All File Changes

v324_base to v325_preview (2015-10-26 to 2015-11-02) v325

• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani
  • lines changed 10, context: html, text, full: html, text
    Adding a dry option to spit out just one of the kallisto commands. refs #16244
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/runKallisto.sh
  • lines changed 5, context: html, text, full: html, text
    Adding a check so that this handles single as well as paired data, refs #16244
    
• src/hg/hgTables/hgTables.c
  • lines changed 10, context: html, text, full: html, text
    Taking back previous gbib-related fix to hgTables that caused a problem
    when filtering non-assembly tables. refs #16158, refs #16188
    
• src/hg/hgTracks/chainTrack.c
  • lines changed 144, context: html, text, full: html, text
    add bigChain support in hgTracks (no redmine)
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    add bigChain support in hgTracks (no redmine)
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    fix a problem with bigGenePred and itemRgb that crept back in to the
    source
    
  • lines changed 10, context: html, text, full: html, text
    add bigChain support in hgTracks (no redmine)
    
• src/hg/hgc/mafClick.c
  • lines changed 2, context: html, text, full: html, text
    fix indent problem in hgc maf display #15935
    
• src/hg/hgc/makefile
  • lines changed 2, context: html, text, full: html, text
    oops somebody lost the beta-specific parts of some lines under the beta target
    
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 24, context: html, text, full: html, text
    fixing blat faq, refs #16173
    
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 3, context: html, text, full: html, text
    Fixing broken links in hgVai help section, no redmine
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 2, context: html, text, full: html, text
    putting hg38 first in navbar
    
• src/hg/htdocs/style/nice_menu.css
  • lines changed 1, context: html, text, full: html, text
    moved nav menu four pixels to the left so users that happen to view two genome browser versions side by side in two different windows on their screen do not get confused
    
• src/hg/htdocs/training/index.html
  • lines changed 22, context: html, text, full: html, text
    added regeneron and karolinska, though not diplaying the latter yet.
    
  • lines changed 14, context: html, text, full: html, text
    encoded email address and added link and changed name for equine workshop at PAG
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 7, context: html, text, full: html, text
    If we get new userRegions from the cart but it's empty (for example because
    we just changed clade/org/db), make sure 'defined regions' is not selected.
    fixes #16291
    
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    add bigChain support in hgTracks (no redmine)
    
• src/hg/makeDb/trackDb/cat/felCat3/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Changing daily to weekly for xenoRefGene tracks, refs #16282
    
• src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGeneNoHs.html
  • lines changed 1, context: html, text, full: html, text
    Changing daily to weekly for xenoRefGene tracks, refs #16282
    
• src/hg/makeDb/trackDb/drosophila/dm6/refGene.html
  • lines changed 1, context: html, text, full: html, text
    Changed daily to weekly on RefSeq Genes description page, refs #16282
    
• src/hg/makeDb/trackDb/drosophila/refGene.html
  • lines changed 1, context: html, text, full: html, text
    Changed daily to weekly on RefSeq Genes description page, refs #16282
    
• src/hg/makeDb/trackDb/drosophila/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Changing daily to weekly for xenoRefGene tracks, refs #16282
    
• src/hg/makeDb/trackDb/human/hg19/tgpPhase3Accessibility.html
  • lines changed 3, context: html, text, full: html, text
    Adding autosomal-only coverage figures from contributor.
    
  • lines changed 10, context: html, text, full: html, text
    Some more description enhancements from the contributors.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV15.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV19.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV20.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV21.html
  • lines changed 2, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.html
  • lines changed 1, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.html
  • lines changed 1, context: html, text, full: html, text
    Correcting wording and removing excess periods in GENCODE description pages, refs #16283
    
• src/hg/makeDb/trackDb/human/snp142.bugFix.html
  • lines changed 9, context: html, text, full: html, text
    Adding explanation of b142 allele frequency bug and fix, release alpha
    only for now.
    
• src/hg/makeDb/trackDb/human/snp142Common_bugFix.html
  • lines changed 29, context: html, text, full: html, text
    Adding explanation of b142 allele frequency bug and fix, release alpha
    only for now.
    
• src/hg/makeDb/trackDb/human/snp142Flagged_bugFix.html
  • lines changed 30, context: html, text, full: html, text
    Adding explanation of b142 allele frequency bug and fix, release alpha
    only for now.
    
