All File Changes

v259_base to v260_preview (2011-11-07 to 2011-11-15) v260

• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 4, context: html, text, full: html, text
    fixed some error print in solo mode with errors
• src/hg/encode/DAFs/3.0/hg19/wgEncodeGisRnaPet.daf
  • lines changed 4, context: html, text, full: html, text
    Version 1.9 of RNA PET DAF
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 13, context: html, text, full: html, text
    Revert "changed how encodeValidate and friends uses packages to allow for same directory location of the packages" This reverts commit 371b1e65141e2a3ef55220fee8a120e8fa90dc26.
  • lines changed 7, context: html, text, full: html, text
    Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 13, context: html, text, full: html, text
    Revert "changed how encodeValidate and friends uses packages to allow for same directory location of the packages" This reverts commit 371b1e65141e2a3ef55220fee8a120e8fa90dc26.
  • lines changed 2, context: html, text, full: html, text
    Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 557, context: html, text, full: html, text
    moved old version to .v09 and moved mkChangeNotes to encodeMkChangeNotes
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes.v09
  • lines changed 565, context: html, text, full: html, text
    moved old version to .v09 and moved mkChangeNotes to encodeMkChangeNotes
• src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.py
  • lines changed 637, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/encodeMkChangeNotes/test/CurrentMkChangeNotes.pyc
  • lines changed 0, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
  • lines changed 0, context: html, text, full: html, text
    accidentally added the compiled library
• src/hg/encode/encodeMkChangeNotes/test/README
  • lines changed 25, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/encodeMkChangeNotes/test/mkChangeTest
  • lines changed 83, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/encodeMkChangeNotes/test/testRunner
  • lines changed 61, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 1, context: html, text, full: html, text
    added information to an error to say that it is fatal
  • lines changed 4, context: html, text, full: html, text
    added more to error message
  • lines changed 5, context: html, text, full: html, text
    made other error message consistent
  • lines changed 8, context: html, text, full: html, text
    added test headers so you know what's up
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 406, context: html, text, full: html, text
    first draft of qaPrepareRelease
  • lines changed 1, context: html, text, full: html, text
    removed hardcoded verbose output
  • lines changed 14, context: html, text, full: html, text
    made a check to see that you have a trackDb.ra in the trackDb dir
  • lines changed 3, context: html, text, full: html, text
    rebalanced whitespace, and made meta db diffs more descriptive
  • lines changed 31, context: html, text, full: html, text
    changed metaDb diff output again, alphabetizes and aggregates dropped and new stanzas
• src/hg/encode/encodeQaPrepareRelease/makefile
  • lines changed 27, context: html, text, full: html, text
    first draft of qaPrepareRelease
• src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease
  • lines changed 2, context: html, text, full: html, text
    changed name in usage statement
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 196, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/config/hg18_chromInfo.txt
  • lines changed 49, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/config/pi.ra
  • lines changed 181, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • lines changed 535, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 14, context: html, text, full: html, text
    Revert "changed how encodeValidate and friends uses packages to allow for same directory location of the packages" This reverts commit 371b1e65141e2a3ef55220fee8a120e8fa90dc26.
  • lines changed 28, context: html, text, full: html, text
    Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
  • lines changed 4, context: html, text, full: html, text
    Revert "removed the code for pi.ra" This reverts commit a8d2cd12a9005d8bb60f1c89c900ea5a76c145b6.
