All File Changes

v266_base to v267_preview (2012-04-24 to 2012-05-01) v267

• python/lib/ucscgenomics/bed.py
  • lines changed 49, context: html, text, full: html, text
    removed bed textstyle from ucscgenomics lib
• python/lib/ucscgenomics/cv.py
  • lines changed 68, context: html, text, full: html, text
    added new changes to cv.py to allow mouseCellType to work from within code
  • lines changed 1, context: html, text, full: html, text
    added small fix for cv.py
• python/lib/ucscgenomics/qa.py
  • lines changed 312, context: html, text, full: html, text
    Moved qa.py to qa/encode/tableCheck.py.
• python/lib/ucscgenomics/qa/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Moved qa.py to qa/encode/tableCheck.py.
• python/lib/ucscgenomics/qa/encode/__init__.py
  • lines changed 0, context: html, text, full: html, text
    Moved qa.py to qa/encode/tableCheck.py.
• python/lib/ucscgenomics/qa/encode/tableCheck.py
  • lines changed 312, context: html, text, full: html, text
    Moved qa.py to qa/encode/tableCheck.py.
  • lines changed 20, context: html, text, full: html, text
    Moved callHgsql function from qa/encode/tableCheck.py to a new file: qa/qaUtils.py. Removed some unused lines from the top of tableCheck.py.
  • lines changed 1, context: html, text, full: html, text
    adding a reference
• python/lib/ucscgenomics/qa/qaUtils.py
  • lines changed 14, context: html, text, full: html, text
    Moved callHgsql function from qa/encode/tableCheck.py to a new file: qa/qaUtils.py. Removed some unused lines from the top of tableCheck.py.
• python/lib/ucscgenomics/textstyle.py
  • lines changed 40, context: html, text, full: html, text
    removed bed textstyle from ucscgenomics lib
• python/style.txt
  • lines changed 6, context: html, text, full: html, text
    Added guidlines for length's of modules, functions and methods. Redmine #7162.
• python/users/kent/django/mysite/README
  • lines changed 3, context: html, text, full: html, text
    Adding READMEs to all of the Django directories.
• python/users/kent/django/mysite/djBook/README
  • lines changed 1, context: html, text, full: html, text
    Adding READMEs to all of the Django directories.
• python/users/kent/django/mysite/jkSp/README
  • lines changed 2, context: html, text, full: html, text
    Adding READMEs to all of the Django directories.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 6, context: html, text, full: html, text
    Added protocol documents view and removed downloadOnly for Junctions. Redmine #7089.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeSydhRnaSeq.daf
  • lines changed 7, context: html, text, full: html, text
    Fixed DAF to use Plus and Minus Raw Signal. Redmine #829.
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 10, context: html, text, full: html, text
    restructiring for new validateFiles and .as and .sql locations
• src/hg/encode/encodeLoad/installSqlSchemas.pl
  • lines changed 52, context: html, text, full: html, text
    reworked installSchemas to actually work and modified make to compensate
• src/hg/encode/encodeLoad/makefile
  • lines changed 1, context: html, text, full: html, text
    reworked installSchemas to actually work and modified make to compensate
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 308, context: html, text, full: html, text
    restructuring for the enw validateFiles
  • lines changed 3, context: html, text, full: html, text
    filtering on bam only for validation settings
  • lines changed 9, context: html, text, full: html, text
    removed some debugging prints
  • lines changed 1, context: html, text, full: html, text
    forgot to pull variable out
  • lines changed 1, context: html, text, full: html, text
    I don't think we meant to drop pdf
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    Adding a missing va_end for tidiness' sake.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    use a union in jsonElement to simplify code and eliminate typecasts (per suggestion of angie and tim); rename jsonHash to jsonObject; fix some obsolete comments
• src/hg/hgTracks/hgTracks.c
  • lines changed 18, context: html, text, full: html, text
    use a union in jsonElement to simplify code and eliminate typecasts (per suggestion of angie and tim); rename jsonHash to jsonObject; fix some obsolete comments
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    use a union in jsonElement to simplify code and eliminate typecasts (per suggestion of angie and tim); rename jsonHash to jsonObject; fix some obsolete comments
• src/hg/hgTracks/imageV2.c
  • lines changed 43, context: html, text, full: html, text
    use a union in jsonElement to simplify code and eliminate typecasts (per suggestion of angie and tim); rename jsonHash to jsonObject; fix some obsolete comments
• src/hg/hgTracks/imageV2.h
  • lines changed 2, context: html, text, full: html, text
    fix things broken by changes in jsHelper
• src/hg/hgTracks/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    use a union in jsonElement to simplify code and eliminate typecasts (per suggestion of angie and tim); rename jsonHash to jsonObject; fix some obsolete comments
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 548, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added region type and positioninputs to UI -- and it actually executes some queries now!
    
