All File Changes

v316_base to v317_preview (2015-05-11 to 2015-05-18) v317

• src/hg/genePredToGtf/genePredToGtf.c
  • lines changed 6, context: html, text, full: html, text
    make genePredToGtf put out the right exon number for start and stop
    codons refs #15216
    
• src/hg/genePredToGtf/tests/expected/basicSimpleTest.gtf
  • lines changed 9, context: html, text, full: html, text
    expected unit test output for genePredToGtf fix refs #15216
    
• src/hg/genePredToGtf/tests/expected/basicTest.gtf
  • lines changed 14, context: html, text, full: html, text
    expected unit test output for genePredToGtf fix refs #15216
    
• src/hg/genePredToGtf/tests/expected/honorTest.gtf
  • lines changed 14, context: html, text, full: html, text
    expected unit test output for genePredToGtf fix refs #15216
    
• src/hg/genePredToGtf/tests/expected/utrSimpleTest.gtf
  • lines changed 9, context: html, text, full: html, text
    expected unit test output for genePredToGtf fix refs #15216
    
• src/hg/genePredToGtf/tests/expected/utrTest.gtf
  • lines changed 14, context: html, text, full: html, text
    expected unit test output for genePredToGtf fix refs #15216
    
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    remove a line of code I recently added that crashes rn4 RGD Gene (no RM)
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 6, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/hgTracks/config.c
  • lines changed 7, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/hgTracks/searchTracks.c
  • lines changed 7, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 191, context: html, text, full: html, text
    Updated some entries with publication info, fixed formatting. Fixed broken links reported by linkchecker.
    
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 8, context: html, text, full: html, text
    Adding note about IP range with Assembly Hub Blat Servers refs #15323
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.css
  • lines changed 5, context: html, text, full: html, text
    Extend trackDbHub doc to include version and support levels for settings. refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    Distinguish trackDb doc and hub doc. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.js
  • lines changed 59, context: html, text, full: html, text
    Extend trackDbHub doc to include version and support levels for settings. refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 5, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 13, context: html, text, full: html, text
    Remove unused function
    
  • lines changed 14, context: html, text, full: html, text
    Identify hub doc so it can be handled differently. refs #10015
    
  • lines changed 0, context: html, text, full: html, text
    whitespace++
    
  • lines changed 25, context: html, text, full: html, text
    Distinguish trackDb doc and hub doc. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 100, context: html, text, full: html, text
    Extend trackDbHub doc to include version and support levels for settings. refs #10015
    
  • lines changed 80, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 115, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 1, context: html, text, full: html, text
    HTML syntax fix. refs #10015
    
  • lines changed 7, context: html, text, full: html, text
    Distinguish trackDb doc and hub doc. refs #10015
    
  • lines changed 43, context: html, text, full: html, text
    Reorder settings so core are at the top of each section. refs #10015
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    Extend trackDbHub doc to include version and support levels for settings. refs #10015
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 290, context: html, text, full: html, text
    Added job posting news item to home page and news archives. Fixed several broken links and lines exceeding 100 chars on newsarch.html.
    
• src/hg/htdocs/indexNews.html
  • lines changed 65, context: html, text, full: html, text
    Added job posting news item to home page and news archives. Fixed several broken links and lines exceeding 100 chars on newsarch.html.
    
  • lines changed 12, context: html, text, full: html, text
    Added staging for abridged version of jobs news item.
    
• src/hg/inc/trackHub.h
  • lines changed 27, context: html, text, full: html, text
    Cleanup hub check code and add new data structs to prep for hub versioning. refs #10015
    
  • lines changed 5, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 3, context: html, text, full: html, text
    Add 'did you mean' suggestion to hubCheck settings check. Similarity test from JK based on axt alignment scoring. refs #10015
    
  • lines changed 3, context: html, text, full: html, text
    Add checkSettings option to hubCheck instead of having setting check be default. This is to maintain current behavior for initial release. Also hide version options for now (they are in additional -help). refs #10015
    
• src/hg/js/hui.js
  • lines changed 20, context: html, text, full: html, text
    Fix behavior of +/- buttons when used without a matrix. Detected during Q/A of hg38 track. refs #14732
    
