CVS changes by file

branch to review (2010-02-02 to 2010-02-10) v225

• src/hg/archaeStuff/data/Genome-info-euk
  • 1.19 lines changed: 17, context: html, text, full: html, text
    update soybean and maize to new versions, add Brachypodium
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.97 lines changed: 8, context: html, text, full: html, text
    change Cenarchaeum to Thaumarchaeota; use NCBI info for Nitr_mari
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.40 lines changed: 1, context: html, text, full: html, text
    add Thaumarchaeota
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.50 lines changed: 11, context: html, text, full: html, text
    Fixed CytoBand band sizes calc for genomes w/plasmids
• src/hg/archaeStuff/scripts/make-genome-info
  • 1.19 lines changed: 15, context: html, text, full: html, text
    fix duplicate dbname problem introduced by similar substrain names
• src/hg/blastToPsl/blast0To8.c
  • 1.3 lines changed: 287, context: html, text, full: html, text
    removed dead programs not being compiled
• src/hg/blastToPsl/blastToPsl.c
  • 1.24 lines changed: 304, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/blastXmlToPsl.c
  • 1.1 lines changed: 203, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/makefile
  • 1.29 lines changed: 9, context: html, text, full: html, text
    try number tree to get link rules to behave
  • 1.28 lines changed: 4, context: html, text, full: html, text
    even more dependency issues
  • 1.27 lines changed: 2, context: html, text, full: html, text
    fixed dependency problem
  • 1.26 lines changed: 5, context: html, text, full: html, text
    attempt to get autobuild working again by forcing a relink
  • 1.25 lines changed: 1, context: html, text, full: html, text
    fixed make issue
  • 1.24 lines changed: 4, context: html, text, full: html, text
    moved pslUniq out of complelely unrelated directory
  • 1.23 lines changed: 60, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/ncbiBlast.c
  • 1.1 lines changed: 4640, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/ncbiBlast.h
  • 1.1 lines changed: 1484, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/pslBuild.c
  • 1.1 lines changed: 284, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/pslBuild.h
  • 1.1 lines changed: 32, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/pslChain.c
  • 1.8 lines changed: 1092, context: html, text, full: html, text
    removed dead programs not being compiled
• src/hg/blastToPsl/pslUniq.c
  • 1.5 lines changed: 56, context: html, text, full: html, text
    moved pslUniq out of complelely unrelated directory
• src/hg/blastToPsl/tests/expected/identityBugTest.psl
  • 1.4 lines changed: 2, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/mrna1Test.bscores
  • 1.1 lines changed: 13, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/mrna1Test.psl
  • 1.1 lines changed: 12, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/prot1Test.bscores
  • 1.1 lines changed: 39, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/prot1Test.psl
  • 1.1 lines changed: 72, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/prot2Test.bscores
  • 1.1 lines changed: 4, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/prot2Test.psl
  • 1.1 lines changed: 3, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/protDnaTest.psl
  • 1.5 lines changed: 52, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/protMrnaEval1Test.psl
  • 1.4 lines changed: 27, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/protMrnaEval2Test.psl
  • 1.4 lines changed: 3, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/protMrnaTest.psl
  • 1.5 lines changed: 59, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/expected/tblastnTest.psl
  • 1.2 lines changed: 2, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/input/blastn+.blast
  • 1.1 lines changed: 206, context: html, text, full: html, text
    added (disabled) test case for blast+
• src/hg/blastToPsl/tests/input/mrna1.blastn.xml
  • 1.1 lines changed: 335, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/input/prot1.tblastn.xml
  • 1.1 lines changed: 1446, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/input/prot2.psiblast.xml
  • 1.1 lines changed: 229, context: html, text, full: html, text
    added blastXmlToPsl
• src/hg/blastToPsl/tests/makefile
  • 1.24 lines changed: 1, context: html, text, full: html, text
    fixed make issue
  • 1.23 lines changed: 41, context: html, text, full: html, text
    added blastXmlToPsl
  • 1.22 lines changed: 13, context: html, text, full: html, text
    added (disabled) test case for blast+
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.26 lines changed: 4, context: html, text, full: html, text
    Added file count at end of html page, by QA request.
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.211 lines changed: 4, context: html, text, full: html, text
    And one more time
  • 1.210 lines changed: 48, context: html, text, full: html, text
    More protocol naming adjustments
  • 1.209 lines changed: 101, context: html, text, full: html, text
    Made protocols more specific to groups. This is the only identification of a cell line to a praticular group
  • 1.208 lines changed: 1, context: html, text, full: html, text
    Marking prostate cell line as provisional since we have no approved protocol
  • 1.207 lines changed: 6, context: html, text, full: html, text
    Three cell lines for Crawford's group are no longer provisional.
  • 1.206 lines changed: 43, context: html, text, full: html, text
    Changed the sex of the human cell lines from Male to Unknown when there was no obvious gender data available.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.30 lines changed: 3, context: html, text, full: html, text
    Show sex for cells
• src/hg/gbToFaRa/gbToFaRa.c
  • 1.25 lines changed: 14, context: html, text, full: html, text
    added option to include version in output fasta
• src/hg/hgCustom/hgCustom.c
  • 1.138 lines changed: 3, context: html, text, full: html, text
    Suppress the '[db]' if db is contained in assembly label (dbDb.description). (Thx Ann!)
  • 1.137 lines changed: 4, context: html, text, full: html, text
    Increased some char[] sizes that caused safef errors with custom track with name longer than 128, and some others that looked like they might.
• src/hg/hgGateway/hgGateway.c
  • 1.113 lines changed: 3, context: html, text, full: html, text
    have default clade mammal if none found
• src/hg/hgSuggest/hgSuggest.c
  • 1.2 lines changed: 36, context: html, text, full: html, text
    support exact matches; fix indentation
  • 1.1 lines changed: 68, context: html, text, full: html, text
    support gene auto-complete
• src/hg/hgSuggest/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    support gene auto-complete
• src/hg/hgTables/gffOut.c
  • 1.20 lines changed: 3, context: html, text, full: html, text
    Removed stray newline from tx IDs generated for tracks that have no name column.