  • lines changed 121, context: html, text, full: html, text
    UI for #6152 (Variant Annotation Tool): position input is now searchedonblur and before we submit the page to execute a query, so that if a position
    is not found or has multiple matches, the user is returned to the UI to fix it.
    
  • lines changed 15, context: html, text, full: html, text
    fix things broken by changes in jsHelper
• src/hg/hgc/pubs.c
  • lines changed 184, context: html, text, full: html, text
    changed almost all html in pubs hgc page to get rid of unnecessary tables (this part does not conform to kent style but really looks better)
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 64, context: html, text, full: html, text
    Put tools into categories and alphabetized per Kate's request (redmine #7701)
  • lines changed 5, context: html, text, full: html, text
    Made changes suggested by Katrina in code review (redmine #7738)
• src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
  • lines changed 1, context: html, text, full: html, text
    Adjust colors of dots (cancer vs. normal cell types for color-blind accomodation
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 26, context: html, text, full: html, text
    Refine Help text, based on input from Donna
  • lines changed 1, context: html, text, full: html, text
    Change help link to a little more formal language
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 1, context: html, text, full: html, text
    Tweak title as per Donna's input
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
  • lines changed 2, context: html, text, full: html, text
    Tweak title as per Donna's input
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryMouse.html
  • lines changed 1, context: html, text, full: html, text
    Tweak title as per Donna's input
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 4, context: html, text, full: html, text
    Added line for PSU Histone (redmine #111)
• src/hg/htdocs/ENCODE/encodeTools.html
  • lines changed 178, context: html, text, full: html, text
    Put tools into categories and alphabetized per Kate's request (redmine #7701)
  • lines changed 1, context: html, text, full: html, text
    Corrected spelling of RSEQtools (redmine #7701)
  • lines changed 13, context: html, text, full: html, text
    Made changes suggested by Katrina in code review (redmine #7738 note 8)
  • lines changed 34, context: html, text, full: html, text
    Made changes suggested by Katrina in code review (redmine #7738)
• src/hg/htdocs/ENCODE/softwareTools.html
  • lines changed 2, context: html, text, full: html, text
    Put tools into categories and alphabetized per Kate's request (redmine #7701)
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    Corrected spelling of bedGraph.
• src/hg/htdocs/admin/mirror.html
  • lines changed 3, context: html, text, full: html, text
    added links to blogs for installing mirror on Ubuntu and CentOS
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 2, context: html, text, full: html, text
    Added links to two words, making things a little easier for the user.
• src/hg/htdocs/images/Casanova_papio_anubis.jpg
  • lines changed 0, context: html, text, full: html, text
    added image of olive baboon - the actual species sequenced
  • lines changed 0, context: html, text, full: html, text
    changed name because the animal's name was Casanova, not his species
• src/hg/htdocs/images/Dipodomys_ordii.jpg
  • lines changed 0, context: html, text, full: html, text
    added kangRat image from wikipedia
• src/hg/htdocs/images/Erinaceus_europaeus.jpg
  • lines changed 0, context: html, text, full: html, text
    added wikipedia image of hedgehog
• src/hg/htdocs/images/Ochotona_princeps.jpg
  • lines changed 0, context: html, text, full: html, text
    added wikipedia image of pika
• src/hg/htdocs/images/Otolemur_garnettii.jpg
  • lines changed 0, context: html, text, full: html, text
    made image smaller (500 to 320 pix wide) to speed loading
• src/hg/htdocs/images/Papio_anubis.jpg
  • lines changed 0, context: html, text, full: html, text
    changed name because the animal's name was Casanova, not his species
• src/hg/htdocs/images/Procavia_capensis.jpg
  • lines changed 0, context: html, text, full: html, text
    added rock hyrax image
• src/hg/htdocs/images/Pteropus_vampyrus.jpg
  • lines changed 0, context: html, text, full: html, text
    added wikipedia vampire (megabat) image
  • lines changed 0, context: html, text, full: html, text
    uploaded wrong version of image (too large). fixed
• src/hg/htdocs/images/Saimiri_boliviensis.jpg
  • lines changed 0, context: html, text, full: html, text
    added image from wikipedia
• src/hg/htdocs/images/Sorex_araneus.jpg
  • lines changed 0, context: html, text, full: html, text
    added image of shrew from wikipedia
• src/hg/htdocs/images/Spermophilus_tridecemlineatus.jpg
  • lines changed 0, context: html, text, full: html, text
    image of 13-lined squirrel from wikipedia
• src/hg/htdocs/images/Tarsius_syrichta.jpg
  • lines changed 0, context: html, text, full: html, text
    added tarsier image from wikipedia
• src/hg/htdocs/images/Trichechus_manatus.jpg
  • lines changed 0, context: html, text, full: html, text
    added image of manatee
• src/hg/htdocs/images/Tursiops_truncatus.jpg
  • lines changed 0, context: html, text, full: html, text
    added image of dolphin from wikipedia
• src/hg/htdocs/inc/encodeProjectSoftware.topbar.html
  • lines changed 38, context: html, text, full: html, text
    Added new menu bar file that includes a link to Software Tools (redmine #7701)
  • lines changed 1, context: html, text, full: html, text
    Added a dash between 'Data Standards' and 'Software Tools' (redmine #7701)
• src/hg/htdocs/mirror.html
  • lines changed 16, context: html, text, full: html, text
    removed Duke mirror. Terry is taking it down.
  • lines changed 2, context: html, text, full: html, text
    temporarily commenting out links to the Queensland mirror, which is down for a bit
• src/hg/htdocs/style/HGStyle.css
  • lines changed 20, context: html, text, full: html, text
    Max noticed that the font-family declarations for 'sans-serif' were often mistyped as 'san-serif'. Fixed that in 18-20 cases.
• src/hg/inc/hCommon.h
  • lines changed 3, context: html, text, full: html, text
    Added hgVarAnnogratorName() (#6152).
• src/hg/inc/hdb.h
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added region type and positioninputs to UI -- and it actually executes some queries now!
    
