All File Changes

v265_preview to v265_preview2 (2012-03-13 to 2012-03-20) v265

• python/lib/README
  • lines changed 23, context: html, text, full: html, text
    Updating Style Guide and README to kent/src standards. Redmine #7162.
• python/lib/ucscgenomics/qa.py
  • lines changed 37, context: html, text, full: html, text
    Changing to conform with new style guide: changed tabs to 4 spaces, changed interpreter directive, put imports on their own lines and removed unused imports, removed repetitive documentation from beginning.
• python/style.txt
  • lines changed 190, context: html, text, full: html, text
    Updating Style Guide and README to kent/src standards. Redmine #7162.
• python/virtual.txt
  • lines changed 1, context: html, text, full: html, text
    Changed default version number of Beautiful soup.
• src/hg/encode/DAFs/3.0/hg19/wgEncodeCshlLongRnaSeq.daf
  • lines changed 33, context: html, text, full: html, text
    adding the elements files
• src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
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    Changed the python executable
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    Updating python path
• src/hg/encode/cellTypeParser/cellTypeParser.py
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    Changed the python executable
• src/hg/encode/encodeValidate/config/fields.ra
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    Why do we still ned to put things in fields.ra
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 11, context: html, text, full: html, text
    fixed a bug where a cvDefined=no term was still trying to be validated against the cv
  • lines changed 31, context: html, text, full: html, text
    added in a new subroutine to validate the ddf header against the cv instead of fields.ra
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    i forgot about the perl hash bug where you need to confirm values in an intermediate nested hash, becuase if you don't, it get automatically created, and that creates phantom entries in the cv term hash
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    removed unecessary comment
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    pushQDescription is no longer used, however a blank value isn't allowed in load.ra, so i put a fake '1' in place of it
• src/hg/hgTables/bam.c
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    Making this escape '<' and '>' tags and the like better.
• src/hg/hgTables/bigWig.c
  • lines changed 8, context: html, text, full: html, text
    Fixes bug #7222 - where required some track name to have the table name for the summary stats to work in the table browser.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 25, context: html, text, full: html, text
    support year filter in t2gUi
  • lines changed 6, context: html, text, full: html, text
    t2g rename start in hgTrackUi
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    disable in-place update when center and left labels are turned off (#7306)
  • lines changed 12, context: html, text, full: html, text
    refactor some makeItems code from hgTracks.c into hgTracks.js b/c (a) it was causing problems in stripJsEmbedded and (b) it really belongs in hgTracks.js
• src/hg/hgTracks/imageV2.c
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    add type to ruler object so it's like all other trackDb objects
• src/hg/hgTracks/simpleTracks.c
  • lines changed 35, context: html, text, full: html, text
    support yearFilter in t2gLoadItems
  • lines changed 102, context: html, text, full: html, text
    use FULLTEXT index for t2g keyword searching
  • lines changed 11, context: html, text, full: html, text
    trim spaces in keywords filter
  • lines changed 24, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    fix #5457, properly treat non-coding refSeq genes by printing out the "there is no protein here" message
  • lines changed 2, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/hgc/hgc.h
  • lines changed 2, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/hgc/pubs.c
  • lines changed 509, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
  • lines changed 15, context: html, text, full: html, text
    fixed wbr bug and added pmid output redmine #6833
• src/hg/hgc/t2g.c
  • lines changed 1, context: html, text, full: html, text
    fix code that was looking for cgiString('hgsid') - this doesn't work if user is coming in with a new cart
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    sciencedirect auto activate app
  • lines changed 494, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 7, context: html, text, full: html, text
    Add blue bar link to Data Summary (on ChIP matrix)
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 9, context: html, text, full: html, text
    Minor wording and usability changes in response to Q/A (#5149-19). 1. Add blue bar link from matrix pages back to summary page. 2. Some title changes on tables and buttons
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 1, context: html, text, full: html, text
    Minor wording and usability changes in response to Q/A (#5149-19). 1. Add blue bar link from matrix pages back to summary page. 2. Some title changes on tables and buttons
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
  • lines changed 4, context: html, text, full: html, text
    Minor wording and usability changes in response to Q/A (#5149-19). 1. Add blue bar link from matrix pages back to summary page. 2. Some title changes on tables and buttons
  • lines changed 3, context: html, text, full: html, text
    Change table titles as per QA
• src/hg/htdocs/inc/encodeProject.topbar.html
  • lines changed 9, context: html, text, full: html, text
    Minor wording and usability changes in response to Q/A (#5149-19). 1. Add blue bar link from matrix pages back to summary page. 2. Some title changes on tables and buttons
• src/hg/htdocs/style/encodeProject.css
  • lines changed 1, context: html, text, full: html, text
    Minor wording and usability changes in response to Q/A (#5149-19). 1. Add blue bar link from matrix pages back to summary page. 2. Some title changes on tables and buttons
• src/hg/js/encodeDataSummary.js
  • lines changed 60, context: html, text, full: html, text
    1. Cleanup repetitive code 2. Exclude bogus Reference Genome experiments (currently 5C) that are actually supplemental files. #5149-18.