  • lines changed 2, context: html, text, full: html, text
    removed the need to labs.ra in encodeValidate only
  • lines changed 9, context: html, text, full: html, text
    fixed the Error: 1 error
  • lines changed 2, context: html, text, full: html, text
    removed comment referencing pi.ra
• src/hg/encode/encodeValidate/doReport.csh
  • lines changed 55, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/manual.all.txt
  • lines changed 22, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/newtest/README
  • lines changed 14, context: html, text, full: html, text
    fleshed out test some more
• src/hg/encode/encodeValidate/newtest/allGood/out/mdb.txt
  • lines changed 3, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/allGood/out/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/notest.cfg
  • lines changed 49, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/badDdfDafs/invalidFiletype/test.cfg
  • lines changed 49, context: html, text, full: html, text
    fleshed out test some more
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/mdb.txt
  • lines changed 2, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/baddafs/badDataVersion/out/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/baddafs/noDataVersionComment/test.cfg
  • lines changed 1, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/newtest/config/pi.ra
  • lines changed 181, context: html, text, full: html, text
    removed pi.ra from teste config directory
• src/hg/encode/encodeValidate/newtest/doEncodeValidate.pl
  • lines changed 2409, context: html, text, full: html, text
    removed copy of doEncodeValidate
• src/hg/encode/encodeValidate/newtest/list
  • lines changed 18, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
  • lines changed 18, context: html, text, full: html, text
    fleshed out test some more
• src/hg/encode/encodeValidate/newtest/tester.pl
  • lines changed 19, context: html, text, full: html, text
    fixed some issues with tester. no long need a copy of doEncodeValidate.pl in the directory
• src/hg/encode/encodeValidate/obsolete/doEncodeReport.pl
  • lines changed 535, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/obsolete/doReport.csh
  • lines changed 55, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/obsolete/expVars.ra
  • lines changed 196, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/obsolete/hg18_chromInfo.txt
  • lines changed 49, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/obsolete/manual.all.txt
  • lines changed 22, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/encodeValidate/obsolete/pi.ra
  • lines changed 181, context: html, text, full: html, text
    These programs or files are obsolete and should not be being used
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 14, context: html, text, full: html, text
    When document link setting in cv.ra contains 'missing' then then rpint that. For redmine 1012
  • lines changed 14, context: html, text, full: html, text
    Extended 'missing' support to individual validation documents.
• src/hg/encode/metaCheck/README.txt
  • lines changed 1, context: html, text, full: html, text
    Spelling
• src/hg/encode/mkChangeNotes/makefile
  • lines changed 27, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/mkChangeNotes/mkChangeNotes
  • lines changed 61, context: html, text, full: html, text
    moved old version to .v09 and moved mkChangeNotes to encodeMkChangeNotes
• src/hg/encode/mkChangeNotes/tests/CurrentMkChangeNotes.py
  • lines changed 637, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/mkChangeNotes/tests/mkChangeTest
  • lines changed 83, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/mkChangeNotes/tests/testRunner
  • lines changed 61, context: html, text, full: html, text
    changed mkChangeNotes test over to encodeMkChangeNotes and added README
• src/hg/encode/qaRaDiff/makefile
  • lines changed 27, context: html, text, full: html, text
    added in qaRaDiff first draft
• src/hg/encode/qaRaDiff/qaRaDiff
  • lines changed 75, context: html, text, full: html, text
    added in qaRaDiff first draft
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    don't puts a string that is null.
• src/hg/hgTables/asObj.c
  • lines changed 111, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/bam.c
  • lines changed 11, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/bigBed.c
  • lines changed 37, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/bigWig.c
  • lines changed 14, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/filterFields.c
  • lines changed 35, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/hgTables.h
  • lines changed 28, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTables/schema.c
  • lines changed 47, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
  • lines changed 2, context: html, text, full: html, text
    Fixed mrna schema bug 5990.
• src/hg/hgTables/vcf.c
  • lines changed 26, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgTracks/hgTracks.c
  • lines changed 15, context: html, text, full: html, text
    Subtracks need groups if there will be sorting later.
  • lines changed 15, context: html, text, full: html, text
    Redmine 5992. Backing out previous fix in order to make a targeted fix for patching. At this checkin, code should be back to 6f7dabcd1d87152560c0b66bb126bce0a0582415.
  • lines changed 3, context: html, text, full: html, text
    Redmine 5992. This is the targetted conservative fix to hgTracks.c. Please make a patch from the difference between this and the previos hgTracks.c check-in
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    Thanks Larry for finding this obscure bug. Handing off pointer instead of pointer to pointer to a routine that takes a void pointer.
  • lines changed 52, context: html, text, full: html, text
    Remove old code that was ifdef'd out.