• src/hg/lib/hui.c
  • lines changed 44, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/lib/jsHelper.c
  • lines changed 6, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/lib/knownBlastTab.as
  • lines changed 17, context: html, text, full: html, text
    add knownBlastTab.as so description will make it into the table browser
    refs #15145
    
  • lines changed 1, context: html, text, full: html, text
    knownGeneMrna.as and knownToVisiGene.as to get descriptions into table
    browser #15145
    
• src/hg/lib/knownGeneMrna.as
  • lines changed 6, context: html, text, full: html, text
    knownGeneMrna.as and knownToVisiGene.as to get descriptions into table
    browser #15145
    
• src/hg/lib/knownToVisiGene.as
  • lines changed 7, context: html, text, full: html, text
    knownGeneMrna.as and knownToVisiGene.as to get descriptions into table
    browser #15145
    
• src/hg/lib/search.c
  • lines changed 7, context: html, text, full: html, text
    Removed ifdef (BUTTONS_BY_CSS). No functional change. This code added in 2011 is unused. (no redmine)
    
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
• src/hg/lib/trackHubCheck.c
  • lines changed 148, context: html, text, full: html, text
    Cleanup hub check code and add new data structs to prep for hub versioning. refs #10015
    
  • lines changed 126, context: html, text, full: html, text
    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
  • lines changed 72, context: html, text, full: html, text
    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
  • lines changed 75, context: html, text, full: html, text
    Finish -core and -extra options to hubCheck. refs #10015
    
  • lines changed 101, context: html, text, full: html, text
    Add 'did you mean' suggestion to hubCheck settings check. Similarity test from JK based on axt alignment scoring. refs #10015
    
  • lines changed 80, context: html, text, full: html, text
    Add checkSettings option to hubCheck instead of having setting check be default. This is to maintain current behavior for initial release. Also hide version options for now (they are in additional -help). refs #10015
    
• src/hg/makeDb/doc/hg38/multiz100way.txt
  • lines changed 108, context: html, text, full: html, text
    done with downloads and everything in the pushQ 007537 refs #14560
    
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 38, context: html, text, full: html, text
    Fix broken URLs from ScienCell (in wgEncodeCell table). refs #14353
    
• src/hg/makeDb/trackDb/apis/chainDm1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chainCi2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chainDm1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chainDm2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chainDm3.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chainNet.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chicken/galGal2/phastConsElements7way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chicken/galGal3/caCondor454.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chicken/galGal3/phastConsElements7way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chimp/panTro1/humanDels.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/cow/bosTau4/phastConsElements5way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/dog/canFam1/mzHg17Mm5_phast.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/dog/canFam2/phastConsElements4way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainAnoGam1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainApiMel2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDm1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDm2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDp2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDp3.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroAna1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroAna2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroEre1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroMoj1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroPer1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroSec1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroSim1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroVir1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroYak1.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/chainDroYak2.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/dm2/phastConsElements15way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/dm3/phastConsElements15way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/drosophila/mzDy1Dp2Ag1_phast.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/fugu/fr2/phastConsElements5way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Added release alpha setting to tgpPhase3 tracks so trackDb leakage wouldn't cause a build warning about lack of html.
    
  • lines changed 2, context: html, text, full: html, text
    Added release tag to tgpPhase3 child entries
    
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
  • lines changed 8, context: html, text, full: html, text
    update to correct newer assemblies refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/cons17way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/hg38/cons20way.html
  • lines changed 3, context: html, text, full: html, text
    tweaking documentation refs #14970
    
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra.beta
  • lines changed 2, context: html, text, full: html, text
    fix a problem with new name for UCSC Genes leaking out to the RR (no
    redmine)
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 3, context: html, text, full: html, text
    turning on frames and correct name for phyloP track refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.20way.ra
  • lines changed 5, context: html, text, full: html, text
    tweaking documentation refs #14970
    
  • lines changed 1, context: html, text, full: html, text
    take out snpTable from hg38 20way for now
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Tweak filter setting. refs #14732
    
• src/hg/makeDb/trackDb/human/placentalChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/primateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/human/vertebrateChainNet.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/lamprey/petMar1/phastConsElements6way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/lancelet/braFlo1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed a character encoding that I missed the first time around. Refs #15330.
    
