All File Changes

v275_base to v276_preview (2012-10-30 to 2012-11-06) v276

• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    I do not think Jim meant to add this line yet. Only when we do a major release number increment.
• src/hg/autoXml/autoXml.c
  • lines changed 12, context: html, text, full: html, text
    Fixing several cases where the attributes name was used where it's mixedCaseName should have been. This fixes a glitch that came up reading NCBI incident database stuff that Hiram is working on.
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    removing the new connFailures capability. it is difficult to distinguish failing sites from struggling sites with this approach -- so leave it out for now.
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    take out swissProt and proteins and databases that will appear in hgTables if present (#8133)
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    removing the new connFailures capability. it is difficult to distinguish failing sites from struggling sites with this approach -- so leave it out for now.
• src/hg/hgTracks/renderMain.c
  • lines changed 1, context: html, text, full: html, text
    removing the new connFailures capability. it is difficult to distinguish failing sites from struggling sites with this approach -- so leave it out for now.
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 7, context: html, text, full: html, text
    Y5Q4 update of portal Experiment Lists (final report). #9315
  • lines changed 1, context: html, text, full: html, text
    Small grammar/punctuation edit.
  • lines changed 1, context: html, text, full: html, text
    Changed link to google spreadsheet to make it consistent with the rest.
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 6, context: html, text, full: html, text
    Y5Q4 update of portal Experiment Lists (final report). #9315
  • lines changed 1, context: html, text, full: html, text
    Small grammar/punctuation edit.
• src/hg/htdocs/ENCODE/index.html
  • lines changed 2, context: html, text, full: html, text
    Final updates of ENCODE portal Experiment Lists. #9315
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 5, context: html, text, full: html, text
    making link to Track Hub doc more prominent
  • lines changed 6, context: html, text, full: html, text
    fine tuning based on Brooke's code review feedback #9489
  • lines changed 2, context: html, text, full: html, text
    fixed one typo
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 10, context: html, text, full: html, text
    Mods based on feedback from paired review.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 8, context: html, text, full: html, text
    Added Goldman NAR pub.
  • lines changed 1, context: html, text, full: html, text
    reverted to abstract until the journal gets its act together and proveds the Open Access we paid for
  • lines changed 1, context: html, text, full: html, text
    added doi to ref
  • lines changed 1, context: html, text, full: html, text
    put the full-text link back is, as they finally got it working at the journal
• src/hg/htdocs/images/Papio_anubis.jpg
  • lines changed 0, context: html, text, full: html, text
    use Papio_hamadryas_anubis.jpg for both papHam1 and papAnu2.
• src/hg/htdocs/images/Papio_hamadryas_anubis.jpg
  • lines changed 0, context: html, text, full: html, text
    use Papio_hamadryas_anubis.jpg for both papHam1 and papAnu2.
• src/hg/htdocs/images/Reconstructed_Centromers.png
  • lines changed 0, context: html, text, full: html, text
    adding 250x250 image for centromers1 db
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 63, context: html, text, full: html, text
    Changes to Mirror dropdown behavior after input from Bob K. #7477
  • lines changed 9, context: html, text, full: html, text
    Use hg.conf browser.node setting to distinguish GEO mirrors. #7477
  • lines changed 19, context: html, text, full: html, text
    Use hg.conf setting (browser.node) to determine GEO mirrors. #7477
• src/hg/htdocs/style/nice_menu.css
  • lines changed 13, context: html, text, full: html, text
    Changes to Mirror dropdown behavior after input from Bob K. #7477
• src/hg/lib/tests/.gitignore
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigBed.
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 35, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigBed.
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 6, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigBed.
• src/hg/lib/tests/expected/annoGrator/bigBedToTabOut.txt
  • lines changed 122, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigBed.
• src/hg/lib/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigBed.
