All File Changes

v309_preview2 to v309_base (2014-11-17 to 2014-11-24) v309

• src/beacon/makefile
  • lines changed 36, context: html, text, full: html, text
    the UCSC GA4GH beacon, refs #14393
• src/beacon/query
  • lines changed 149, context: html, text, full: html, text
    the UCSC GA4GH beacon, refs #14393
  • lines changed 7, context: html, text, full: html, text
    making the beacon help message a little bit better, refs #14393
  • lines changed 4, context: html, text, full: html, text
    more beacon bugfixes, refs #14393
• src/hg/hgGateway/hgGateway.c
  • lines changed 2, context: html, text, full: html, text
    when hubs disappear out from under us, put out a kindler, gentler errormessage that gives people a clue what's happened. #14365
    
• src/hg/hgTables/identifiers.c
  • lines changed 26, context: html, text, full: html, text
    Fixes #14409. Instead of showing only 1 example missing identifier, show up to the first 20.
  • lines changed 14, context: html, text, full: html, text
    Fixes #12687. Changed to show only the first 10 missing identifiers, AND it provides a link that the user can click to get a complete list of all missing identifiers.
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    when hubs disappear out from under us, put out a kindler, gentler errormessage that gives people a clue what's happened. #14365
    
• src/hg/hgTracks/chainTrack.c
  • lines changed 2, context: html, text, full: html, text
    chains are filtered on normScore
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    when hubs disappear out from under us, put out a kindler, gentler errormessage that gives people a clue what's happened. #14365
    
• src/hg/htdocs/ENCODE/index.html
  • lines changed 17, context: html, text, full: html, text
    Layout fixes (size graphic rather than table cell). refs #14407
  • lines changed 24, context: html, text, full: html, text
    Remove News panel. refs #14407
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/Neandertal/index.html
  • lines changed 1, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/ebolaPortal/index.html
  • lines changed 4, context: html, text, full: html, text
    Add link to ebola antibody sequence file. refs #14404
  • lines changed 1, context: html, text, full: html, text
    Capitalizing Ebola, refs #14404
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 7, context: html, text, full: html, text
    Replacing accented characters with their html names.
  • lines changed 10, context: html, text, full: html, text
    Removing links to dbs not on RR and adding monDom assemblies, per code review #14380 #14336
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 2, context: html, text, full: html, text
    Small typo fixes on gbib help page, refs #14381
  • lines changed 3, context: html, text, full: html, text
    Small left-handed style change refs #14381
  • lines changed 1, context: html, text, full: html, text
    fixed wording on GBiB firewall requirements
  • lines changed 3, context: html, text, full: html, text
    further wording changes to the gbib help docs - remote servers and ports
  • lines changed 3, context: html, text, full: html, text
    adding port 80 to gbib firewall list
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/images/Plasmodium_falciparum_3D7.jpg
  • lines changed 0, context: html, text, full: html, text
    added temporary genome db plasFalc3D7V12
• src/hg/htdocs/index.html
  • lines changed 1, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training.html
  • lines changed 119, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/adv.html
  • lines changed 38, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/bigTrees.jpg
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/cincyData.html
  • lines changed 27, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/cincyData1.html
  • lines changed 58, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/cincyData2.html
  • lines changed 49, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/emoryData.html
  • lines changed 27, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/emoryData1.html
  • lines changed 55, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/emoryData2.html
  • lines changed 55, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/hawaiiLogo.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/home.topbar.html
  • lines changed 21, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/index.html
  • lines changed 31, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/ldb2.jpg
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/pageAdvTwo.html
  • lines changed 394, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/pageOne.html
  • lines changed 53, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/pageTwo.html
  • lines changed 322, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/quake.html
  • lines changed 56, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen01.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen02.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen03.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen04.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen11.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen12.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen13.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen14.jpg
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/screen15.gif
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/ashg2009/sidebar.html
  • lines changed 59, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
  • lines changed 1, context: html, text, full: html, text
    found an overlooked ref to training.html
• src/hg/htdocs/training/ashg2009/tbx1.jpg
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
• src/hg/htdocs/training/index.html
  • lines changed 119, context: html, text, full: html, text
    moved training.html to training/index.html use git --follow to see history from before the move
  • lines changed 23, context: html, text, full: html, text
    making changes to links to accomodate being one dir lower
• src/hg/htdocs/training/ucscGeneFishing.pdf
  • lines changed 0, context: html, text, full: html, text
    refactoring training.html to training/index.html. still having trouble with the top bluebar, but otherwise it is working. refs #14408
  • lines changed 0, context: html, text, full: html, text
    removing large pdf
• src/hg/inc/cart.h
  • lines changed 6, context: html, text, full: html, text
    when hubs disappear out from under us, put out a kindler, gentler errormessage that gives people a clue what's happened. #14365
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v309
• src/hg/lib/annoFormatVep.c
  • lines changed 1, context: html, text, full: html, text
    Case-sensitive comparison of strings with differing case was causing us to drop many dbNSFP annotations, ouch.refs #14360, #14367
    