• src/hg/hgc/bigBedClick.c
  • lines changed 47, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/hgc/hgc.c
  • lines changed 72, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
  • lines changed 55, context: html, text, full: html, text
    Get DNA color feature: added support for composites and limited to currently visible tracks. This is for redmine 685.
  • lines changed 3, context: html, text, full: html, text
    When searching geneReviews using disease name, instead of useing '&search_param==begins_with', use '&search_param==begins_with'.
• src/hg/hgc/hgc.h
  • lines changed 5, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/htdocs/ENCODE/dataPlansMouse.html
  • lines changed 3, context: html, text, full: html, text
    Improve titles and links, based on Q/A review (redmine 5702)
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 1, context: html, text, full: html, text
    Improve titles and links, based on Q/A review (redmine 5702)
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 1, context: html, text, full: html, text
    Improve titles and links, based on Q/A review (redmine 5702)
  • lines changed 1, context: html, text, full: html, text
    Tweak window size so scrollers appear more conveniently
• src/hg/htdocs/ENCODE/index.html
  • lines changed 147, context: html, text, full: html, text
    Archive old news. Add New indicators to left blue bar for new or completely updated pages
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 139, context: html, text, full: html, text
    Archive old news. Add New indicators to left blue bar for new or completely updated pages
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 43, context: html, text, full: html, text
    Add Contents panel with explanatory sentences and navigation
  • lines changed 2, context: html, text, full: html, text
    <p> tags are inline elements which should never have block elements <ul> contained within them. Moved the <p> tag to be proper html. Redmine# 5919.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 10, context: html, text, full: html, text
    Added 4 new assemblies to releaae table.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 187, context: html, text, full: html, text
    Added credits for new turkey, microbat, Xenopus, and cow assemblies.
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 1, context: html, text, full: html, text
    adding in note that specifically states that bedGraphToBigWig does not accept gzipped bedGraph input files per Vanessa's suggestion in code review, redmine #5912
• src/hg/inc/bedDetail.h
  • lines changed 4, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/encode/wgEncodeGencodeAnnotationRemark.h
  • lines changed 62, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/inc/encode/wgEncodeGencodePolyAFeature.h
  • lines changed 74, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/inc/hui.h
  • lines changed 15, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/makeItemsItem.h
  • lines changed 3, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/pgSnp.h
  • lines changed 3, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/samAlignment.h
  • lines changed 6, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/trackDb.h
  • lines changed 30, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/inc/trackHub.h
  • lines changed 2, context: html, text, full: html, text
    add an option to hubCheck to not check all the tracks, just check the trackDb. Useful in crawling the hubs to pull the trackDb's into the udc cache where they can be parsed. #5088
• src/hg/lib/bedDetail.c
  • lines changed 7, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/encode/wgEncodeGencodeAnnotationRemark.as
  • lines changed 6, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/lib/encode/wgEncodeGencodeAnnotationRemark.c
  • lines changed 124, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/lib/encode/wgEncodeGencodeAnnotationRemark.sql
  • lines changed 12, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/lib/encode/wgEncodeGencodePolyAFeature.as
  • lines changed 12, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/lib/encode/wgEncodeGencodePolyAFeature.c
  • lines changed 162, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/lib/encode/wgEncodeGencodePolyAFeature.sql
  • lines changed 18, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/lib/ensGene.as
  • lines changed 19, context: html, text, full: html, text
    adding ensembl gene table definitions and fixing the score column of genePredExt
• src/hg/lib/ensemblSource.as
  • lines changed 6, context: html, text, full: html, text
    adding ensembl gene table definitions and fixing the score column of genePredExt
• src/hg/lib/ensemblToGeneName.as
  • lines changed 6, context: html, text, full: html, text
    adding ensembl gene table definitions and fixing the score column of genePredExt
• src/hg/lib/genePredExt.as
  • lines changed 1, context: html, text, full: html, text
    adding ensembl gene table definitions and fixing the score column of genePredExt
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    add some magic to make hgFind open hidden subTracks of hidden composites. #5412
• src/hg/lib/hgFind.c
  • lines changed 10, context: html, text, full: html, text
    add some magic to make hgFind open hidden subTracks of hidden composites. #5412
• src/hg/lib/hui.c
  • lines changed 189, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
  • lines changed 3, context: html, text, full: html, text
    Fixed newly introduced filterBy bug.
