All File Changes

v289_preview2 to v289_base (2013-09-02 to 2013-09-09) v289

• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c
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    2 changes made per Jim's note in CR 11663
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
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    2 changes made per Jim's note in CR 11663
• src/hg/hgGenome/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    Fixing linker warnings that appear on Mac OS X 10.8, caused byarguments passed to functions that don't take any arguments.
    
• src/hg/hgTables/compositeTrack.c
  • lines changed 1, context: html, text, full: html, text
    Fixing linker warnings that appear on Mac OS X 10.8, caused byarguments passed to functions that don't take any arguments.
    
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    Fixing linker warnings that appear on Mac OS X 10.8, caused byarguments passed to functions that don't take any arguments.
    
• src/hg/hgTrackUi/hgTrackUi.c
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    added pack and squish modes to snake display, big clean up. #10637
• src/hg/hgTracks/pubsTracks.c
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    comment change
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    various small changes to pubs tracks to be able to show bing.com crawl results
• src/hg/hgTracks/snakeTrack.c
  • lines changed 814, context: html, text, full: html, text
    added pack and squish modes to snake display, big clean up. #10637
  • lines changed 2, context: html, text, full: html, text
    Fixing Mac OS X portability issue.
  • lines changed 1, context: html, text, full: html, text
    Fixing compiler warning that appears only when compiling with -O.
• src/hg/hgVai/hgVai.c
  • lines changed 34, context: html, text, full: html, text
    hgVai can now handle assembly hubs, but if they have no genePred tracks, itcan't really do anything useful so it just suggests that the user choose a different assembly.
    fixes #11306
    
• src/hg/hgc/hgc.c
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    don't crash in Human Proteins detail page if proteome.uniProtAliasdoesn't exist fixes #11653
    
• src/hg/hgc/pubs.c
  • lines changed 37, context: html, text, full: html, text
    various small changes to pubs tracks to be able to show bing.com crawl results
• src/hg/htdocs/ENCODE/index.html
  • lines changed 3, context: html, text, full: html, text
    Removing link to mouseeencode.org until they do not require login, commented out section on ENCODE portal
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    Added entry for echTel2 (redmine #9693)
  • lines changed 2, context: html, text, full: html, text
    Editing static docs for oviAri3 release, refs #9409
• src/hg/htdocs/contacts.html
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    Corrected spelling of 'Commercial'
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 4880, context: html, text, full: html, text
    Essentially overhauled page; removed references to WUSTL's data use policy page and replaced with standard section; standardized references to WUSTL and BCM-HGSC; ordered sections based on order of links at top of page; changed references to Agencourt Bioscience to Beckman Coulter Genomics (redmine #9984)
  • lines changed 3, context: html, text, full: html, text
    Added entry for echTel2 (redmine #9693)
  • lines changed 33, context: html, text, full: html, text
    Changed references to Beckman Coulter Genomics back to Agencourt Bioscience (redmine #9984)
  • lines changed 3, context: html, text, full: html, text
    Editing static docs for oviAri3 release, refs #9409
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 47, context: html, text, full: html, text
    Rewording FTP html page to emphasize using rsync refs #11643
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 27, context: html, text, full: html, text
    Adding announcement about oviAri3 release, refs #9409
  • lines changed 2, context: html, text, full: html, text
    Editing static docs for oviAri3 release, refs #9409
  • lines changed 27, context: html, text, full: html, text
    Added entries for the tenrec release (redmine #9693)
• src/hg/htdocs/images/17.jpg
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    adding 19.jpg and fixing edges of other #.jpgs to better match bluish new hgTracks background
• src/hg/htdocs/images/18.jpg
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    adding 19.jpg and fixing edges of other #.jpgs to better match bluish new hgTracks background
• src/hg/htdocs/images/19.jpg
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    adding 19.jpg and fixing edges of other #.jpgs to better match bluish new hgTracks background
• src/hg/htdocs/images/2.jpg
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    adding 19.jpg and fixing edges of other #.jpgs to better match bluish new hgTracks background
• src/hg/htdocs/images/4.jpg
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    adding 19.jpg and fixing edges of other #.jpgs to better match bluish new hgTracks background
• src/hg/htdocs/images/5.jpg
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    adding 19.jpg and fixing edges of other #.jpgs to better match bluish new hgTracks background
• src/hg/htdocs/images/6.jpg
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    adding 19.jpg and fixing edges of other #.jpgs to better match bluish new hgTracks background
• src/hg/htdocs/images/9.jpg
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    adding 19.jpg and fixing edges of other #.jpgs to better match bluish new hgTracks background
• src/hg/htdocs/images/pubs_bing.png
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    adding microsoft research logo for upcoming web-publications track
• src/hg/htdocs/indexNews.html
  • lines changed 102, context: html, text, full: html, text
    Adding announcement about oviAri3 release, refs #9409
  • lines changed 3, context: html, text, full: html, text
    Editing static docs for oviAri3 release, refs #9409
  • lines changed 47, context: html, text, full: html, text
    Added entries for the tenrec release (redmine #9693)
• src/hg/inc/versionInfo.h
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    New version number v289
• src/hg/lib/annoFormatVep.c
  • lines changed 18, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 3, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/hg/lib/hgFind.c
  • lines changed 51, context: html, text, full: html, text
    While hgFind exhaustive search may cause a CGI timeout (#11626), at least one app (hgGetAnn) requires an exhaustive search (#11665). So I have enforced a results limit for mRNA searches only, and have allowed hgGetAnn to override the limit. Will not be surprised if some other obscure case pops up where an hgFind call needs to be exhaustive, but have yet to code-browse discover one.
• src/hg/lib/sqlProg.c
  • lines changed 13, context: html, text, full: html, text
    cleaning up unneeded switch
• src/hg/lib/tests/expected/annoGrator/snpBigWigToTabOut.txt
  • lines changed 3, context: html, text, full: html, text
    snp135 got some new rows when it was rebuilt (#11544), so we get some new rows of output.
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 11, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 310, context: html, text, full: html, text
    starting lastz for neoBri1 hapBur1 punNye1 astMex1 lepOcu1 refs #10272
  • lines changed 46, context: html, text, full: html, text
    wrapping up lastz runs for gadMor1 chrPic1 myoLuc2 chiLan1 pelSin1 mesAur1 myoDav1 eptFus1 takFla1 refs #10272
  • lines changed 71, context: html, text, full: html, text
    starting lastz run on allSin1 refs #10272
  • lines changed 56, context: html, text, full: html, text
    wrapping up lastz runs for gadMor1 mesAur1 pteAle1 myoDav1 eptFus1 takFla1 neoBri1 hapBur1 punNye1 astMex1 lepOcu1 allSin1 refs #10272
  • lines changed 99, context: html, text, full: html, text
    finishing up lastz runs for criGri1 neoBri1 hapBur1 punNye1 astMex1 lepOcu1 mayZeb1 refs #10272
  • lines changed 17, context: html, text, full: html, text
    done with lastz for criGri1 pteAle1 mayZeb1 refs #10272
  • lines changed 1, context: html, text, full: html, text
    restarting lastz run on allSin1 to fix chrM missing refs #10272
  • lines changed 13, context: html, text, full: html, text
    finishing up allSin1 lastz run refs #10272
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    added alpaca (vicPac2)
• src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra
  • lines changed 2, context: html, text, full: html, text
    Staging hg19 to oviAri3 chain/net on hgwbeta, refs #9409
  • lines changed 1, context: html, text, full: html, text
    Releasing hg19 to oviAri3 chain/net to RR, refs #9409
  • lines changed 1, context: html, text, full: html, text
    Correcting mistake from my last edit for releasing oviAri/hg19 chain/net to RR, refs #9409
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 132, context: html, text, full: html, text
    remove snake tracks that used chains as the format. Add map viewergenes track
    