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Fixed too-small char[] size, found by Ann w/ENCODE tracks w/giant names, RT 1621.
• src/hg/hgTracks/bigBedTrack.c
  • 1.5 lines changed: 33, context: html, text, full: html, text
    Hopefully fixing bigBed so that it works in dense mode on a clean cart _and_ it works with custom tracks. Have tested these two anyway.
  • 1.4 lines changed: 12, context: html, text, full: html, text
    Moving bigBedFileOpen to a better place.
• src/hg/hgTracks/config.c
  • 1.90 lines changed: 7, context: html, text, full: html, text
    If the result of 'hFreezeName' (dbDb.description) contains the database name, as I intend to make happen, don't also show the database name in parens.
  • 1.89 lines changed: 19, context: html, text, full: html, text
    Changes that I have been sitting on awhile. More info on unexpected errors. Fixes to dragReorder. Support for simpler navigation links.
• src/hg/hgTracks/hgTracks.c
  • 1.1623 lines changed: 11, context: html, text, full: html, text
    If the result of 'hFreezeName' (dbDb.description) contains the database name, as I intend to make happen, don't also show the database name in parens.
  • 1.1622 lines changed: 72, context: html, text, full: html, text
    Changes that I have been sitting on awhile. More info on unexpected errors. Fixes to dragReorder. Support for simpler navigation links.
  • 1.1621 lines changed: 10, context: html, text, full: html, text
    Increased some char[] sizes that caused safef errors with custom track with name longer than 128, and some others that looked like they might.
• src/hg/hgTracks/hgTracks.h
  • 1.199 lines changed: 2, context: html, text, full: html, text
    Changes that I have been sitting on awhile. More info on unexpected errors. Fixes to dragReorder. Support for simpler navigation links.
• src/hg/hgTracks/imageV2.c
  • 1.22 lines changed: 45, context: html, text, full: html, text
    Safegaurds against empty tracks which can legitimately happen when there is no centerLabel
  • 1.21 lines changed: 200, context: html, text, full: html, text
    Changes that I have been sitting on awhile. More info on unexpected errors. Fixes to dragReorder. Support for simpler navigation links.
  • 1.20 lines changed: 4, context: html, text, full: html, text
    Increased some char[] sizes that caused safef errors with custom track with name longer than 128, and some others that looked like they might.
• src/hg/hgTracks/imageV2.h
  • 1.14 lines changed: 4, context: html, text, full: html, text
    Safegaurds against empty tracks which can legitimately happen when there is no centerLabel
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Changes that I have been sitting on awhile. More info on unexpected errors. Fixes to dragReorder. Support for simpler navigation links.
• src/hg/hgTracks/simpleTracks.c
  • 1.126 lines changed: 1, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
  • 1.125 lines changed: 3, context: html, text, full: html, text
    pgSnpHeight: if we're in dense mode, no need to double the track height.
  • 1.124 lines changed: 2, context: html, text, full: html, text
    pgSnpDrawAt: removed the ceiling of 50 items for drawing the cool stacked colored bars -- performance is just fine, and display snaps into squish/dense anyway when there are thousands of items.
  • 1.123 lines changed: 3, context: html, text, full: html, text
    Increased some char[] sizes that caused safef errors with custom track with name longer than 128, and some others that looked like they might.
• src/hg/inc/suggest.h
  • 1.1 lines changed: 16, context: html, text, full: html, text
    code to support suggesting genes given a prefix typed by the user
• src/hg/inc/trackDb.h
  • 1.53 lines changed: 3, context: html, text, full: html, text
    Adding trackDbUpdateOldTag function to convert older format trackDb tags to current format. Specifically converting superTrack, compositeTrack, and subTrack tags to use the new container and parent tags instead.
• src/hg/instinct/hgGeneset/drawingCode.c
  • 1.6 lines changed: 10, context: html, text, full: html, text
    fixed width,height
  • 1.5 lines changed: 1, context: html, text, full: html, text
    fixed silly bug
• src/hg/instinct/hgGeneset/frontend/css/hgHeatmapStyle.css
  • 1.6 lines changed: 10, context: html, text, full: html, text
    Added clustering button and made buttons look clickable
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_dots-small_75_2636d1_2x2.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_fine-grain_25_aaaaaa_60x60.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_flat_0_aaaaaa_40x100.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_flat_75_ffffff_40x100.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_glass_55_fbf9ee_1x400.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_glass_65_ffffff_1x400.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_glass_75_d9e4f8_1x400.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_glass_75_dadada_1x400.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-bg_inset-soft_95_fef1ec_1x100.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-icons_222222_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-icons_2e83ff_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-icons_3d3d3d_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-icons_454545_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-icons_cd0a0a_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/css/images/ui-icons_ffffff_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding UI Images
• src/hg/instinct/hgGeneset/frontend/genesetView.html
  • 1.7 lines changed: 3, context: html, text, full: html, text
    More fixes
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Added clustering button and made buttons look clickable
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Started zoom in/out
• src/hg/instinct/hgGeneset/frontend/js/hgHeatmapGeneset.js
  • 1.9 lines changed: 6, context: html, text, full: html, text
    More fixes
  • 1.8 lines changed: 23, context: html, text, full: html, text
    Added clustering button and made buttons look clickable
  • 1.7 lines changed: 14, context: html, text, full: html, text
    Fixed thumbnail, auto request on load
  • 1.6 lines changed: 36, context: html, text, full: html, text
    Started zoom in/out
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_grayCellLines.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fixed name of neveClass
  • 1.3 lines changed: 78, context: html, text, full: html, text
    Changed default vis of a bunch of the clinical features
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/index.html
  • 1.37 lines changed: 1, context: html, text, full: html, text
    
• src/hg/instinct/hgMicroscope/makefile
  • 1.1 lines changed: 20, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope.as
  • 1.1 lines changed: 60, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope.sql