• src/hg/lib/web.c
  • lines changed 7, context: html, text, full: html, text
    Use hg.conf browser.node setting to distinguish GEO mirrors. #7477
  • lines changed 4, context: html, text, full: html, text
    Just comments about future direcction for GEO mirror support
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 61, context: html, text, full: html, text
    cow v. rhino lastz done
• src/hg/makeDb/doc/centromers1.txt
  • lines changed 46, context: html, text, full: html, text
    adding a centromers1 browser, only for hgwdev, shows kahayden's / Jim's work on mapping encode data to reconstructed centromer sequences
• src/hg/makeDb/doc/cerSim1.txt
  • lines changed 23, context: html, text, full: html, text
    completed Lamprey petMar2 and Rhino cerSim1 lastz to Opossum
  • lines changed 24, context: html, text, full: html, text
    cow v. rhino lastz done
• src/hg/makeDb/doc/geoFor1.txt
  • lines changed 16, context: html, text, full: html, text
    revisit the phyloP histogram graph
• src/hg/makeDb/doc/monDom5.txt
  • lines changed 141, context: html, text, full: html, text
    completed Lamprey petMar2 and Rhino cerSim1 lastz to Opossum
• src/hg/makeDb/doc/papAnu2.txt
  • lines changed 101, context: html, text, full: html, text
    Put papAnu2 in pushQ.
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 220, context: html, text, full: html, text
    starting 7-way alignment
  • lines changed 239, context: html, text, full: html, text
    gap and frame annotation added to the 7-way
  • lines changed 140, context: html, text, full: html, text
    phylo tree estimate done from the 7-way maf file
  • lines changed 277, context: html, text, full: html, text
    done with phastCons7way
  • lines changed 187, context: html, text, full: html, text
    done with phyloP7way
  • lines changed 13, context: html, text, full: html, text
    correct histogram of the phyloP data
• src/hg/makeDb/doc/rn5.txt
  • lines changed 16, context: html, text, full: html, text
    liftOver to rn4 done
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 2, context: html, text, full: html, text
    use UDR to transfer genbank files to the euronode
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    another assembly that already has xenoMrna in it...
  • lines changed 2, context: html, text, full: html, text
    fix yet another assembly that has xenoMrna
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 3, context: html, text, full: html, text
    Added gadMor1, latCha1, melUnd1
• src/hg/makeDb/genbank/src/copy/gbCopyStep
  • lines changed 16, context: html, text, full: html, text
    use UDR to transfer genbank files to the euronode
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Review #9495 feedback from Hiram: combined papAnu2 with papHam1 to to include both name in *papAnuNames[] and papHamNames[].
• src/hg/makeDb/trackDb/baboon/papAnu2/description.html
  • lines changed 1, context: html, text, full: html, text
    Remove underscore from Papio_anubis name.
• src/hg/makeDb/trackDb/baboon/papHam1/description.html
  • lines changed 3, context: html, text, full: html, text
    Changed nonexistent NCBI link to a Baylor link. RM 7679#note-19.
• src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    fixup petMar2 and geoFor1 priority overrides
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.html
  • lines changed 2, context: html, text, full: html, text
    Fixed Tom Tullius email link (redmine #9487)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 153, context: html, text, full: html, text
    added accessions to Duke Affy Exon
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 2, context: html, text, full: html, text
    fixed objStatus as per code review for v275
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1.html
  • lines changed 4, context: html, text, full: html, text
    Track #7964 (1000 Genomes variants) description: Phase 1 publicationhas been released on Nature's web site, but is not yet in PubMed, so
    I'm adding links to Nature for the pilot and Phase 1 refs.