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Shortened INSDC long label to be under 80 characters, refs #11348
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 203, context: html, text, full: html, text
    Ensembl v73 update and their FTP server has changed its output refs #11675
  • lines changed 4, context: html, text, full: html, text
    fixup a couple of broken names refs #11675
• src/hg/utils/automation/findEnsFtpNames.sh
  • lines changed 15, context: html, text, full: html, text
    Ensembl v73 update and their FTP server has changed its output refs #11675
• src/hg/utils/phyloTrees/112way.commonNames.nh
  • lines changed 112, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/112way.nh
  • lines changed 111, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/112way.scientificNames.nh
  • lines changed 112, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/benchMark100.commonNames.nh
  • lines changed 15, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/benchMark100.nh
  • lines changed 15, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/benchMark100.scientificNames.nh
  • lines changed 15, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/benchMark100.sh
  • lines changed 1, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 2, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 7, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 14, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 3, context: html, text, full: html, text
    adding allSin1 and updating tree based upon input from Klaus-Peter Koepfli refs #10272
• src/inc/vcf.h
  • lines changed 2, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/lib/annoGrator.c
  • lines changed 13, context: html, text, full: html, text
    In order to detect the overlap of two 0-length (insertion) items, we needto expand at least one of their ranges to the two surrounding bases.
    
• src/lib/annoStreamVcf.c
  • lines changed 1, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/lib/vcf.c
  • lines changed 4, context: html, text, full: html, text
    VCF annoRows need to have corrected coords for indels, otherwise it messesup coord comparison in annoGrator. Also, that lets us get rid of the
    ugly skippedFirstBase hack in annoFormatVep and annoGratorGpVar.
    
• src/userApps/Makefile
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    correct testing for existence of downloaded source refs #9149
• src/utils/qa/weeklybld/buildEnv.csh
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    v289 final build

• lines changed: 7589
• files changed: 80