• src/hg/lib/lincRNAsCTTemp.as
  • lines changed 11, context: html, text, full: html, text
    add lincRNAsCTTemp.as for two extra field description.
• src/hg/lib/makeItemsItem.c
  • lines changed 7, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/lib/pgSnp.c
  • lines changed 7, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/samAlignment.c
  • lines changed 8, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/trackDbCustom.c
  • lines changed 12, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/hg/lib/trackHub.c
  • lines changed 10, context: html, text, full: html, text
    add an option to hubCheck to not check all the tracks, just check the trackDb. Useful in crawling the hubs to pull the trackDb's into the udc cache where they can be parsed. #5088
• src/hg/makeDb/doc/encodeDccHg19/gencodeV9.txt
  • lines changed 164, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
  • lines changed 50, context: html, text, full: html, text
    Added TssHmm files
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 1, context: html, text, full: html, text
    Correct the name of the tree model used in the 6 way conservation. redmine bug #5771.
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 17, context: html, text, full: html, text
    done with tarSyr1 lastz
  • lines changed 239, context: html, text, full: html, text
    construct download files, place in pushQ and start 11-way alignment
• src/hg/makeDb/doc/hg19.txt
  • lines changed 5, context: html, text, full: html, text
    Stuff for new agilent array (subtrack Ag Can 4x180k to Arrays track in hg19 variation/repeat group)
  • lines changed 64, context: html, text, full: html, text
    LASTZ for Gibbon (nomLeu1) vs Human (hg19)
  • lines changed 380, context: html, text, full: html, text
    Track #5710 (dbSNP 135): built SNP tracks and aux tables & files used by hgc.
• src/hg/makeDb/doc/nomLeu1.txt
  • lines changed 25, context: html, text, full: html, text
    LASTZ for Gibbon (nomLeu1) vs Human (hg19)
  • lines changed 2, context: html, text, full: html, text
    add WGS link
  • lines changed 3, context: html, text, full: html, text
    Finished html for gibbon nomLeu1 assembly
  • lines changed 38, context: html, text, full: html, text
    Finished initial release of gibbon nomLeu1.
• src/hg/makeDb/doc/sacCer3.txt
  • lines changed 32, context: html, text, full: html, text
    Provide liftOver files from sacCer3 to sacCer1 and sacCer2.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 5, context: html, text, full: html, text
    Fixing some bugs that turned up in joinerCheck, where knownTo* tables were built against the wrong version of UCSC Genes. This came from something in the buildscript using the hg19 version of UCSC Genes rather than the new version being built in the temporary database
  • lines changed 2, context: html, text, full: html, text
    Added a command to drop the chromInfo table from the temporary database before all the tables are copied from the temporary database to hg19.
  • lines changed 1, context: html, text, full: html, text
    Responding to excellent code review feedback from Dr. Raney, Code Review # 5910
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    Added cosmicId.
  • lines changed 1, context: html, text, full: html, text
    Added basic entry for all.joiner for new Agilent track
  • lines changed 2, context: html, text, full: html, text
    Removing hg19 dependencies involving a couple tables that are exclusive to the proteome browser, given that those tables are presenting joinerCheck problems and we're not supporting the proteome browser anymore
  • lines changed 28, context: html, text, full: html, text
    Ignore tables for geneReviews and lincRNAs tracks.
  • lines changed 8, context: html, text, full: html, text
    Add geneReviews tables to the geneReviews rule. No need to ignore them
  • lines changed 2, context: html, text, full: html, text
    Add minCheck=0.85 filter to geneReviews and geneReviewRefGene table.
  • lines changed 13, context: html, text, full: html, text
    Track #5710 (dbSNP 135): added snp135 tables. Removed snp134 tables because only snp135 is going to QA.