    
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 388, context: html, text, full: html, text
    initial display of the 7-way conservation
• src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.7way.ra
  • lines changed 103, context: html, text, full: html, text
    initial display of the 7-way conservation
  • lines changed 4, context: html, text, full: html, text
    setting the phyloP viewLimits
• src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    initial display of the 7-way conservation
• src/hg/makeDb/trackDb/lamprey/trackDb.chainNet.ra
  • lines changed 19, context: html, text, full: html, text
    tuning up the chain net tracks to be accurate locations and parameters
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    fix typo in trackDb/makefile
  • lines changed 4, context: html, text, full: html, text
    adding a centromers1 browser, only for hgwdev, shows kahayden's / Jim's work on mapping encode data to reconstructed centromer sequences
  • lines changed 1, context: html, text, full: html, text
    accidentally checked in an uncomment in the trackDb makefile, correcting with this commit
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    correct priority for petMar2 chain net
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    correct priority for petMar2 chain net
• src/hg/makeDb/trackDb/other/centromers1/description.html
  • lines changed 53, context: html, text, full: html, text
    adding a centromers1 browser, only for hgwdev, shows kahayden's / Jim's work on mapping encode data to reconstructed centromer sequences
• src/hg/makeDb/trackDb/other/centromers1/gap.html
  • lines changed 37, context: html, text, full: html, text
    adding a centromers1 browser, only for hgwdev, shows kahayden's / Jim's work on mapping encode data to reconstructed centromer sequences
• src/hg/makeDb/trackDb/other/centromers1/gold.html
  • lines changed 4, context: html, text, full: html, text
    adding a centromers1 browser, only for hgwdev, shows kahayden's / Jim's work on mapping encode data to reconstructed centromer sequences
• src/hg/makeDb/trackDb/other/centromers1/trackDb.encode.ra
  • lines changed 196, context: html, text, full: html, text
    adding a centromers1 browser, only for hgwdev, shows kahayden's / Jim's work on mapping encode data to reconstructed centromer sequences
  • lines changed 1, context: html, text, full: html, text
    add color
  • lines changed 101, context: html, text, full: html, text
    adding colors
  • lines changed 2, context: html, text, full: html, text
    correcting header
  • lines changed 23, context: html, text, full: html, text
    correcting header
  • lines changed 15, context: html, text, full: html, text
    adding colors
• src/hg/makeDb/trackDb/other/centromers1/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    adding a centromers1 browser, only for hgwdev, shows kahayden's / Jim's work on mapping encode data to reconstructed centromer sequences
  • lines changed 1, context: html, text, full: html, text
    adding monomer color
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/trackDb.genbank.new.ra
  • lines changed 3, context: html, text, full: html, text
    fix genbank searching on assemblies without all_mrna (#7686)
• src/hg/makeDb/trackDb/trackDb.genbank.ra
  • lines changed 2, context: html, text, full: html, text
    fix genbank searching on assemblies without all_mrna (#7686)
• src/inc/annoStreamBigBed.h
  • lines changed 13, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigBed.
• src/inc/bbiFile.h
  • lines changed 1, context: html, text, full: html, text
    Adding missing #include, for includers of bbiFile.h that haven't already included linefile.h.
• src/inc/net.h
  • lines changed 15, context: html, text, full: html, text
    removing the new connFailures capability. it is difficult to distinguish failing sites from struggling sites with this approach -- so leave it out for now.
• src/inc/trix.h
  • lines changed 6, context: html, text, full: html, text
    Improving documentation of text search interface.
• src/index/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding trixSearch to index utilities.
• src/index/trixSearch/trixSearch.c
  • lines changed 20, context: html, text, full: html, text
    Updating comments and usage statement per Angie's review. Adding -full option.
• src/lib/annoStreamBigBed.c
  • lines changed 119, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigBed.
• src/lib/dtdParse.c
  • lines changed 1, context: html, text, full: html, text
    Improving a comment.
• src/lib/https.c
  • lines changed 9, context: html, text, full: html, text
    removing the new connFailures capability. it is difficult to distinguish failing sites from struggling sites with this approach -- so leave it out for now.
• src/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigBed.
• src/lib/net.c
  • lines changed 92, context: html, text, full: html, text
    removing the new connFailures capability. it is difficult to distinguish failing sites from struggling sites with this approach -- so leave it out for now.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v276 preview1
• src/utils/qa/weeklybld/buildUtils.csh
  • lines changed 15, context: html, text, full: html, text
    Commented out all 32-bit build statements.
• src/utils/qa/weeklybld/cherryPickCommits.csh
  • lines changed 14, context: html, text, full: html, text
    Commented out all 32-bit build statements.
• src/utils/qa/weeklybld/coBranch.csh
  • lines changed 5, context: html, text, full: html, text
    Commented out all 32-bit build statements.
• src/utils/qa/weeklybld/configureSandbox.csh
  • lines changed 5, context: html, text, full: html, text
    Commented out all 32-bit build statements.
• src/utils/qa/weeklybld/doHgDownloadUtils.csh
  • lines changed 12, context: html, text, full: html, text
    Commented out all 32-bit build statements.
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 13, context: html, text, full: html, text
    Commented out all 32-bit build statements.
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 17, context: html, text, full: html, text
    Commented out all 32-bit build statements.
• src/utils/qa/weeklybld/moveBranchTag.csh
  • lines changed 8, context: html, text, full: html, text
    Commented out all 32-bit build statements.
• src/utils/qa/weeklybld/patchBranch.csh
  • lines changed 6, context: html, text, full: html, text
    Commented out all 32-bit build statements.

• lines changed: 3416
• files changed: 106