• src/hg/inc/jsHelper.h
  • lines changed 74, context: html, text, full: html, text
    use a union in jsonElement to simplify code and eliminate typecasts (per suggestion of angie and tim); rename jsonHash to jsonObject; fix some obsolete comments
• src/hg/inc/soterm.h
  • lines changed 2, context: html, text, full: html, text
    ongoing #6152. Added support for variants longer than 1 in CDS.
  • lines changed 1, context: html, text, full: html, text
    more work on #6152. Now with in-frame deletions!
• src/hg/inc/variant.h
  • lines changed 5, context: html, text, full: html, text
    ongoing #6152. Added support for variants longer than 1 in CDS.
• src/hg/inc/web.h
  • lines changed 3, context: html, text, full: html, text
    UI for #6152 (Variant Annotation Tool): position input is now searchedonblur and before we submit the page to execute a query, so that if a position
    is not found or has multiple matches, the user is returned to the UI to fix it.
    
• src/hg/js/encodeMatrix.js
  • lines changed 1, context: html, text, full: html, text
    URI encode mdb values (e.g. CD20+) in search URL
• src/hg/js/hgVarAnnogrator.js
  • lines changed 62, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added region type and positioninputs to UI -- and it actually executes some queries now!
    
  • lines changed 37, context: html, text, full: html, text
    UI for #6152 (Variant Annotation Tool): position input is now searchedonblur and before we submit the page to execute a query, so that if a position
    is not found or has multiple matches, the user is returned to the UI to fix it.
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 2, context: html, text, full: html, text
    more work on #6152. Now with in-frame deletions!
• src/hg/lib/gpFx.c
  • lines changed 58, context: html, text, full: html, text
    ongoing #6152. Added support for variants longer than 1 in CDS.
  • lines changed 101, context: html, text, full: html, text
    more work on #6152. Now with in-frame deletions!
• src/hg/lib/hCommon.c
  • lines changed 7, context: html, text, full: html, text
    Added hgVarAnnogratorName() (#6152).
• src/hg/lib/hdb.c
  • lines changed 36, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Tool): Added region type and positioninputs to UI -- and it actually executes some queries now!
    
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    Bugfix (#7101): Tim found that the BAM UI code was not using ClosestToHome.That caused subtrack config controls to show incorrect values.
    Fixed according to Tim's suggestion to do like hgTracks code.
    
• src/hg/lib/jsHelper.c
  • lines changed 10, context: html, text, full: html, text
    cleanup per review items from tim
  • lines changed 138, context: html, text, full: html, text
    use a union in jsonElement to simplify code and eliminate typecasts (per suggestion of angie and tim); rename jsonHash to jsonObject; fix some obsolete comments
  • lines changed 2, context: html, text, full: html, text
    fix compiler error
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 6, context: html, text, full: html, text
    ongoing #6152. Added support for variants longer than 1 in CDS.
  • lines changed 4, context: html, text, full: html, text
    more work on #6152. Now with in-frame deletions!
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 5, context: html, text, full: html, text
    ongoing #6152. Added support for variants longer than 1 in CDS.
  • lines changed 7, context: html, text, full: html, text
    more work on #6152. Now with in-frame deletions!
• src/hg/lib/variant.c
  • lines changed 46, context: html, text, full: html, text
    ongoing #6152. Added support for variants longer than 1 in CDS.
  • lines changed 21, context: html, text, full: html, text
    more work on #6152. Now with in-frame deletions!
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    Moving a freeMem inside an if where it belongs (according to commentsabout docRoot above, the problem should only manifest in command line mode
    when docRoot can be NULL).
    