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/lancelet/braFlo1/phastConsElements5way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/medaka/oryLat2/phastConsElements5way.html
  • lines changed 1, context: html, text, full: html, text
    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mostConserved.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mouse/mm10/chainNet.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM2.ra
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    added trackHander attribute toe mouse gencode trackDb entries. The removed requirement to have code explictly match versioned table names (RM 14781)
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM3.ra
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    added trackHander attribute toe mouse gencode trackDb entries. The removed requirement to have code explictly match versioned table names (RM 14781)
    
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM4.ra
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    added trackHander attribute toe mouse gencode trackDb entries. The removed requirement to have code explictly match versioned table names (RM 14781)
    
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/mouse/phastConsElements17way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/opossum/monDom4/phastConsElements7way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/opossum/multiz5way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/orangutan/ponAbe2/phastConsElements8way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/phastConsElements.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/platypus/ornAna1/phastConsElements6way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/rat/rn4/phastConsElements9way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/stickleback/gasAcu1/phastConsElements8way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons20way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/tetraodon/chainSelf.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/trackDb.ra
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    turning on augustusGene track refs #13088
    
• src/hg/makeDb/trackDb/worm/cb1/blastzCe1.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/cb1/blastzCe2.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/cb1/ce1Chain.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/cb1/chainCe2.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/ce2/blastzCb1.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/ce2/chainCb1.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/ce6/phastConsElements6way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainCaeJap1.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainCaePb1.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainCaePb2.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainCaeRem2.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainCaeRem3.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainCb3.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainCe4.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainCe6.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainPriPac1.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/worm/chainSelf.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/xenTro/xenTro2/phastConsElements7way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/zebrafish/danRer3/chainSelf.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
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    Fixing links to paper after Stanford slightly modified the URL, (no redmine)
    
• src/hg/utils/automation/doAugustus.pl
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    beginning of augustus gene prediction procedure refs #13088
    
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    now running through cleanup refs #13088
    
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    now running through cleanup refs #13088
    
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    now running through cleanup refs #13088
    
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    fixup chicken mis reference and add production of rna fasta and protein fasta refs #13088
    
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    use the gp file instead of the database table for the getRnaPred conversions does not always work with the db table refs #13088
    
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    better batch building fasta and sizing kluster run and gzip result before moving around refs #13088
    
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    fixing process error procedure refs #13088
    
• src/hg/utils/automation/doBlastzChainNet.pl
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    correct README comments for syntenic nets and reciprocal best download files refs #15144
    
• src/hg/utils/automation/doRecipBest.pl
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    correct README comments for syntenic nets and reciprocal best download files refs #15144
    
• src/hg/utils/automation/makefile
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    adding doAugustus.pl doCpgIslands.pl and doGenscan.pl to the delivered script files list refs #13088
    
• src/hg/utils/checkUrlsInTable/checkUrlsInTable.c
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    Add -strict option. Suppress 302 (Temp redirect) errors unless strict is on. Sometimes redirects work, sometimes not... refs #14353
    
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    Add -strict option. Suppress 302 (Temp redirect) errors unless strict is on. Sometimes redirects work, sometimes not... refs #14353
    
• src/hg/utils/checkUrlsInTable/makefile
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    Add -strict option. Suppress 302 (Temp redirect) errors unless strict is on. Sometimes redirects work, sometimes not... refs #14353
    
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    Add -strict option. Suppress 302 (Temp redirect) errors unless strict is on. Sometimes redirects work, sometimes not... refs #14353
    
• src/hg/utils/hubCheck/hubCheck.c
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    Cleanup hub check code and add new data structs to prep for hub versioning. refs #10015
    
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    Add version check features to hubCheck (-version, -core, -extra, -settings). Initial coding, not yet functional. Also added levels (for testing only) to settings spec. refs #10015
    
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    1. Change level-alpha to level-new (input from group review). Add -settings option to hubCheck (doesn't check, just shows settings and level). Add level to all settings (very initial proposed set based on input from Ensembl). refs #10015
    
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    Finish -core and -extra options to hubCheck. refs #10015
    
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    Add checkSettings option to hubCheck instead of having setting check be default. This is to maintain current behavior for initial release. Also hide version options for now (they are in additional -help). refs #10015
    
• src/lib/udc.c
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    Lower verbosity of this low-level module
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v317 preview1 refs #15355
    
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
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    Fixing email addresses so that replies to the thread will be sent successfully
    

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• files changed: 216