: html, text
    Forgot thes files in commit:652519aed933b3d975c3feaa034873160f55cbf3 Fixes issues in Redmine #4154 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.new.ra
  • lines changed 668, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 4, context: html, text, full: html, text
    Forgot thes files in commit:652519aed933b3d975c3feaa034873160f55cbf3 Fixes issues in Redmine #4154 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 183, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 4, context: html, text, full: html, text
    Fixes issues in Redmine #4154 1. Set diplay for Peaks to dense 2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item. 3. Decreassed header size for "Rationale for the Mouse ENCODE project" 4. Updated the the following "An" -> "A" "consiting" -> "consisting" deleted duplicate the "contructed " -> "constructed" "avaialble " -> "available" "paramteres " -> "parameters"
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 243, context: html, text, full: html, text
    Added 10 submission, three of which were previously submitted 3041,3042,3043. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 55, context: html, text, full: html, text
    Added 3 submissions for track. Redmine #110.
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 18, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • lines changed 14, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/pig/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/rat/rn4/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    extend ctgPos search rule to function OK here
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • lines changed 11, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
• src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra
  • lines changed 33, context: html, text, full: html, text
    update ensGene search rules to match the names in this genome
  • lines changed 33, context: html, text, full: html, text
    same ensGene search rules for all sacCer assemblies
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • lines changed 33, context: html, text, full: html, text
    same ensGene search rules for all sacCer assemblies
• src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
  • lines changed 34, context: html, text, full: html, text
    fixup ensGene name searches for the extra letters in the ENS gene names
• src/hg/makeDb/trackDb/stickleback/gasAcu1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
• src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/tetraodon/tetNig1/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    fixup some of the checkHgFindSpec errors
• src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
  • lines changed 34, context: html, text, full: html, text
    fixing up search rules
  • lines changed 16, context: html, text, full: html, text
    search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
  • lines changed 1, context: html, text, full: html, text
    fixup checkHgFindSpec errors
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
  • lines changed 33, context: html, text, full: html, text
    fixup checkHgFindSpec errors
• src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/hg/makeDb/trackDb/zebrafish/UMassChIP-Seq.html
  • lines changed 76, context: html, text, full: html, text
    UMassChIP-Seq.html in danRer5 and 7 were identical. I moved danRer7's copy one dir up and removed the copy from danRer5.
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fixup ctgPos2 search rule
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    fixup search for gold and ctgPos2
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassChIP-Seq.html
  • lines changed 31, context: html, text, full: html, text
    UMassChIP-Seq.html in danRer5 and 7 were identical. I moved danRer7's copy one dir up and removed the copy from danRer5.
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    fixup checkHgFindSpec errors
• src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    fixup checkHgFindSpec errors
• src/hg/makeDb/trackDb/zebrafish/danRer7/UMassChIP-Seq.html
  • lines changed 34, context: html, text, full: html, text
    Cleaned up grammar, html, and citations.....a lot.
  • lines changed 49, context: html, text, full: html, text
    Set hard line wrap to 100 chars. Obfuscated email address.
  • lines changed 76, context: html, text, full: html, text
    UMassChIP-Seq.html in danRer5 and 7 were identical. I moved danRer7's copy one dir up and removed the copy from danRer5.
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    fixup gold search rule to allow all fragment names to match
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    merge conflict resolved
• src/hg/protein/lib/spKgMap.c
  • lines changed 11, context: html, text, full: html, text
    merge conflict resolved
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 38, context: html, text, full: html, text
    Adding new UCSC exception flag for dbSNP: InconsistentAlleles (the setof alleles for which frequencies are given does not match the set of observed alleles). This is in response to Ben and Ngan's finding some inconsistencies, and MLQ #5794 in which a user reported some strange non-base characters used as alleles for allele frequencies. Sent a couple test cases of inconsistent bases to dbSNP, and when build 135 FTP files are available, I can send them a more comprehensive list.
• src/hg/txCds/txInfoAssemble/txInfoAssemble.c
  • lines changed 1, context: html, text, full: html, text
    Addressing code review #5758 feedback: I'd written a nice new function but then had forgotten to call it
• src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
  • lines changed 1, context: html, text, full: html, text
    update expected results to match database
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 33, context: html, text, full: html, text
    add the ability to check for shortLabel and longLabel max lengths #5799
• src/lib/chainBlock.c
  • lines changed 2, context: html, text, full: html, text
    merge conflict resolved
• src/lib/cheapcgi.c
  • lines changed 2, context: html, text, full: html, text
    removing an unused variable as gcc 4.6 complained
  • lines changed 1, context: html, text, full: html, text
    This variable is used and does need to be initialized.
  • lines changed 2, context: html, text, full: html, text
    oops that must have been the wrong unused instance of ct being reported by gcc 4.6 warning
• src/lib/udc.c
  • lines changed 1, context: html, text, full: html, text
    fix problem with udcCleanup on tiny corrupt bitmap files
• src/lib/vcf.c
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
• src/utils/qa/alertBqueue.csh
  • lines changed 1, context: html, text, full: html, text
    Removed extra echo.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v259 preview2

• lines changed: 158491
• files changed: 481