• src/hg/lib/cart.c
  • lines changed 22, context: html, text, full: html, text
    when hubs disappear out from under us, put out a kindler, gentler errormessage that gives people a clue what's happened. #14365
    
• src/hg/lib/cosmicNew.as
  • lines changed 18, context: html, text, full: html, text
    Created new autoSql definition for updated COSMIC track format
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    when hubs disappear out from under us, put out a kindler, gentler errormessage that gives people a clue what's happened. #14365
    
• src/hg/lib/hubConnect.c
  • lines changed 3, context: html, text, full: html, text
    when hubs disappear out from under us, put out a kindler, gentler errormessage that gives people a clue what's happened. #14365
    
• src/hg/lib/tests/expected/annoGrator/gpFx.txt
  • lines changed 6, context: html, text, full: html, text
    Oof, expected output glossed over some missing info. :(
• src/hg/lib/trackHub.c
  • lines changed 6, context: html, text, full: html, text
    make sure that description HTML ends in .html, but not twice. #13516
• src/hg/makeDb/doc/dm6.txt
  • lines changed 187, context: html, text, full: html, text
    added phyloP and phastCons to 27-way refs #4049
• src/hg/makeDb/doc/eboVir3/antibodySequence.txt
  • lines changed 10, context: html, text, full: html, text
    Add ebola sequences collected by Pauline to downloads. refs #14404
• src/hg/makeDb/doc/eboVir3/newSequences.txt
  • lines changed 147, context: html, text, full: html, text
    new sequence procedure under construction refs #14278
• src/hg/makeDb/doc/encodeAwgHg19.txt
  • lines changed 23, context: html, text, full: html, text
    metadata fixes. refs #13230
• src/hg/makeDb/doc/hg19.txt
  • lines changed 29, context: html, text, full: html, text
    snp142: rebuilt tables that use dbSNP's Allele dump file because itwas incomplete when downloaded, then updated a couple weeks after the
    release.
    refs #14189
    
  • lines changed 6, context: html, text, full: html, text
    small makedoc change for hgmd update
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 29, context: html, text, full: html, text
    snp142: rebuilt tables that use dbSNP's Allele dump file because itwas incomplete when downloaded, then updated a couple weeks after the
    release.
    refs #14189
    