  • lines changed 9, context: html, text, full: html, text
    UI for #6152 (Variant Annotation Tool): position input is now searchedonblur and before we submit the page to execute a query, so that if a position
    is not found or has multiple matches, the user is returned to the UI to fix it.
    
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/ce6.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/choHof1.txt
  • lines changed 17, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/chrPic1.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 18, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/ci2.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/danRer6.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/dasNov3.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/dipOrd1.txt
  • lines changed 14, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 20, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/dm3.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/echTel1.txt
  • lines changed 16, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 21, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release3.notes
  • lines changed 2136, context: html, text, full: html, text
    Adding in a notes file for Riken Cage
  • lines changed 45, context: html, text, full: html, text
    Adding CD20 cell line
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechRnaSeq.release1.notes
  • lines changed 93, context: html, text, full: html, text
    add release note
• src/hg/makeDb/doc/eriEur1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/fr3.txt
  • lines changed 3, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 21, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 19, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/hetGla2.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 28, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/hg19.txt
  • lines changed 31, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/latCha1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/melUnd1.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 17, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/micMur1.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 21, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/mm9.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/nomLeu2.txt
  • lines changed 9, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/ochPri2.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 21, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/oreNil1.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/oreNil2.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 19, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/oryLat2.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/otoGar3.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 18, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/papHam1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/proCap1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 17, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/pteVam1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 1, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/rn4.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/rn5.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/sacCer2.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/doc/saiBol1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 26, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/sorAra1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 18, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/speTri2.txt
  • lines changed 11, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 18, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/tarSyr1.txt
  • lines changed 19, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 12, context: html, text, full: html, text
    completed genscan track
• src/hg/makeDb/doc/triMan1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 21, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/tupBel1.txt
  • lines changed 10, context: html, text, full: html, text
    adding cpgIslandExt track
• src/hg/makeDb/doc/turTru2.txt
  • lines changed 12, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 20, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/vicPac1.txt
  • lines changed 15, context: html, text, full: html, text
    adding cpgIslandExt track
  • lines changed 17, context: html, text, full: html, text
    done with genscan track build
• src/hg/makeDb/doc/xenTro2.txt
  • lines changed 32, context: html, text, full: html, text
    makeDoc additions for hg19 mm9 rn4 danRer6 dm3 xentro2 oryLat2 ci2 ce6 sacCer2 via script /hive/data/inside/literature/pubtools/addToMakeDbDoc.sh for publications track
• src/hg/makeDb/trackDb/baboon/papHam1/description.html
  • lines changed 5, context: html, text, full: html, text
    added image of olive baboon - the actual species sequenced
  • lines changed 7, context: html, text, full: html, text
    changed name of image lik and corrected foto source info. added link to baylor project page
  • lines changed 1, context: html, text, full: html, text
    added s to Science in outlink
  • lines changed 1, context: html, text, full: html, text
    added name of the baboon
  • lines changed 1, context: html, text, full: html, text
    after noticing that the horse has his name, added baboob name, Casanova
• src/hg/makeDb/trackDb/bushbaby/otoGar1/description.html
  • lines changed 2, context: html, text, full: html, text
    changed size tags on one bushbaby image and added photo to the other
• src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html
  • lines changed 6, context: html, text, full: html, text
    changed size tags on one bushbaby image and added photo to the other
• src/hg/makeDb/trackDb/cat/felCat5/description.html
  • lines changed 140, context: html, text, full: html, text
    added a dir a description.html for felCat5
• src/hg/makeDb/trackDb/cow/bosTau4/description.html
  • lines changed 2, context: html, text, full: html, text
    made box around cow image full size
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 6, context: html, text, full: html, text
    Added stanza for Harvard control. Redmine #4486.
  • lines changed 15, context: html, text, full: html, text
    Adding labels to blood cells that have the same naming schema
  • lines changed 1, context: html, text, full: html, text
    Fixing draw ID for CD20+ cell line
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    Fixed TGF-b to TGF-beta.
  • lines changed 24, context: html, text, full: html, text
    Removing CD20+_RO01746 from CV
  • lines changed 8, context: html, text, full: html, text
    Adding Monocytes-CD14+_RO01826 and fixing a few inconsistencies
  • lines changed 36, context: html, text, full: html, text
    Fixes for the CV
  • lines changed 6, context: html, text, full: html, text
    Fixing MRT tags in CV
  • lines changed 26, context: html, text, full: html, text
    Removing term B_cells_CD20+, undeprecated CD20+, labeled CD20+ as B_cells_CD20+, changed childOf term for children to CD20+ in CV
  • lines changed 2, context: html, text, full: html, text
    Adding a couple labels to CV
  • lines changed 40, context: html, text, full: html, text
    Fixing protocol names for BioChain samples
  • lines changed 1, context: html, text, full: html, text
    Correcting vendorId in cv
  • lines changed 2, context: html, text, full: html, text
    Fixed naming of Provisional tags.
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling of Provisional.
  • lines changed 2, context: html, text, full: html, text
    Changing the + and - in the label to Plus an Minus
  • lines changed 2, context: html, text, full: html, text
    Adding label for SKMC
  • lines changed 32, context: html, text, full: html, text
    Added protocols for CSHL lab.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 204, context: html, text, full: html, text
    Moving alpha cv to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 129, context: html, text, full: html, text
    Approved changes in beta/cv.ra. Redmine #7723.
• src/hg/makeDb/trackDb/dog/canFam1/description.html
  • lines changed 2, context: html, text, full: html, text
    adjusted box to make room for full image
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • lines changed 2, context: html, text, full: html, text
    adjusted box to make room for full image
• src/hg/makeDb/trackDb/dolphin/turTru1/description.html
  • lines changed 6, context: html, text, full: html, text
