All File Changes

v286_preview2 to v286_base (2013-07-02 to 2013-07-09) v286

• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 21, context: html, text, full: html, text
    Updated getTrackReferences to add PMID and PMCID with hyperlinks, set -o to default on, refs #10192
• src/hg/hgConvert/hgConvert.c
  • lines changed 33, context: html, text, full: html, text
    clean up the liftOverChain to allow choices for toDb where it is actually in dbDb refs #10272
• src/hg/hgGene/ctd.c
  • lines changed 8, context: html, text, full: html, text
    simplifying sql abuses of sqlGetField
• src/hg/hgGene/gad.c
  • lines changed 12, context: html, text, full: html, text
    simplifying sql abuses of sqlGetField
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    Fixing some broken HTML and JS in hgVai and hgTables when the position/search term can't be found. refs 6152 10964
• src/hg/hgTracks/menu.c
  • lines changed 7, context: html, text, full: html, text
    was missing the Ensembl blue bar nav help for all assemblies with ucscToEnsembl table refs #11114
• src/hg/hgc/geneReviewsClick.c
  • lines changed 108, context: html, text, full: html, text
    RM To Do 10993 path for the files necessary to compute the links has changed.
• src/hg/hgc/geneReviewsClick.h
  • lines changed 8, context: html, text, full: html, text
    RM To Do 10993 path for the files necessary to compute the links has changed.
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    simplifying sql code to ease sqli checking
  • lines changed 103, context: html, text, full: html, text
    RM To Do 10993 path for the files necessary to compute the links has changed.
  • lines changed 3, context: html, text, full: html, text
    fixed unvetted query from sql in a trackDbSetting idInUrlSql
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    RM To Do 10993 path for the files necessary to compute the links has changed.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 4, context: html, text, full: html, text
    More edits to hub help doc. refs #8072
  • lines changed 38, context: html, text, full: html, text
    Added new section to describe what is *special* about assembly hubs. refs #8072
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    Adding link to new instructions for building bigBeg index. refs #8072
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 2, context: html, text, full: html, text
    Adding instructions on where to get necessary utils for these processes. refs #8072
• src/hg/htdocs/goldenPath/help/twoBit.html
  • lines changed 5, context: html, text, full: html, text
    Adding instructions on where to get necessary utils for these processes. refs #8072
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 72, context: html, text, full: html, text
    Adding assembly hubs and gene alleles announcements to news page.
  • lines changed 2, context: html, text, full: html, text
    Making a link in newsarch.html redirect from goldenPath/ directory MLQ# 11219
  • lines changed 1, context: html, text, full: html, text
    fixed a link
• src/hg/htdocs/indexNews.html
  • lines changed 159, context: html, text, full: html, text
    Adding assembly hubs and gene alleles announcements to news page.
  • lines changed 1, context: html, text, full: html, text
    added a colon I left out earlier
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v286
• src/hg/inc/web.h
  • lines changed 2, context: html, text, full: html, text
    Fixing some broken HTML and JS in hgVai and hgTables when the position/search term can't be found. refs 6152 10964
• src/hg/lib/annoFormatVep.c
  • lines changed 2, context: html, text, full: html, text
    When abbreviating frameshift alleles, don't use "bases" to refer to both nucleotides and amino acids (thx Brooke). refs #6152
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    Fixing some broken HTML and JS in hgVai and hgTables when the position/search term can't be found. refs 6152 10964
• src/hg/lib/web.c
  • lines changed 15, context: html, text, full: html, text
    Fixing some broken HTML and JS in hgVai and hgTables when the position/search term can't be found. refs 6152 10964
• src/hg/makeDb/doc/allMis1.txt
  • lines changed 7, context: html, text, full: html, text
    in the pushQ 007055 refs #8750
• src/hg/makeDb/doc/eriEur2.txt
  • lines changed 70, context: html, text, full: html, text
    ready to do the hg19 chain net then into the pushQ refs #9419
• src/hg/makeDb/doc/hg19.txt
  • lines changed 21, context: html, text, full: html, text
    finish up lastz swaps to tarSyr1 papHam1 otoGar3 refs #10272
  • lines changed 74, context: html, text, full: html, text
    running lastz swaps to pteVam1 choHof1 proCap1 dipOrd1 refs #10272
  • lines changed 137, context: html, text, full: html, text
    finish off lastz swaps to pteVam1 proCap1 starting lastz runs to tupChi1 and octDeg1 refs #10272
  • lines changed 15, context: html, text, full: html, text
    finishing off tupChi1 lastz run on chaining chr19 on octDeg1 lastz refs #10272
  • lines changed 241, context: html, text, full: html, text
    starting lastz runs on oryAfe1 chrAsi1 eleEdw1 dasNov3 refs #10272
  • lines changed 57, context: html, text, full: html, text
    starting lastz on eriEur2 refs #9419
• src/hg/makeDb/genbank/src/inc/gbDefs.h
  • lines changed 3, context: html, text, full: html, text
    adding the moltype DNA to gbProcess, to make it possible to pull out BACs and other weird things out of genbank
• src/hg/makeDb/genbank/src/lib/gbDefs.c
  • lines changed 2, context: html, text, full: html, text
    adding the moltype DNA to gbProcess, to make it possible to pull out BACs and other weird things out of genbank
• src/hg/makeDb/genbank/src/process/gbProcess.c
  • lines changed 17, context: html, text, full: html, text
    adding the moltype DNA to gbProcess, to make it possible to pull out BACs and other weird things out of genbank
  • lines changed 4, context: html, text, full: html, text
    forgot to remove some printfs
  • lines changed 13, context: html, text, full: html, text
    adding -org filter to gbProcess and deactivating the section filters for the dna moltype
• src/hg/makeDb/schema/all.joiner
  • lines changed 16, context: html, text, full: html, text
    adding eriEur2 refs #9149
• src/hg/makeDb/trackDb/human/hg19/knownGeneOld6.html
  • lines changed 27, context: html, text, full: html, text
    added description for updated Old UCSC Genes track
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    make the Old Known Genes track point to the most recent old version
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    changing link to the right uniprot section
• src/hg/utils/phyloTrees/108way.dissect.txt
  • lines changed 1505, context: html, text, full: html, text
    working up new scheme to order all the new assemblies in between the existing ones refs #10272
• src/hg/utils/phyloTrees/108way.nh
  • lines changed 1, context: html, text, full: html, text
    update ficAlb1 to ficAlb2 refs #10272
• src/hg/utils/phyloTrees/108wayChainNet.pl
  • lines changed 212, context: html, text, full: html, text
    working up new scheme to order all the new assemblies in between the existing ones refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 1, context: html, text, full: html, text
    update ficAlb1 to ficAlb2 refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    update ficAlb1 to ficAlb2 refs #10272
• src/lib/annoStreamVcf.c
  • lines changed 10, context: html, text, full: html, text
    Partially fixing the vcf tabix region logic in annoStreamVcf.c.Still need to figure out a way to skip to the next row of VCF *after*
    a minChrom region that has no elements! refs #6152
    
• src/userApps/README
  • lines changed 14, context: html, text, full: html, text
    add note about pre-compiled binaries refs #9149
• src/userApps/fetchKentSource.sh
  • lines changed 4, context: html, text, full: html, text
    moving to beta branch for version 286 build refs #9149
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v286 preview2
  • lines changed 8, context: html, text, full: html, text
    v286 final build
• src/utils/qa/weeklybld/revertCommits.csh
  • lines changed 185, context: html, text, full: html, text
    oops. adding utility revertCommits.csh to git repo. should have done it earlier.

• lines changed: 3271
• files changed: 55