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 16, context: html, text, full: html, text
    added cytoBandIdeo track
• src/hg/makeDb/doc/plasFalc3D7V12.txt
  • lines changed 35, context: html, text, full: html, text
    added temporary genome db plasFalc3D7V12
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added dm6 refs #4049
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    dm6 GeneTbl upstreamMaf set to 27-way refs #4049
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added dm6 refs #4049
• src/hg/makeDb/schema/all.joiner
  • lines changed 5, context: html, text, full: html, text
    Add linked table. refs #14054
• src/hg/makeDb/trackDb/cat/felCat8/description.html
  • lines changed 63, context: html, text, full: html, text
    adding felCat8 to the build refs #14412
• src/hg/makeDb/trackDb/cat/felCat8/gap.html
  • lines changed 32, context: html, text, full: html, text
    adding felCat8 to the build refs #14412
• src/hg/makeDb/trackDb/cat/felCat8/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding felCat8 to the build refs #14412
• src/hg/makeDb/trackDb/cat/felCat8/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding felCat8 to the build refs #14412
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 411, context: html, text, full: html, text
    descr page for 27-way refs #4049
  • lines changed 2, context: html, text, full: html, text
    correct reference to 27 refs #4049
  • lines changed 67, context: html, text, full: html, text
    Updating references, refs #13461
• src/hg/makeDb/trackDb/drosophila/dm6/flyBaseGene.ra
  • lines changed 2, context: html, text, full: html, text
    turning on phastCons phyloP and reset default viz refs #4049
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.27way.ra
  • lines changed 68, context: html, text, full: html, text
    turning on phastCons phyloP and reset default viz refs #4049
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    turning on phastCons phyloP and reset default viz refs #4049
• src/hg/makeDb/trackDb/ebola/eboVir2/spMut.html
  • lines changed 1, context: html, text, full: html, text
    Changing occuring to occurring, refs #14062
• src/hg/makeDb/trackDb/ebola/eboVir3/spMut.html
  • lines changed 1, context: html, text, full: html, text
    Changing occuring to occurring, refs #14062
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra
  • lines changed 74, context: html, text, full: html, text
    adding four new sequences refs #14278
  • lines changed 2, context: html, text, full: html, text
    using correct Snp table refs #14278
• src/hg/makeDb/trackDb/human/cooperDevDelay.html
  • lines changed 32, context: html, text, full: html, text
    Moved Cooper description page doc from hg19 level to human level; refs #9391
• src/hg/makeDb/trackDb/human/encodeStanfordNRSF.html
  • lines changed 1, context: html, text, full: html, text
    Changing occuring to occurring, refs #14062
• src/hg/makeDb/trackDb/human/hg19/cooperDevDelay.html
  • lines changed 32, context: html, text, full: html, text
    Moved Cooper description page doc from hg19 level to human level; refs #9391
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding wgEncodeAwgDnaseMasterSites.ra to makefile for metadata in hg19 on beta/public, and making beta/public similar by adding space after wgEncodeOpenChromDnase.ra refs #13230
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding wgEncodeAwgDnaseMasterSites.ra to makefile for metadata in hg19 on beta/public, and making beta/public similar by adding space after wgEncodeOpenChromDnase.ra refs #13230
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    Moved entry for Cooper Dev Delay track from hg19 to human trackDb doc; made into a composite track; just preliminary settings - will need to be updated at some point before release; refs #9391
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.html
  • lines changed 1, context: html, text, full: html, text
    Changing occuring to occurring, refs #14062
• src/hg/makeDb/trackDb/human/stanfordNRSF.html
  • lines changed 1, context: html, text, full: html, text
    Changing occuring to occurring, refs #14062
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    Moved entry for Cooper Dev Delay track from hg19 to human trackDb doc; made into a composite track; just preliminary settings - will need to be updated at some point before release; refs #9391
• src/hg/makeDb/trackDb/makefile
  • lines changed 2, context: html, text, full: html, text
    added temporary genome db plasFalc3D7V12
  • lines changed 1, context: html, text, full: html, text
    adding tarSyr2 to the build refs #14410
  • lines changed 1, context: html, text, full: html, text
    adding felCat8 to the build refs #14412
• src/hg/makeDb/trackDb/plasFalc3D7/plasFalc3D7V12/description.html
  • lines changed 63, context: html, text, full: html, text
    added temporary genome db plasFalc3D7V12
• src/hg/makeDb/trackDb/plasFalc3D7/plasFalc3D7V12/gap.html
  • lines changed 37, context: html, text, full: html, text
    added temporary genome db plasFalc3D7V12
• src/hg/makeDb/trackDb/plasFalc3D7/plasFalc3D7V12/gold.html
  • lines changed 29, context: html, text, full: html, text
    added temporary genome db plasFalc3D7V12
• src/hg/makeDb/trackDb/plasFalc3D7/plasFalc3D7V12/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    added temporary genome db plasFalc3D7V12
  • lines changed 4, context: html, text, full: html, text
    change default plasmodium GC wiggle range is it is very AT-rich
• src/hg/makeDb/trackDb/sheep/oviAri3/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    turning off default tracks introEst and genscan. turning on ensGene by default
• src/hg/makeDb/trackDb/spMut.html
  • lines changed 1, context: html, text, full: html, text
    Changing occuring to occurring, refs #14062
• src/hg/makeDb/trackDb/tarsier/tarSyr2/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb refs #14410
• src/hg/makeDb/trackDb/tarsier/tarSyr2/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb refs #14410
• src/hg/makeDb/trackDb/tarsier/tarSyr2/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb refs #14410
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb refs #14410
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 2, context: html, text, full: html, text
    new includes for top level trackDb for joinedRmsk refs #14410
• src/hg/utils/gff3ToGenePred/tests/expected/errCases1Test.out
  • lines changed 6, context: html, text, full: html, text
    backout change to allow gff3 files to not specify phase on exons (perMark)
    
• src/lib/gff3.c
  • lines changed 1, context: html, text, full: html, text
    backout change to allow gff3 files to not specify phase on exons (perMark)
    
• src/utils/apacheLogParse
  • lines changed 903, context: html, text, full: html, text
    adding apacheLogParse to git, better than having only a single copy in/cluster/bin/scripts.
    
• src/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    adding apacheLogParse to git, better than having only a single copy in/cluster/bin/scripts.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v309 final build refs #14342

• lines changed: 4472
• files changed: 124