    added dolphin photo to both assemblies
  • lines changed 2, context: html, text, full: html, text
    changed wording on image license
• src/hg/makeDb/trackDb/dolphin/turTru2/description.html
  • lines changed 6, context: html, text, full: html, text
    added dolphin photo to both assemblies
  • lines changed 2, context: html, text, full: html, text
    changed wording on image license
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 2, context: html, text, full: html, text
    changed size tags on one gibbon image and added photo to the other
  • lines changed 1, context: html, text, full: html, text
    fixed size bug around image
• src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
  • lines changed 5, context: html, text, full: html, text
    changed size tags on one gibbon image and added photo to the other
• src/hg/makeDb/trackDb/guineaPig/cavPor3/description.html
  • lines changed 2, context: html, text, full: html, text
    fixed bounding box size around image and added height tag
• src/hg/makeDb/trackDb/hedgehog/eriEur1/description.html
  • lines changed 6, context: html, text, full: html, text
    added image of hedgehog
  • lines changed 2, context: html, text, full: html, text
    changed wording on image license
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • lines changed 0, context: html, text, full: html, text
    Made change suggested by Katrina in code review (redmine #7738 note 4)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 4158, context: html, text, full: html, text
    Cleaning up the labels and the metaDb for this track, dropping redundant information in the metaData and dropping donor ids out of the long labels, removing the lab rep dcc rep thing in place of rank
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 80, context: html, text, full: html, text
    Removing restriction dates due to publication
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 6, context: html, text, full: html, text
    restored the object type after some discoveries were made about how the files were uploaded
  • lines changed 2, context: html, text, full: html, text
    added series accession number to RikenCage
  • lines changed 17, context: html, text, full: html, text
    revoking old TssHmm's
  • lines changed 313, context: html, text, full: html, text
    added in seqPlayform where known
  • lines changed 3, context: html, text, full: html, text
    resolving merge
  • lines changed 45, context: html, text, full: html, text
    missed this metaDAta somehow
  • lines changed 13, context: html, text, full: html, text
    fixing metadata errors
  • lines changed 29, context: html, text, full: html, text
    Cleaning up Riken to get rid of Generation 0 and to sort out the weird HepG2 TssHmm issue that originated in submission 5610
  • lines changed 23, context: html, text, full: html, text
    Fixing the bioRep and the expId for the new data
  • lines changed 13, context: html, text, full: html, text
    Updating md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 8, context: html, text, full: html, text
    Added md5sum's for files. Redmine #4486.
  • lines changed 276, context: html, text, full: html, text
    Updated names for objects to use Harvard Control. Also added Harvard Control to track. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 2, context: html, text, full: html, text
    adding treatment to expVars
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 10195, context: html, text, full: html, text
    Staging RIKEN CAGE Loc (Release 3) on beta (redmine #6579)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    expand list of chroms for vegaGene redmine 7403
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging RIKEN CAGE Loc (Release 3) on beta (redmine #6579)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html
  • lines changed 38, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 9, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html
  • lines changed 9, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html
  • lines changed 9, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 27, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.html
  • lines changed 27, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 1361, context: html, text, full: html, text
    Cleaning up the labels and the metaDb for this track, dropping redundant information in the metaData and dropping donor ids out of the long labels, removing the lab rep dcc rep thing in place of rank
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 19, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 82, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html
  • lines changed 82, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 4, context: html, text, full: html, text
    Adding allButtonPair to multiWigs.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html
  • lines changed 7, context: html, text, full: html, text
    Cleaning up Riken to get rid of Generation 0 and to sort out the weird HepG2 TssHmm issue that originated in submission 5610
  • lines changed 7, context: html, text, full: html, text
    Changing some methods text and the view limits according to tha approval call
  • lines changed 5, context: html, text, full: html, text
    qa fixes for html riken
  • lines changed 2, context: html, text, full: html, text
    more html fixes for riken, this time capitalization
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra
  • lines changed 7, context: html, text, full: html, text
    resolving merge
  • lines changed 1, context: html, text, full: html, text
    reverting an error made earlier
  • lines changed 137, context: html, text, full: html, text
    Cleaning up Riken to get rid of Generation 0 and to sort out the weird HepG2 TssHmm issue that originated in submission 5610
  • lines changed 2, context: html, text, full: html, text
    Changing some methods text and the view limits according to tha approval call
  • lines changed 115, context: html, text, full: html, text
    trackDb fixes and promotes tier 2.5 cell lines
  • lines changed 323, context: html, text, full: html, text
    Fixing Ticket 6579 note 30
  • lines changed 250, context: html, text, full: html, text
    Fixing Ticket 6579 note 30
  • lines changed 1, context: html, text, full: html, text
    removing a bad search and replace change
  • lines changed 0, context: html, text, full: html, text
    removing space that was causing default to not be checked
  • lines changed 1, context: html, text, full: html, text
    removing another bad search and replace
  • lines changed 67, context: html, text, full: html, text
    qa fixes
  • lines changed 8, context: html, text, full: html, text
    more qa fixes
  • lines changed 16, context: html, text, full: html, text
    changed alignments to off, and removed replicate from fileSortOrder
  • lines changed 1, context: html, text, full: html, text
    changed max window on minus to be the same as plus
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html
  • lines changed 23, context: html, text, full: html, text
    Updated publications sections. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra
  • lines changed 34, context: html, text, full: html, text
    Fixed matrix labels. Redmine #4486.
  • lines changed 58, context: html, text, full: html, text
    Updated names for objects to use Harvard Control. Also added Harvard Control to track. Redmine #4486.
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    vicVic1 is actually vicPac1
• src/hg/makeDb/trackDb/manatee/triMan1/description.html
  • lines changed 5, context: html, text, full: html, text
    added credit for manatee photo
• src/hg/makeDb/trackDb/megabat/pteVam1/description.html
  • lines changed 6, context: html, text, full: html, text
    adding picture for megabat
  • lines changed 1, context: html, text, full: html, text
    corrected photo credit
  • lines changed 2, context: html, text, full: html, text
    changed wording on image license
• src/hg/makeDb/trackDb/microbat/myoLuc1/description.html
  • lines changed 2, context: html, text, full: html, text
    added dimensions around image
• src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
  • lines changed 1, context: html, text, full: html, text
    fixed one and add other image stuff for naked mole rat
• src/hg/makeDb/trackDb/moleRat/hetGla2/description.html
  • lines changed 8, context: html, text, full: html, text
    fixed one and add other image stuff for naked mole rat
• src/hg/makeDb/trackDb/mouse/ikmc.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    update expId for Signal subtracks