• src/hg/makeDb/trackDb/human/snp142Mult_bugFix.html
  • lines changed 26, context: html, text, full: html, text
    Adding explanation of b142 allele frequency bug and fix, release alpha
    only for now.
    
• src/hg/makeDb/trackDb/human/snp142_bugFix.html
  • lines changed 37, context: html, text, full: html, text
    Adding explanation of b142 allele frequency bug and fix, release alpha
    only for now.
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 90, context: html, text, full: html, text
    Adding explanation of b142 allele frequency bug and fix, release alpha
    only for now.
    
• src/hg/makeDb/trackDb/mouse/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Changing daily to weekly for xenoRefGene tracks, refs #16282
    
• src/hg/makeDb/trackDb/refGene.html
  • lines changed 1, context: html, text, full: html, text
    Changed daily to weekly on RefSeq Genes description page, refs #16282
    
• src/hg/makeDb/trackDb/refGene.new.html
  • lines changed 1, context: html, text, full: html, text
    Changing daily to weekly on RefSeq Genes track description page, refs #16282
    
• src/hg/makeDb/trackDb/squirt/refGene.html
  • lines changed 1, context: html, text, full: html, text
    Changed daily to weekly on RefSeq Genes description page, refs #16282
    
• src/hg/makeDb/trackDb/squirt/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Changing daily to weekly for xenoRefGene tracks, refs #16282
    
• src/hg/makeDb/trackDb/worm/refGene.html
  • lines changed 1, context: html, text, full: html, text
    Changed daily to weekly on RefSeq Genes description page, refs #16282
    
• src/hg/makeDb/trackDb/xenoRefGene.html
  • lines changed 1, context: html, text, full: html, text
    Changing daily to weekly for xenoRefGene tracks, refs #16282
    
• src/hg/utils/automation/ncbiToUcsc.sh
  • lines changed 178, context: html, text, full: html, text
    garbage obsolete file removed refs #16274
    
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    improved so no false positives allowed
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v325 preview1
    
• src/utils/qa/weeklybld/buildGbibAndZip
  • lines changed 4, context: html, text, full: html, text
    added warning not to use the obsolete script
    
• src/utils/qa/weeklybld/buildGbibAndZip.csh
  • lines changed 50, context: html, text, full: html, text
    Since our current build bash shell is broken, I cloned and tweaked it to be a bood little cshell script. It should now be working. Noted in the wiki.
    
  • lines changed 10, context: html, text, full: html, text
    added delay to wait for vm startup. fixed path problem.
    
  • lines changed 5, context: html, text, full: html, text
    adding script for updating the qateam browserboxbeta
    
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
  • lines changed 5, context: html, text, full: html, text
    Making the naming convention more consistent. Not sure why, but Hiram likes the version to come first in the log names. I had it at the end before.
    
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 8, context: html, text, full: html, text
    Making the naming convention more consistent. Not sure why, but Hiram likes the version to come first in the log names. I had it at the end before.
    
• src/utils/qa/weeklybld/doLiftOverTestRobot.csh
  • lines changed 3, context: html, text, full: html, text
    Making the naming convention more consistent. Not sure why, but Hiram likes the version to come first in the log names. I had it at the end before.
    
  • lines changed 1, context: html, text, full: html, text
    fixing email addresses to suffix @soe.ucsc.edu
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 2, context: html, text, full: html, text
    added a comment
    
  • lines changed 2, context: html, text, full: html, text
    fixing email addresses to suffix @soe.ucsc.edu
    
• src/utils/qa/weeklybld/doRobots.csh
  • lines changed 3, context: html, text, full: html, text
    getting rid of redundant ssh to host machine bits
    
• src/utils/qa/weeklybld/doTrackCheckRobot.csh
  • lines changed 1, context: html, text, full: html, text
    Making the naming convention more consistent. Not sure why, but Hiram likes the version to come first in the log names. I had it at the end before.
    
  • lines changed 2, context: html, text, full: html, text
    fixing email addresses to suffix @soe.ucsc.edu
    
• src/utils/qa/weeklybld/makeStrictBeta.csh
  • lines changed 1, context: html, text, full: html, text
    fixing email addresses to suffix @soe.ucsc.edu
    
• src/utils/qa/weeklybld/updateBrowserboxbeta.csh
  • lines changed 113, context: html, text, full: html, text
    adding script for updating the qateam browserboxbeta
    

• lines changed: 921
• files changed: 66