  • 1.1 lines changed: 88, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/README
  • 1.1 lines changed: 12, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/bigImage.html
  • 1.1 lines changed: 1098, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/configPage.c
  • 1.1 lines changed: 37, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/configPage.h
  • 1.1 lines changed: 10, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/dot_clear.gif
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/hgMicroscope.c
  • 1.1 lines changed: 729, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/hgMicroscope.h
  • 1.1 lines changed: 51, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/makefile
  • 1.1 lines changed: 31, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/microscopeSearch.c
  • 1.1 lines changed: 488, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/microscopeSearch.h
  • 1.1 lines changed: 38, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/testMicroscopeSearch
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/testMicroscopeSearch.c
  • 1.1 lines changed: 67, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/testMicroscopeSearch.o
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscope/testVisiSearch.c
  • 1.1 lines changed: 67, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscopeLoad/exampleLoadingScript/makefile
  • 1.1 lines changed: 17, context: html, text, full: html, text
    
• src/hg/instinct/hgMicroscope/microscopeLoad/exampleLoadingScript/vgLoadTest.c
  • 1.1 lines changed: 160, context: html, text, full: html, text
    
• src/hg/instinct/hgMicroscope/microscopeLoad/exampleLoadingScript/vgLoadTest.o
  • 1.1 lines changed: 0, context: html, text, full: html, text
    
• src/hg/instinct/hgMicroscope/microscopeLoad/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscopeLoad/microscopeLoad.c
  • 1.1 lines changed: 438, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscopeLoad/retest
  • 1.1 lines changed: 5, context: html, text, full: html, text
    Cancer version of visiGene
• src/hg/instinct/hgMicroscope/microscopeLoad/test/test.ra
  • 1.1 lines changed: 7, context: html, text, full: html, text
    
• src/hg/instinct/hgMicroscope/microscopeLoad/test/test.tab
  • 1.1 lines changed: 4, context: html, text, full: html, text
    
• src/hg/instinct/hgMicroscope/microscopeLoad/test/testcaptions.txt
  • 1.1 lines changed: 3, context: html, text, full: html, text
    
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.64 lines changed: 7, context: html, text, full: html, text
    fixed json wrapper to be to spec
• src/hg/instinct/lib/json.c
  • 1.6 lines changed: 8, context: html, text, full: html, text
    cleaned up
  • 1.5 lines changed: 11, context: html, text, full: html, text
    fixed json wrapper to be to spec
• src/hg/instinct/webUserAdmin/webUserAdmin.c
  • 1.13 lines changed: 10, context: html, text, full: html, text
    Made checking for admin email more verbose
• src/hg/js/autocomplete.js
  • 1.2 lines changed: 3, context: html, text, full: html, text
    ../cgi-bin/suggest => ../cgi-bin/hgSuggest
  • 1.1 lines changed: 50, context: html, text, full: html, text
    support stuff for auto-complete using jquery.autocomplete.js
• src/hg/js/hgGateway.js
  • 1.1 lines changed: 12, context: html, text, full: html, text
    javascript for hgGateway CGI
• src/hg/js/hui.js
  • 1.50 lines changed: 38, context: html, text, full: html, text
    Big changes to move matrix CB normalizeAll code from js to C. These changes should make the large composites less sluggish
• src/hg/js/jquery.autocomplete.js
  • 1.2 lines changed: 8, context: html, text, full: html, text
    patch which fixes following problem: up/down arrows didn't work on IE, Safari and Chrome; patch downloaded from: http://code.google.com/p/jqac/issues/detail?id=1
  • 1.1 lines changed: 481, context: html, text, full: html, text
    version 1.4.2 downloaded from http://code.google.com/p/jqac/
• src/hg/js/utils.js
  • 1.27 lines changed: 14, context: html, text, full: html, text
    Added some timing routines to help focus on selfish, inefficient code
• src/hg/lib/customFactory.c
  • 1.116 lines changed: 2, context: html, text, full: html, text
    limit custom tracks short label to 128 characters to avoid buffer overflow elsewhere
• src/hg/lib/genomicSuperDups.as
  • 1.3 lines changed: 7, context: html, text, full: html, text
    Added some missing fields compared tot the sql definition and changed some of the descriptions as suggested by the data provider for this track.
• src/hg/lib/genomicSuperDups.sql
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Minor edits.
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Changed descriptions for table columns based on feedback from data provider.
• src/hg/lib/hdb.c
  • 1.418 lines changed: 2, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/lib/hgFind.c
  • 1.224 lines changed: 54, context: html, text, full: html, text
    Added hook for specifying a search type: CGI var (not cart) singleSearch=knownCanonical (and maybe other types someday). This will support stable links to hgTracks views of gene symbols short-circuited to knownCanonical locations.
  • 1.223 lines changed: 7, context: html, text, full: html, text
    If the result of 'hFreezeName' (dbDb.description) contains the database name, as I intend to make happen, don't also show the database name in parens.
• src/hg/lib/hui.c
  • 1.259 lines changed: 349, context: html, text, full: html, text
    Big changes to move matrix CB normalizeAll code from js to C. These changes should make the large composites less sluggish
  • 1.258 lines changed: 3, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
  • 1.257 lines changed: 14, context: html, text, full: html, text
    a little more fix on the items in the conservation dialog to get views
  • 1.256 lines changed: 4, context: html, text, full: html, text
    fix up control in multiz's that changes how codon translation happens
• src/hg/lib/makefile
  • 1.401 lines changed: 1, context: html, text, full: html, text
    add suggest.o
• src/hg/lib/rgdGene2.sql
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Added rgdGene2.sql.
• src/hg/lib/rgdGeneXref2.sql
  • 1.1 lines changed: 7, context: html, text, full: html, text
    Created rgdGeneXref2.sql
• src/hg/lib/simpleRepeat.sql
  • 1.9 lines changed: 1, context: html, text, full: html, text
    the extra ; in the comment causes it to be invalid SQL ?
• src/hg/lib/suggest.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    one more try at rcsid
  • 1.2 lines changed: 2, context: html, text, full: html, text
    forgot the rcsid
  • 1.1 lines changed: 18, context: html, text, full: html, text
    code to support suggesting genes given a prefix typed by the user
• src/hg/lib/trackDbCustom.c
  • 1.80 lines changed: 30, context: html, text, full: html, text
    Making hgTracks be backwards compatible with older trackDb tables in case they didn't run hgTrackDb.