• src/hg/makeDb/trackDb/README
  • lines changed 81, context: html, text, full: html, text
    Updated README as per redmine 5963. Documented filterComposite which was a major oversight and viewLimitsMax which has existed since the reign of dinosaurs. Also removed mention of 'metadata' lines, 'hierarchy' and 'dividers' which are no longer supported.
• src/hg/makeDb/trackDb/affyExonTissues.html
  • lines changed 1, context: html, text, full: html, text
    fix URL doesn't like pound sign in hgTablesTest. but it links to the same place
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 6, context: html, text, full: html, text
    Correct the name of the tree model used in the 6 way conservation. redmine bug #5771.
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Changed chainMinScore override for monDom5 to 5000 as reported by getChainLines.csh
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 4, context: html, text, full: html, text
    Fixing NB100 and ZNF274
  • lines changed 55, context: html, text, full: html, text
    Updating validation documents
  • lines changed 10, context: html, text, full: html, text
    Fixing antibody labels
  • lines changed 5, context: html, text, full: html, text
    Fixing RNA Labels
  • lines changed 2, context: html, text, full: html, text
    Fixing Estrogen Label
  • lines changed 2, context: html, text, full: html, text
    Fixing Brenda Tissue Link
  • lines changed 1, context: html, text, full: html, text
    Fixing GATA3 validation
  • lines changed 3, context: html, text, full: html, text
    Fixing cell line protocol links
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 14, context: html, text, full: html, text
    Fixing antibody labels
  • lines changed 5, context: html, text, full: html, text
    Fixing RNA Labels
  • lines changed 1, context: html, text, full: html, text
    Fixing Estrogen Label
  • lines changed 2, context: html, text, full: html, text
    Fixing CD14 Brenda Tissue Link
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 1097, context: html, text, full: html, text
    pushing reviewed changes copied from beta/cv.ra, no code review needed
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 28, context: html, text, full: html, text
    Initial description of gibbon nomLeu1
  • lines changed 28, context: html, text, full: html, text
    Change the search term for nomLeu1
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gap.html
  • lines changed 26, context: html, text, full: html, text
    Finished html for gibbon nomLeu1 assembly
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gold.html
  • lines changed 22, context: html, text, full: html, text
    Finished html for gibbon nomLeu1 assembly
• src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
  • lines changed 9, context: html, text, full: html, text
    fixup example searches
• src/hg/makeDb/trackDb/human/geneReviews.html
  • lines changed 13, context: html, text, full: html, text
    Correct singular version of 'GeneReviews'. Changed 'detail' to 'details' for consistency. Cleaned up html.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo
• src/hg/makeDb/trackDb/human/hg19/agilentCgh.html
  • lines changed 9, context: html, text, full: html, text
    Stuff for new agilent array (subtrack Ag Can 4x180k to Arrays track in hg19 variation/repeat group)
  • lines changed 4, context: html, text, full: html, text
    possibly fixing HTML error? seen in hgTables (redmine issue 5769 chatter)
• src/hg/makeDb/trackDb/human/hg19/cosmic.html
  • lines changed 2, context: html, text, full: html, text
    Corrected spelling, fixed an & character.