  • lines changed 13, context: html, text, full: html, text
    make md5sum
  • lines changed 119, context: html, text, full: html, text
    correct date due to multiple resubmission
  • lines changed 40, context: html, text, full: html, text
    removed commented out date entries, as it seems to cause KeyErr when running MkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    fix freeze dataVersion
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 35, context: html, text, full: html, text
    Moved Junctions from downloadOnly to displayed. Redmine #7089.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed Peak file. Redmine #6703.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 305, context: html, text, full: html, text
    Fixed metaDb to remove old file names.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging Caltech RNA-Seq (Release 1) on beta (redmine #4156)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 577, context: html, text, full: html, text
    Staging Caltech RNA-Seq (Release 1) on beta (redmine #4156)
  • lines changed 1, context: html, text, full: html, text
    Ruihua added freeze date to one entry (redmine #4156)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuHistone.ra
  • lines changed 3, context: html, text, full: html, text
    Venkat fixed peak file (redmine #6703)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    Releasing PSU Histone (Release 1) to RR (redmine #111)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuHistone.ra
  • lines changed 8044, context: html, text, full: html, text
    Releasing PSU Histone (Release 1) to RR (redmine #111)
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging Caltech RNA-Seq (Release 1) on beta (redmine #4156)
  • lines changed 2, context: html, text, full: html, text
    Moved Junctions from downloadOnly to displayed. Redmine #7089.
  • lines changed 1, context: html, text, full: html, text
    Releasing PSU Histone (Release 1) to RR (redmine #111)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.html
  • lines changed 4, context: html, text, full: html, text
    fix description
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html
  • lines changed 55, context: html, text, full: html, text
    new description sent by Georgi
  • lines changed 24, context: html, text, full: html, text
    correct reference format, the one form Georgi is old
  • lines changed 3, context: html, text, full: html, text
    Removed ms-dos CRLF characters.
  • lines changed 37, context: html, text, full: html, text
    fix descriptions
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    fix description
  • lines changed 16, context: html, text, full: html, text
    fix description
  • lines changed 7, context: html, text, full: html, text
    fix dispaly convention and view selectio label
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra
  • lines changed 5, context: html, text, full: html, text
    fix typo, remove Raw from Raw Signal
  • lines changed 6, context: html, text, full: html, text
    fix differentiation time points in long label so to be consistent with caltechHistone
  • lines changed 8, context: html, text, full: html, text
    fix short label length
  • lines changed 3, context: html, text, full: html, text
    add view column to sort list
  • lines changed 1, context: html, text, full: html, text
    fix label
  • lines changed 0, context: html, text, full: html, text
    fix label
  • lines changed 1, context: html, text, full: html, text
    fix dispaly convention and view selectio label
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 162, context: html, text, full: html, text
    Moved Junctions from downloadOnly to displayed. Redmine #7089.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
  • lines changed 9, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.html
  • lines changed 36, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed Peak file. Redmine #6703.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
  • lines changed 9, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html
  • lines changed 15, context: html, text, full: html, text
    Added new 'Publications' section with specified citations (redmine #7514)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
  • lines changed 147, context: html, text, full: html, text
    fix labels
• src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html
  • lines changed 1, context: html, text, full: html, text
    fixed bounding box size around image
• src/hg/makeDb/trackDb/pika/ochPri2/description.html
  • lines changed 6, context: html, text, full: html, text
    added image of pika
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    changed wording on image license
• src/hg/makeDb/trackDb/pubs.html
  • lines changed 16, context: html, text, full: html, text
    Made several grammar corrections and edited for clarity. More edits needed.
  • lines changed 13, context: html, text, full: html, text
    small corrections to pubs html page after QA
• src/hg/makeDb/trackDb/rockHyrax/proCap1/description.html
  • lines changed 6, context: html, text, full: html, text
    added photo credit for rock hyrax
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • lines changed 2, context: html, text, full: html, text
    fixed bounding box size around image
• src/hg/makeDb/trackDb/shrew/sorAra1/description.html
  • lines changed 6, context: html, text, full: html, text
    added photo to shrew description
  • lines changed 2, context: html, text, full: html, text
    changed wording on image license
• src/hg/makeDb/trackDb/squirrel/speTri1/description.html
  • lines changed 7, context: html, text, full: html, text
    added images for both squirrel assemblies
• src/hg/makeDb/trackDb/squirrel/speTri2/description.html
  • lines changed 7, context: html, text, full: html, text
    added images for both squirrel assemblies
• src/hg/makeDb/trackDb/tarsier/tarSyr1/description.html
  • lines changed 7, context: html, text, full: html, text
    adding tarsier photo from wikipedia
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html
  • lines changed 1, context: html, text, full: html, text
    changed name of photo contributor
• src/hg/makeDb/trackDb/tenrec/echTel1/description.html
  • lines changed 1, context: html, text, full: html, text
    adjusted bounding box to make room for full image
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Removed release tags for Max's Publications track as I'm staging on beta and pushing to RR.
• src/hg/makeDb/trackDb/transMap.html
  • lines changed 3, context: html, text, full: html, text
    Changed journal references to point to journal pages rather than NCBI as suggested by Katrina in code review (redmine #7738 notes 5,6)
• src/hg/makeDb/trackDb/transMapAlnMRna.html
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    Changed journal references to point to journal pages rather than NCBI as suggested by Katrina in code review (redmine #7738 notes 5,6)
• src/hg/makeDb/trackDb/transMapAlnRefSeq.html
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    Changed journal references to point to journal pages rather than NCBI as suggested by Katrina in code review (redmine #7738 notes 5,6)
• src/hg/makeDb/trackDb/transMapAlnSplicedEst.html
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    Changed journal references to point to journal pages rather than NCBI as suggested by Katrina in code review (redmine #7738 notes 5,6)
• src/hg/makeDb/trackDb/transMapAlnUcscGenes.html
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    Changed journal references to point to journal pages rather than NCBI as suggested by Katrina in code review (redmine #7738 notes 5,6)
• src/hg/makeDb/trackDb/treeShrew/tupBel1/description.html
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    fixed bounding box size around image
• src/hg/mouseStuff/netFilter/netFilter.c
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    added -maxAli option to netFilter
• src/hg/oneShot/encodeExpToCvDb/encodeExpToCvDb.c
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    Making optional fields ok with null values (seems to be required for drop-down editing of foreign keys, blank ok not enough. Making md5sum tolerate longer strings since can be comma separated currently.
• src/hg/utils/automation/Encode.pm
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    removed deprecated types from extended types list
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    shouldnt have removed gappedPeak
    