  • 1.79 lines changed: 8, context: html, text, full: html, text
    If the result of 'hFreezeName' (dbDb.description) contains the database name, as I intend to make happen, don't also show the database name in parens.
  • 1.78 lines changed: 8, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
  • 1.77 lines changed: 12, context: html, text, full: html, text
    Ifdeffing out some of the new code until I finish baking it.
  • 1.76 lines changed: 40, context: html, text, full: html, text
    Adding trackDbUpdateOldTag function to convert older format trackDb tags to current format. Specifically converting superTrack, compositeTrack, and subTrack tags to use the new container and parent tags instead.
• src/hg/lib/wikiTrack.c
  • 1.27 lines changed: 19, context: html, text, full: html, text
    do not error out just because the wiki WEB site has disappeared
• src/hg/makeDb/doc/aplCal1.txt
  • 1.11 lines changed: 22, context: html, text, full: html, text
    adding trackDb.ra entry for aplCal1 chains/nets
• src/hg/makeDb/doc/calJac3.txt
  • 1.1 lines changed: 62, context: html, text, full: html, text
    Downloading new Marmoset assembly
• src/hg/makeDb/doc/equCab2.txt
  • 1.29 lines changed: 5, context: html, text, full: html, text
    enabled xeno refgene
• src/hg/makeDb/doc/hg18.txt
  • 1.397 lines changed: 27, context: html, text, full: html, text
    Added tRNAs track section.
• src/hg/makeDb/doc/hg19.txt
  • 1.81 lines changed: 28, context: html, text, full: html, text
    Added tRNAs track section.
  • 1.80 lines changed: 9, context: html, text, full: html, text
    Loaded new data for segmental duplications.
  • 1.79 lines changed: 16, context: html, text, full: html, text
    Added a 40mer sequence subtrack to the Mapability track.
  • 1.78 lines changed: 32, context: html, text, full: html, text
    Loaded corrected data for the Seg Dupes track.
• src/hg/makeDb/doc/mm9.txt
  • 1.124 lines changed: 28, context: html, text, full: html, text
    Added tRNAs track section.
  • 1.123 lines changed: 54, context: html, text, full: html, text
    Documented adding mapability track.
  • 1.122 lines changed: 18, context: html, text, full: html, text
    re-run the Panda chain net
• src/hg/makeDb/doc/monDom5.txt
  • 1.18 lines changed: 9, context: html, text, full: html, text
    re-run the Panda chain net
• src/hg/makeDb/doc/rn4.txt
  • 1.37 lines changed: 27, context: html, text, full: html, text
    Added tRNAs track section.
• src/hg/makeDb/doc/sacCer2.txt
  • 1.17 lines changed: 5, context: html, text, full: html, text
    grammar
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.110 lines changed: 1, context: html, text, full: html, text
    turning ailMel1 back on after reload
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.363 lines changed: 17, context: html, text, full: html, text
    adding marmoset calJac3
  • 1.362 lines changed: 1, context: html, text, full: html, text
    adding multiz6way to genbank danRer6
  • 1.361 lines changed: 2, context: html, text, full: html, text
    adding multiz6way to genbank danRer6
  • 1.360 lines changed: 1, context: html, text, full: html, text
    enable xeno refseq on equCab2
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.114 lines changed: 1, context: html, text, full: html, text
    turning ailMel1 back on after reload
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.101 lines changed: 3, context: html, text, full: html, text
    fixed samples in grayCelllineSNPSeg
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.61 lines changed: 2, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/makeDb/schema/all.joiner
  • 1.772 lines changed: 1, context: html, text, full: html, text
    Added dupeOk to tRNAs identifier since, per Fan, it is known & OK for the name to be duplicated
  • 1.771 lines changed: 12, context: html, text, full: html, text
    Moved set for tRNAs and CGAP SAGE tracks from being above their identifier to the location with all the other set information
  • 1.770 lines changed: 1, context: html, text, full: html, text
    Fixed a typo.
  • 1.769 lines changed: 9, context: html, text, full: html, text
    Added section for tRNA tracks.
  • 1.768 lines changed: 1, context: html, text, full: html, text
    Added crgMapability subtracks to list of tables to be ignored for mm9.
• src/hg/makeDb/trackDb/README
  • 1.100 lines changed: 6, context: html, text, full: html, text
    Tweaking MATRIX section a bit as per Angie's suggestions.
  • 1.99 lines changed: 47, context: html, text, full: html, text
    Clarifying some view info.