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    Addressing feedback from Lauren: Redmine #20, Question #6
• src/hg/makeDb/trackDb/human/hg19/knownGeneOld5.html
  • lines changed 25, context: html, text, full: html, text
    added a track description page for the old known genes track, and included a breakdown of the correspondence between the old and new builds
  • lines changed 4, context: html, text, full: html, text
    Cleaning up based on feedback from Brooke
  • lines changed 2, context: html, text, full: html, text
    Changed a plural to a singular and added a comma.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 265, context: html, text, full: html, text
    Added 2 new submissions, and expanded subGroups to includ treatment.Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 310, context: html, text, full: html, text
    changing spikeInPool 14 to spikeInPool NIST14
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 69, context: html, text, full: html, text
    adding some geo accession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 443, context: html, text, full: html, text
    adding in release2 data, as specified in issue 5942
  • lines changed 125, context: html, text, full: html, text
    tweaked V2s to be more like their predecessors
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 44, context: html, text, full: html, text
    Adding subgroup for obtainedBy and had a renaming go wrong
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 93, context: html, text, full: html, text
    Added Caltech fastqs
  • lines changed 109, context: html, text, full: html, text
    revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
  • lines changed 2, context: html, text, full: html, text
    correcting the 'composite' lines for the two new subtracks; was causing an error in hgFileSearch that I noticed while trying to test redmine 5408
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 127, context: html, text, full: html, text
    adding the md5sums and the dccaccessions
  • lines changed 43, context: html, text, full: html, text
    added origAssembly hg19 lines to TssHmm objects
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
  • lines changed 11267, context: html, text, full: html, text
    staging UW Histone on hgwbeta, redmine# 4459
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    Stuff for new agilent array (subtrack Ag Can 4x180k to Arrays track in hg19 variation/repeat group)
  • lines changed 43, context: html, text, full: html, text
    Track #5710 (dbSNP 135): Adding track def's and overrides (exceptthose that would require a new tag...) for snp135 tracks.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    adding in release2 data, as specified in issue 5942
  • lines changed 2, context: html, text, full: html, text
    staging UW Histone on hgwbeta, redmine# 4459
  • lines changed 2, context: html, text, full: html, text
    Taking the .new offline until make works
  • lines changed 1, context: html, text, full: html, text
    revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
  • lines changed 1, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 477, context: html, text, full: html, text
    Added 2 new submissions, and expanded subGroups to includ treatment.Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
  • lines changed 266, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 190, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
  • lines changed 158, context: html, text, full: html, text
    adding in release2 data, as specified in issue 5942
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
  • lines changed 955, context: html, text, full: html, text
    adding in release2 data, as specified in issue 5942
  • lines changed 38, context: html, text, full: html, text
    tweaked V2s to be more like their predecessors
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 16, context: html, text, full: html, text
    Use the RGB settings
  • lines changed 70, context: html, text, full: html, text
    Adding subgroup for obtainedBy and had a renaming go wrong
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
  • lines changed 8921, context: html, text, full: html, text
    revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 8929, context: html, text, full: html, text
    revoked all the HEY1 entries, lab is not confident the antibody is binding to HEY1, looks like POL2 results
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 1, context: html, text, full: html, text
    Changed a short label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
  • lines changed 4, context: html, text, full: html, text
    converted celsius to an ascii character, fixed some typos and changed the release month for UW Histone, redmine #4459
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    changed visibility of hotspots to match the expected default behavior
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 41, context: html, text, full: html, text
    Made edits as requested by track contributors, redmine #34
• src/hg/makeDb/trackDb/mouse/agilentCgh.html
  • lines changed 6, context: html, text, full: html, text
    possibly fixing HTML error? seen in hgTables (redmine issue 5769 chatter)
• src/hg/makeDb/trackDb/rat/agilentCgh.html
  • lines changed 6, context: html, text, full: html, text
    possibly fixing HTML error? seen in hgTables (redmine issue 5769 chatter)
• src/hg/makeDb/trackDb/rmsk.html
  • lines changed 2, context: html, text, full: html, text
    replacing double quotes with ASCII format per Vanessa's code review
• src/hg/makeDb/trackDb/snp135.html
  • lines changed 36, context: html, text, full: html, text
    Track #5710 (dbSNP 135): Adding html descriptions.
• src/hg/makeDb/trackDb/snp135.shared.html
  • lines changed 362, context: html, text, full: html, text
    Track #5710 (dbSNP 135): Adding html descriptions.
• src/hg/makeDb/trackDb/snp135Common.html
  • lines changed 28, context: html, text, full: html, text
    Track #5710 (dbSNP 135): Adding html descriptions.
• src/hg/makeDb/trackDb/snp135Flagged.html
  • lines changed 29, context: html, text, full: html, text
    Track #5710 (dbSNP 135): Adding html descriptions.
• src/hg/makeDb/trackDb/snp135Mult.html
  • lines changed 25, context: html, text, full: html, text
    Track #5710 (dbSNP 135): Adding html descriptions.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    basic import and changes for gencode V9;
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 54, context: html, text, full: html, text
    LASTZ for Gibbon (nomLeu1) vs Human (hg19)
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 88, context: html, text, full: html, text
    Track #5710 (dbSNP 135): Adding track def's and overrides (exceptthose that would require a new tag...) for snp135 tracks.