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    Merge branch 'master' into newValidateFiles
• src/hg/utils/automation/doCpgIslands.pl
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    fix error in using head in a pipe in csh
• src/hg/utils/automation/doGenscan.pl
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    similar to doCpgIslands.pl and more robust
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    properly protect each step from repeats or missing previous step
• src/hg/utils/automation/grcIncidentUpdate.sh
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    present copy of update.sh used by grcIncidentDb.pl
• src/hg/utils/automation/grcRunIncidentUpdate.sh
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    current copy of runUpdate.sh used by grcIncidentDb.pl
• src/hg/utils/automation/ncbiIncidentDb.pl
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    now taken care of in grcIncidentDb.pl
• src/hg/utils/automation/ncbiIncidentUpdate.sh
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    now contained in grcRunIncidentUpdate.sh and grcIncidentUpdate.sh
• src/hg/utils/automation/ncbiRunIncidentUpdate.sh
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    now contained in grcRunIncidentUpdate.sh and grcIncidentUpdate.sh
• src/hg/utils/phyloTrees/60way.nh
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    update mm9 to mm10
• src/hg/utils/phyloTrees/placentals.txt
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    updating comments about which is what
• src/hg/utils/phyloTrees/vertebrates.txt
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    adding melUnd1 lepOcu1 hapBur1 neoBri1 mayZeb1 punNye1 xipMac1 oreNil1
• src/inc/asParse.h
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    Feature #6152 (Variant Annotation Tool): Added region type and positioninputs to UI -- and it actually executes some queries now!
    