• src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
  • 1.27 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.26 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/cat/trackDb.chainNet.ra
  • 1.6 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.5 lines changed: 7, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.4 lines changed: 1, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/cat/trackDb.ra
  • 1.11 lines changed: 28, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.10 lines changed: 28, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.chainNet.ra
  • 1.8 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.7 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.6 lines changed: 1, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.ra
  • 1.78 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.77 lines changed: 28, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.chainNet.ra
  • 1.5 lines changed: 9, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.ra
  • 1.22 lines changed: 8, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.21 lines changed: 22, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.20 lines changed: 4, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
  • 1.22 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.21 lines changed: 6, context: html, text, full: html, text
    fixed shortLabel for chainNetDanRer2 for galGal2
  • 1.20 lines changed: 7, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.19 lines changed: 3, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.25 lines changed: 6, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.24 lines changed: 6, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.23 lines changed: 7, context: html, text, full: html, text
    moved all anoCar1 chains and nets to composite and dropped individual tracks
  • 1.22 lines changed: 5, context: html, text, full: html, text
    moved all taeGut1 chains and nets to composite and dropped individual tracks
  • 1.21 lines changed: 8, context: html, text, full: html, text
    moved all taeGut1 chains and nets to composite and dropped individual tracks
  • 1.20 lines changed: 20, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.chainNet.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.4 lines changed: 3, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.chainNet.ra
  • 1.3 lines changed: 4, context: html, text, full: html, text
    moved chainNet from trackDb.ra to trackDb.chainNet.ra
  • 1.2 lines changed: 0, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.1 lines changed: 11, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.54 lines changed: 10, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.53 lines changed: 3, context: html, text, full: html, text
    moved chainNet from trackDb.ra to trackDb.chainNet.ra
  • 1.52 lines changed: 2, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • 1.14 lines changed: 9, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.13 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.12 lines changed: 2, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.35 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.34 lines changed: 28, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.33 lines changed: 5, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.32 lines changed: 6, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.31 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/cow/bosTau1/trackDb.ra
  • 1.20 lines changed: 9, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.chainNet.ra
  • 1.6 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.5 lines changed: 7, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.ra
  • 1.11 lines changed: 18, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/cow/bosTau3/trackDb.chainNet.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.3 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
  • 1.2 lines changed: 6, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.chainNet.ra
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.1 lines changed: 4, context: html, text, full: html, text
    moved chainNet from trackDb.ra to trackDb.chainNet.ra
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.22 lines changed: 9, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.21 lines changed: 4, context: html, text, full: html, text
    moved chainNet from trackDb.ra to trackDb.chainNet.ra
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.10 lines changed: 4, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/cow/trackDb.ra
  • 1.7 lines changed: 7, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.6 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.chainNet.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.ra
  • 1.40 lines changed: 22, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.chainNet.ra
  • 1.6 lines changed: 0, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.49 lines changed: 8, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • 1.18 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.17 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.16 lines changed: 7, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.45 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.44 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.43 lines changed: 26, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.42 lines changed: 9, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.41 lines changed: 28, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.40 lines changed: 33, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • 1.60 lines changed: 3, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
  • 1.4 lines changed: 15, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/fugu/fr1/description.html
  • 1.28 lines changed: 1, context: html, text, full: html, text
    changed spp half of name to lower case
• src/hg/makeDb/trackDb/fugu/fr1/trackDb.chainNet.ra
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/fugu/fr2/description.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    changes spp half of name to lower case
• src/hg/makeDb/trackDb/fugu/fr2/trackDb.chainNet.ra
  • 1.2 lines changed: 7, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/fugu/trackDb.chainNet.ra
  • 1.9 lines changed: 17, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.8 lines changed: 1, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.78 lines changed: 17, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.77 lines changed: 26, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.76 lines changed: 9, context: html, text, full: html, text
    moved all fr2 chains and nets to composite and dropped individual tracks
  • 1.75 lines changed: 12, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.74 lines changed: 28, context: html, text, full: html, text
    moved all gasAcu1 chains and nets to composite and dropped individual tracks
  • 1.73 lines changed: 35, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.72 lines changed: 2, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
  • 1.11 lines changed: 9, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.10 lines changed: 6, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.9 lines changed: 7, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/guineaPig/trackDb.chainNet.ra
  • 1.7 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/horse/equCab1/trackDb.chainNet.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.3 lines changed: 9, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/horse/trackDb.chainNet.ra
  • 1.9 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • 1.26 lines changed: 16, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.25 lines changed: 23, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.24 lines changed: 21, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/gwasCatalog.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    added hyphen to Genome-Wide
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.586 lines changed: 8, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.585 lines changed: 20, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra
  • 1.19 lines changed: 6, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.18 lines changed: 6, context: html, text, full: html, text
    Changed xenTro1 chain and net shortLabels to match chainNet shortLabels.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.452 lines changed: 24, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.451 lines changed: 8, context: html, text, full: html, text
    moved all fr2 chains and nets to composite and dropped individual tracks
  • 1.450 lines changed: 13, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.449 lines changed: 8, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.448 lines changed: 22, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.447 lines changed: 20, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.446 lines changed: 6, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.445 lines changed: 26, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg18/pgVenter.html
  • 1.2 lines changed: 31, context: html, text, full: html, text
    Long since obsoleted by composite track details (pgSnp.html). thx Pauline!
• src/hg/makeDb/trackDb/human/hg18/pgWatson.html
  • 1.2 lines changed: 29, context: html, text, full: html, text
    Long since obsoleted by composite track details (pgSnp.html). thx Pauline!
• src/hg/makeDb/trackDb/human/hg18/trackDb.chainNet.ra
  • 1.16 lines changed: 9, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.15 lines changed: 3, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.465 lines changed: 24, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.464 lines changed: 28, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.463 lines changed: 8, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.462 lines changed: 22, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.461 lines changed: 22, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.460 lines changed: 28, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.459 lines changed: 28, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.865 lines changed: 65, context: html, text, full: html, text
    Standardized metadata to 'antibody=Input'.
  • 1.864 lines changed: 22, context: html, text, full: html, text
    take out fileName for signals in CSHL short RNA
  • 1.863 lines changed: 9, context: html, text, full: html, text
    get Caltech directional data to be colored by strand
  • 1.862 lines changed: 60, context: html, text, full: html, text
    properly attach directional metadata to mislabeled tables
  • 1.861 lines changed: 72, context: html, text, full: html, text
    removed entire blocks for subtracks being dropped from ENCODE UW DNaseI HS track (release 2) rather than my previous change of just removing release beta tag
  • 1.860 lines changed: 9, context: html, text, full: html, text
    removed release beta from subtracks being dropped from ENCODE UW DNaseI HS track (release 2)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.html
  • 1.14 lines changed: 11, context: html, text, full: html, text
    Added CRG Alignablity track details.