• src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Removed override for xenTro3 for 'X. tropicalis Chain/Net' would show as short label
• src/hg/makeDb/trackDb/zebrafish/UMassChIP-Seq.html
  • lines changed 4, context: html, text, full: html, text
    Changed wording in one sentence to correct the meaning. Corrected < character to hex code.
• src/hg/oneShot/doOmimGene2/doOmimGene2.c
  • lines changed 22, context: html, text, full: html, text
    Added logic to cover cases where one Entrez gene mapped to multiple chroms.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 15, context: html, text, full: html, text
    Track #5710 (dbSNP 135): minor adjustments to deal with the firstround of dbSNP's FTP files. They will dump a new version, hopefully available next week and hopefully with fewer anomalies.
  • lines changed 34, context: html, text, full: html, text
    Track #5710 (dbSNP 135): most of the 2.8M InconsistentAlleles caseswere caused by homozygous non-reference singleton variants submitted by personal genome projects, so I added a new exception, SingleAlleleFreq (2.3M of those in snp135). Now InconsistentAlleles is only for non-singletons (474k in snp135). Also, snp135 has a lot of items with locType="between" but unexpected coords and/or alleles; seems like locType should be something else, and I emailed dbSNP some examples. Meanwhile, those coords need to be adjusted as if their locType weren't "between" in order to avoid other errors that are simply side-effects of the root inconsistency. I removed the error check for refNCBI having the wrong length because it usually overlapped with another error or exception and doesn't really warrant dropping the SNP if there's no other error.
• src/hg/utils/automation/Encode.pm
  • lines changed 21, context: html, text, full: html, text
    Revert "removed the need for labs.ra" This reverts commit 8dc382b443d003200c40eb60b1957d6bfcec5493.
  • lines changed 13, context: html, text, full: html, text
    Revert "removed the code for pi.ra" This reverts commit a8d2cd12a9005d8bb60f1c89c900ea5a76c145b6.
  • lines changed 3, context: html, text, full: html, text
    added comments to functions to be deprecated
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 1, context: html, text, full: html, text
    SNP automation: more efficient way to summarize exceptions at end.
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 5, context: html, text, full: html, text
    add an option to hubCheck to not check all the tracks, just check the trackDb. Useful in crawling the hubs to pull the trackDb's into the udc cache where they can be parsed. #5088
• src/hg/utils/phyloTrees/51way.dissect.txt
  • lines changed 707, context: html, text, full: html, text
    constructed from: /cluster/bin/phast/tree_doctor --dissect 51way.nh > 51way.dissect.txt
• src/hg/utils/phyloTrees/51way.nh
  • lines changed 24, context: html, text, full: html, text
    adding gibbon nomLeu1 and update versions on genomes
• src/hg/utils/phyloTrees/chainNet.pl
  • lines changed 3, context: html, text, full: html, text
    update to 51way tree
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 3, context: html, text, full: html, text
    only check leaves for label limits #5799
• src/inc/bigBed.h
  • lines changed 8, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/inc/htmshell.h
  • lines changed 3, context: html, text, full: html, text
    add attributeEncode
• src/inc/vcf.h
  • lines changed 4, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/lib/bigBed.c
  • lines changed 22, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/lib/common.c
  • lines changed 5, context: html, text, full: html, text
    Performance improvement for safencpy when src is a very long string(e.g. chrom sequence): don't do a full strlen; count chars and stop counting if/when we get to specified limit n.
• src/lib/htmshell.c
  • lines changed 6, context: html, text, full: html, text
    add attributeEncode
• src/lib/mime.c
  • lines changed 1, context: html, text, full: html, text
    no upload limits, no tempfile usage for huge input
• src/lib/vcf.c
  • lines changed 22, context: html, text, full: html, text
    Moved as code in hgTables down to lib and access it from hgc and hgTrackUi. This is to remove 'extraFields' support as per Jim's request in redmine 5883 and 5582
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v260 preview1

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• files changed: 250