• src/inc/options.h
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    options.h was missing its #define OPTIONS_H -- apparently my codewas the first so far to have multiple includes of options.h. :)
    
• src/kehayden/alphaChain/DYZ3_alphaChain.txt
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    update alphaChain stdin files
• src/kehayden/alphaChain/alphaChain.c
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    KEH: corrected rand
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    updated alphaChain.c normalized counter
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    consolidated alphaChain between kent libraries, with parent
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    Tweaked comment at head of file.
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    changed header of file
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    fixed merge conflict
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    Adding in dummy nodes to help deal with missing data from reads not being infinite.
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    Fixed a bug in the useCounts from double counting once per line of input. Starting to implement the output, but it's still rough and buggy.
• src/kehayden/alphaChain/doIt
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    update alphaChain stdin files
• src/kehayden/alphaChain/makefile
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    update alphaChain stdin files
• src/lib/asParse.c
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    Feature #6152 (Variant Annotation Tool): Added region type and positioninputs to UI -- and it actually executes some queries now!
    
• src/lib/basicBed.c
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    fixes for 32-bit compile
• src/lib/common.c
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    more work on #6152. Now with in-frame deletions!
• src/lib/linefile.c
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    fixes for 32-bit compile
• src/product/scripts/allDatabaseUpdate.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/fetchFullGbdb.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/fetchFullGoldenPath.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/fetchMinimalGbdb.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/fetchMinimalGoldenPath.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/kentSrcUpdate.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/loadDb.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/loadUpdateGoldenPath.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/tagGoldenPath.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/product/scripts/updateHtml.sh
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    using bash instead of just sh so the include of browserEnvironment.txt will work without a full path
• src/utils/bedToBigBed/bedToBigBed.c
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    fixes for 32-bit compile
• src/utils/qa/weeklybld/buildEnv.csh
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    v267 preview1
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    The following tables were added to the hgcentral dump to sql... gbMembers, namedSessions. This was for redmine 6845.
• src/utils/qa/weeklybld/buildZip.csh
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    Building zips was still hanging.

• lines changed: 37583
• files changed: 385