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.2 lines changed: 10, context: html, text, full: html, text
    Added a 40mer sequence subtrack to the Mapability track.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.96 lines changed: 2, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.95 lines changed: 2, context: html, text, full: html, text
    moved all petMar1 chains and nets to composite and dropped individual tracks
  • 1.94 lines changed: 2, context: html, text, full: html, text
    moved all anoCar1 chains and nets to composite and dropped individual tracks
  • 1.93 lines changed: 2, context: html, text, full: html, text
    moved all taeGut1 chains and nets to composite and dropped individual tracks
  • 1.92 lines changed: 5, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
  • 1.91 lines changed: 2, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.90 lines changed: 4, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.89 lines changed: 2, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.88 lines changed: 5, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • 1.34 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.512 lines changed: 6, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.511 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.510 lines changed: 13, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.509 lines changed: 14, context: html, text, full: html, text
    moved all braFlo1 chains and nets to composite and dropped individual tracks
  • 1.508 lines changed: 8, context: html, text, full: html, text
    moved all petMar1 chains and nets to composite and dropped individual tracks
  • 1.507 lines changed: 13, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
  • 1.506 lines changed: 7, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.505 lines changed: 6, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.504 lines changed: 12, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.503 lines changed: 10, context: html, text, full: html, text
    moved all gasAcu1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/lamprey/trackDb.ra
  • 1.8 lines changed: 8, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/lizard/trackDb.chainNet.ra
  • 1.8 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.7 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/lizard/trackDb.ra
  • 1.10 lines changed: 7, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/makefile
  • 1.283 lines changed: 1, context: html, text, full: html, text
    adding calJac3 to the build
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • 1.1 lines changed: 129, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/marmoset/calJac3/gap.html
  • 1.1 lines changed: 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/marmoset/calJac3/gold.html
  • 1.1 lines changed: 22, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.1 lines changed: 40, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
  • 1.13 lines changed: 12, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.12 lines changed: 7, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/medaka/oryLat1/trackDb.chainNet.ra
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/medaka/oryLat1/trackDb.ra
  • 1.14 lines changed: 3, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • 1.8 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/medaka/trackDb.ra
  • 1.27 lines changed: 28, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.26 lines changed: 9, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.25 lines changed: 6, context: html, text, full: html, text
    moved all petMar1 chains and nets to composite and dropped individual tracks
  • 1.24 lines changed: 40, context: html, text, full: html, text
    moved all gasAcu1 chains and nets to composite and dropped individual tracks
  • 1.23 lines changed: 30, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/mm5/trackDb.ra
  • 1.53 lines changed: 15, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/mm6/trackDb.chainNet.ra
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/mouse/mm6/trackDb.ra
  • 1.57 lines changed: 3, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.56 lines changed: 2, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.chainNet.ra
  • 1.17 lines changed: 9, context: html, text, full: html, text
    moved all fr1chains and nets to composite and dropped individual tracks
  • 1.16 lines changed: 6, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.15 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.14 lines changed: 6, context: html, text, full: html, text
    Changed xenTro1 chain and net shortLabels to match chainNet shortLabels.
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.64 lines changed: 8, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.63 lines changed: 8, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.62 lines changed: 3, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.chainNet.ra
  • 1.12 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.65 lines changed: 8, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/mouse/mm9/mapability.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Changed assembly name.
  • 1.1 lines changed: 20, context: html, text, full: html, text
    Description for mapability track.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
  • 1.9 lines changed: 42, context: html, text, full: html, text
    moved all TetNig1 chains and nets to composite and dropped individual tracks
  • 1.8 lines changed: 51, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.82 lines changed: 5, context: html, text, full: html, text
    Minor edit of track name.
  • 1.81 lines changed: 1, context: html, text, full: html, text
    Minor edit of track name.
  • 1.80 lines changed: 50, context: html, text, full: html, text
    Added Mapability track with subtracks from CRG.
  • 1.79 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.78 lines changed: 6, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
  • 1.77 lines changed: 7, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.32 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.31 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.205 lines changed: 6, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.204 lines changed: 9, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.203 lines changed: 28, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.202 lines changed: 7, context: html, text, full: html, text
    moved all fr2 chains and nets to composite and dropped individual tracks
  • 1.201 lines changed: 9, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.200 lines changed: 6, context: html, text, full: html, text
    moved all braFlo1 chains and nets to composite and dropped individual tracks
  • 1.199 lines changed: 11, context: html, text, full: html, text
    moved all petMar1 chains and nets to composite and dropped individual tracks
  • 1.198 lines changed: 10, context: html, text, full: html, text
    moved all anoCar1 chains and nets to composite and dropped individual tracks
  • 1.197 lines changed: 25, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
  • 1.196 lines changed: 28, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.195 lines changed: 10, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.194 lines changed: 18, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.193 lines changed: 4, context: html, text, full: html, text
    moved all gasAcu1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom1/trackDb.chainNet.ra
  • 1.6 lines changed: 8, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.5 lines changed: 8, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom1/trackDb.ra
  • 1.27 lines changed: 5, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/opossum/monDom2/trackDb.ra
  • 1.4 lines changed: 17, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.chainNet.ra
  • 1.12 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.11 lines changed: 1, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.ra
  • 1.28 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.27 lines changed: 5, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
  • 1.6 lines changed: 21, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.33 lines changed: 14, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.32 lines changed: 38, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.31 lines changed: 13, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • 1.21 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.20 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.19 lines changed: 16, context: html, text, full: html, text
    fixed shortLabel for chainNet{mm6,danRer2} for monDom1
  • 1.18 lines changed: 3, context: html, text, full: html, text
    dropped two errant tildes
  • 1.17 lines changed: 16, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.50 lines changed: 7, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.49 lines changed: 29, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.48 lines changed: 7, context: html, text, full: html, text
    moved all fr2 chains and nets to composite and dropped individual tracks
  • 1.47 lines changed: 34, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.46 lines changed: 28, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.45 lines changed: 28, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/orangutan/ponAbe2/trackDb.ra
  • 1.20 lines changed: 10, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • 1.10 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.9 lines changed: 1, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • 1.13 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.12 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.15 lines changed: 9, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/rat/rn3/trackDb.chainNet.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
  • 1.67 lines changed: 26, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/rat/rn4/rgdGene2.html
  • 1.1 lines changed: 25, context: html, text, full: html, text
    Created rgdGene2.html.
• src/hg/makeDb/trackDb/rat/rn4/trackDb.chainNet.ra
  • 1.1 lines changed: 9, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.56 lines changed: 9, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.55 lines changed: 2, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.54 lines changed: 12, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
  • 1.53 lines changed: 8, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
  • 1.4 lines changed: 10, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • 1.22 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.21 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.20 lines changed: 7, context: html, text, full: html, text
    changed animal name to o_Organism for several
  • 1.19 lines changed: 6, context: html, text, full: html, text
    Changed bosTau4 chain and net shortLabels to match chainNet shortLabels.
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.77 lines changed: 26, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.76 lines changed: 26, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.75 lines changed: 13, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
  • 1.74 lines changed: 28, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.73 lines changed: 28, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rhesus/rheMac1/trackDb.chainNet.ra
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/rhesus/rheMac1/trackDb.ra
  • 1.9 lines changed: 11, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.53 lines changed: 12, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.10 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.9 lines changed: 7, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • 1.23 lines changed: 26, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.22 lines changed: 28, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.21 lines changed: 26, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
  • 1.11 lines changed: 7, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.10 lines changed: 7, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed typo. Thanks, tdbQuery.
  • 1.8 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/stickleback/trackDb.ra
  • 1.32 lines changed: 27, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.31 lines changed: 27, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.30 lines changed: 7, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.29 lines changed: 5, context: html, text, full: html, text
    moved all anoCar1 chains and nets to composite and dropped individual tracks
  • 1.28 lines changed: 28, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.27 lines changed: 28, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.26 lines changed: 26, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/tRNAs.html
  • 1.3 lines changed: 13, context: html, text, full: html, text
    Edited the credits & references to fit the pubMed format
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/makeDb/trackDb/tetraodon/trackDb.chainNet.ra
  • 1.13 lines changed: 7, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.12 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.11 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.58 lines changed: 17, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.57 lines changed: 7, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.56 lines changed: 26, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.55 lines changed: 6, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.54 lines changed: 7, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.53 lines changed: 26, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.52 lines changed: 13, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.51 lines changed: 26, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.79 lines changed: 5, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.78 lines changed: 3, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.77 lines changed: 3, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.76 lines changed: 5, context: html, text, full: html, text
    moved all fr2 chains and nets to composite and dropped individual tracks
  • 1.75 lines changed: 8, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.74 lines changed: 4, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.73 lines changed: 4, context: html, text, full: html, text
    moved all braFlo1 chains and nets to composite and dropped individual tracks
  • 1.72 lines changed: 4, context: html, text, full: html, text
    moved all petMar1 chains and nets to composite and dropped individual tracks
  • 1.71 lines changed: 4, context: html, text, full: html, text
    moved all TetNig1 chains and nets to composite and dropped individual tracks
  • 1.70 lines changed: 4, context: html, text, full: html, text
    moved all taeGut1 chains and nets to composite and dropped individual tracks
  • 1.69 lines changed: 4, context: html, text, full: html, text
    moved all taeGut1 chains and nets to composite and dropped individual tracks
  • 1.68 lines changed: 4, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
  • 1.67 lines changed: 4, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.66 lines changed: 4, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.65 lines changed: 6, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.64 lines changed: 4, context: html, text, full: html, text
    moved all gasAcu1 chains and nets to composite and dropped individual tracks
  • 1.63 lines changed: 49, context: html, text, full: html, text
    adding aplCal1 chain/net
  • 1.62 lines changed: 4, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.61 lines changed: 4, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.60 lines changed: 4, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
  • 1.59 lines changed: 1, context: html, text, full: html, text
    Removed a stray release alpha from netMm7 track.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.616 lines changed: 28, context: html, text, full: html, text
    moved all danRer3 chains and nets to composite and dropped individual tracks
  • 1.615 lines changed: 24, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.614 lines changed: 26, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.613 lines changed: 26, context: html, text, full: html, text
    moved all fr2 chains and nets to composite and dropped individual tracks
  • 1.612 lines changed: 42, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.611 lines changed: 25, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.610 lines changed: 27, context: html, text, full: html, text
    moved all braFlo1 chains and nets to composite and dropped individual tracks
  • 1.609 lines changed: 27, context: html, text, full: html, text
    moved all petMar1 chains and nets to composite and dropped individual tracks
  • 1.608 lines changed: 27, context: html, text, full: html, text
    moved all taeGut1 chains and nets to composite and dropped individual tracks
  • 1.607 lines changed: 27, context: html, text, full: html, text
    moved all taeGut1 chains and nets to composite and dropped individual tracks
  • 1.606 lines changed: 52, context: html, text, full: html, text
    moved all cavPor3 chains and nets to composite and dropped individual tracks
  • 1.605 lines changed: 76, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.604 lines changed: 25, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.603 lines changed: 81, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.602 lines changed: 27, context: html, text, full: html, text
    moved all gasAcu1 chains and nets to composite and dropped individual tracks
  • 1.601 lines changed: 28, context: html, text, full: html, text
    moved all ornAna1 chains and nets to composite and dropped individual tracks
  • 1.600 lines changed: 27, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.599 lines changed: 27, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/urchin/strPur1/trackDb.ra
  • 1.10 lines changed: 24, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
  • 1.12 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.10 lines changed: 1, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/xenTro/trackDb.ra
  • 1.32 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.31 lines changed: 3, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.30 lines changed: 28, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.29 lines changed: 11, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
  • 1.28 lines changed: 26, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.chainNet.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.4 lines changed: 3, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
  • 1.45 lines changed: 7, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.44 lines changed: 27, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.chainNet.ra
  • 1.5 lines changed: 9, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
  • 1.26 lines changed: 24, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.25 lines changed: 6, context: html, text, full: html, text
    moved all rn4 chains and nets to composite and dropped individual tracks
  • 1.24 lines changed: 6, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebraFinch/trackDb.chainNet.ra
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
  • 1.10 lines changed: 8, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
• src/hg/makeDb/trackDb/zebrafish/danRer1/trackDb.ra
  • 1.38 lines changed: 6, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.37 lines changed: 6, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.chainNet.ra
  • 1.6 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.5 lines changed: 3, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
  • 1.61 lines changed: 28, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.60 lines changed: 7, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.59 lines changed: 20, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.58 lines changed: 48, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.chainNet.ra
  • 1.7 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.6 lines changed: 9, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.5 lines changed: 3, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
  • 1.46 lines changed: 28, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.45 lines changed: 28, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.44 lines changed: 8, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.43 lines changed: 8, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.42 lines changed: 15, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • 1.32 lines changed: 10, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.31 lines changed: 6, context: html, text, full: html, text
    moved all danRer1 chains and nets to composite and dropped individual tracks
  • 1.30 lines changed: 21, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.29 lines changed: 46, context: html, text, full: html, text
    moved all mm9 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • 1.16 lines changed: 6, context: html, text, full: html, text
    Changing netHg18 and chainHg18 to composites.
  • 1.15 lines changed: 6, context: html, text, full: html, text
    moved chainNet from trackDb.ra to trackDb.chainNet.ra
  • 1.14 lines changed: 1, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.71 lines changed: 9, context: html, text, full: html, text
    Changing netHg17 and chainHg17 to chainNetHg17 composite tracks.
  • 1.70 lines changed: 8, context: html, text, full: html, text
    moved all fr1 chains and nets to composite and dropped individual tracks
  • 1.69 lines changed: 43, context: html, text, full: html, text
    moved chainNet from trackDb.ra to trackDb.chainNet.ra
  • 1.68 lines changed: 27, context: html, text, full: html, text
    moved all oryLat2 chains and nets to composite and dropped individual tracks
  • 1.67 lines changed: 16, context: html, text, full: html, text
    moved all mm8 chains and nets to composite and dropped individual tracks
• src/hg/oneShot/freen/freen.c
  • 1.97 lines changed: 36, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/oneShot/tdbRewriteViewsToSubtracks1/makefile
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Making a single file rewriter for track in the middle.
• src/hg/oneShot/tdbRewriteViewsToSubtracks1/tdbRewriteViewsToSubtracks1.c
  • 1.1 lines changed: 696, context: html, text, full: html, text
    Making a single file rewriter for track in the middle.
• src/hg/utils/automation/doRecipBest.pl
  • 1.12 lines changed: 9, context: html, text, full: html, text
    allow use of lastz or blastz directory
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.27 lines changed: 5, context: html, text, full: html, text
    handle chrom names for chromInfo that are longer than 16 chars
  • 1.26 lines changed: 11, context: html, text, full: html, text
    fixup usage of AGP files with comments and FASTA with Genbank ID lines
• src/hg/utils/makefile
  • 1.20 lines changed: 2, context: html, text, full: html, text
    moved pslUniq out of complelely unrelated directory
• src/hg/utils/mutationClassifier/mutationClassifier.c
  • 1.4 lines changed: 67, context: html, text, full: html, text
    code cleanup per jim's feedback
• src/hg/utils/pslUniq/makefile
  • 1.1 lines changed: 17, context: html, text, full: html, text
    moved pslUniq out of complelely unrelated directory
• src/hg/utils/pslUniq/pslUniq.c
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Clean up pslUniq and place it into the build
  • 1.3 lines changed: 18, context: html, text, full: html, text
    added option to allow for N entries (dumb name then eh?)
  • 1.2 lines changed: 3, context: html, text, full: html, text
    some clean up
  • 1.1 lines changed: 47, context: html, text, full: html, text
    only one record of each query name gets through
• src/hg/utils/rgdGeneXref2/makefile
  • 1.1 lines changed: 36, context: html, text, full: html, text
    Created makefile.
• src/hg/utils/rgdGeneXref2/rgdGeneXref2.c
  • 1.1 lines changed: 115, context: html, text, full: html, text
    Created rgdGeneXref2.c.
• src/hg/utils/tdbQuery/tdbQuery.c
  • 1.29 lines changed: 3, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
  • 1.28 lines changed: 3, context: html, text, full: html, text
    Taking out a half-baked change.
  • 1.27 lines changed: 63, context: html, text, full: html, text
    Getting rid of settingsByView stuff. Adding in converter to container/parent syntax. Fix to parent-not-found error message.
• src/hg/utils/tdbQuery/tdbRecord.c
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Getting to compile in Linux.
  • 1.6 lines changed: 75, context: html, text, full: html, text
    Getting rid of settingsByView stuff. Adding in converter to container/parent syntax. Fix to parent-not-found error message.
• src/hg/utils/tdbQuery/tdbRecord.h
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Getting rid of settingsByView stuff. Adding in converter to container/parent syntax. Fix to parent-not-found error message.
• src/hg/visiGene/README.txt
  • 1.1 lines changed: 11, context: html, text, full: html, text
    hgMicroscope stuff
• src/hg/visiGene/makefile
  • 1.2 lines changed: 20, context: html, text, full: html, text
    hgMicroscope dir
• src/hg/visiGene/microscope.as
  • 1.1 lines changed: 60, context: html, text, full: html, text
    hgMicroscope stuff
• src/hg/visiGene/microscope.sql
  • 1.1 lines changed: 88, context: html, text, full: html, text
    hgMicroscope stuff
• src/inc/bigBed.h
  • 1.18 lines changed: 30, context: html, text, full: html, text
    Removing bigBedFileCreate which is no longer in library.
• src/inc/cheapcgi.h
  • 1.71 lines changed: 7, context: html, text, full: html, text
    Needed to rewrite the 2way CB routines. Now called fourWay
• src/lib/bigBed.c
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Making bigBedCoverageIntervals() static.
  • 1.26 lines changed: 4, context: html, text, full: html, text
    Fixed memory leaks.
• src/lib/cheapcgi.c
  • 1.131 lines changed: 30, context: html, text, full: html, text
    Needed to rewrite the 2way CB routines. Now called fourWay
• src/lib/htmshell.c
  • 1.65 lines changed: 5, context: html, text, full: html, text
    Fixed the warnbox to make hidden 'OK' not be picked up by select all.
• src/utils/qa/findLevel.csh
  • 1.20 lines changed: 6, context: html, text, full: html, text
    cheap fix to find more-or-less only the track you're looking for. the better way to fix this would be to figure out the quotes, and include the tableName in the tdbQuery statement.
• src/utils/qa/getDbSize.csh
  • 1.16 lines changed: 5, context: html, text, full: html, text
    adjust column width to allow for Tb-level files
• src/utils/qa/qaEncodeTracks.csh
  • 1.7 lines changed: 2, context: html, text, full: html, text
    grammar tweak
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.99 lines changed: 2, context: html, text, full: html, text
    v225 preview
• src/utils/qa/weeklybld/doNewBranch.csh
  • 1.34 lines changed: 46, context: html, text, full: html, text
    re-arranging to run utils early

• lines changed: 23843
• files changed: 294