  • lines changed 12, context: html, text, full: html, text
    Fixes to search problems
• src/hg/js/encodeMatrix.js
  • lines changed 1, context: html, text, full: html, text
    Open hgEncodeVocab in targeted window (response to Q/A)
• src/hg/js/hgTracks.js
  • lines changed 23, context: html, text, full: html, text
    refactor some makeItems code from hgTracks.c into hgTracks.js b/c (a) it was causing problems in stripJsEmbedded and (b) it really belongs in hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    watch out for empty rec.type
• src/hg/lib/pgSnp.c
  • lines changed 18, context: html, text, full: html, text
    Edits to pgSnp detail page format, the coding sequence displays inresponse to redmine #7054. Includes computing frameshifts on size of deletion rather than count of '-', treating multiple substitutions that affect length of sequence as indels, hr between genes, and skipping reference matches.
• src/hg/lib/pubsArticle.sql
  • lines changed 18, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/pubsBlat.sql
  • lines changed 19, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/pubsMarkerAnnot.sql
  • lines changed 14, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/pubsMarkerBand.sql
  • lines changed 11, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/pubsMarkerGene.sql
  • lines changed 11, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/pubsMarkerSnp.sql
  • lines changed 11, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/pubsSequence.sql
  • lines changed 8, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/pubsSequenceAnnot.sql
  • lines changed 13, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/t2gArticle.sql
  • lines changed 2, context: html, text, full: html, text
    add FULLTEXT index
  • lines changed 17, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/t2gBlat.sql
  • lines changed 19, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/t2gMarkerAnnot.sql
  • lines changed 14, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/t2gMarkerBand.sql
  • lines changed 11, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/t2gMarkerGene.sql
  • lines changed 11, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/t2gMarkerSnp.sql
  • lines changed 11, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/t2gSequence.sql
  • lines changed 8, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/lib/t2gSequenceAnnot.sql
  • lines changed 13, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/makeDb/doc/ailMel1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/bosTau7.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 3, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/choHof1.txt
  • lines changed 4, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/dasNov2.txt
  • lines changed 5, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/echTel1.txt
  • lines changed 5, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisChiaPet.release1.notes
  • lines changed 232, context: html, text, full: html, text
    willy's chia pet fixes
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrHistone.release2.notes
  • lines changed 72, context: html, text, full: html, text
    add release2 notes file
  • lines changed 1120, context: html, text, full: html, text
    add correct notes
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release2.notes
  • lines changed 723, context: html, text, full: html, text
    creating notes file
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuHistone.release1.notes
  • lines changed 4, context: html, text, full: html, text
    Replaced Peaks files, to fix error that qa found. Redmine #111.
• src/hg/makeDb/doc/eriEur1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/felCat4.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/galGal4.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/hg19.txt
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    trivial tweak
• src/hg/makeDb/doc/loxAfr3.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/macEug2.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/micMur1.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/mm10.txt
  • lines changed 134, context: html, text, full: html, text
    panTro3, otoGar3, micMur1 lastz done
  • lines changed 226, context: html, text, full: html, text
    done with speTri2 hetGla1 dipOrd1 lastz
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    running equCab3 cavPor3 vicPac1 lastz
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    lastz running oryCun2 susScr2 tupBel1 turTru1 vicPac1 and cavPor3
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    starting lastz runs for choHof1 pteVam1 loxAfr3 felCat4 ailMel1 and canFam3
• src/hg/makeDb/doc/myoLuc2.txt
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/ochPri2.txt
  • lines changed 5, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/ornAna1.txt
  • lines changed 3, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 4, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/otoGar3.txt
  • lines changed 170, context: html, text, full: html, text
    masking done
• src/hg/makeDb/doc/oviAri1.txt
  • lines changed 3, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 9, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/petMar1.txt
  • lines changed 6, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/proCap1.txt
  • lines changed 5, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/pteVam1.txt
  • lines changed 4, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/rn5.obsolete.txt
  • lines changed 361, context: html, text, full: html, text
    previous rn5 experiment is now obsolete with new rn5 release
• src/hg/makeDb/doc/rn5.txt
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    buildign a new RN5 release
• src/hg/makeDb/doc/sarHar1.txt
  • lines changed 81, context: html, text, full: html, text
    Finished sarHar1 genscan track.
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    add NCBI URL information
• src/hg/makeDb/doc/sorAra1.txt
  • lines changed 2, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/speTri1.txt
  • lines changed 5, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/speTri2.txt
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    initial browser build
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    starting masking procedures
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    adding URL information to NCBI information pages
• src/hg/makeDb/doc/susScr2.txt
  • lines changed 4, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/taeGut1.txt
  • lines changed 4, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/tarSyr1.txt
  • lines changed 22, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/tupBel1.txt
  • lines changed 5, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/turTru1.txt
  • lines changed 5, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/doc/vicPac1.txt
  • lines changed 4, context: html, text, full: html, text
    adding URL information to NCBI information pages
• src/hg/makeDb/genbank/doc/to-do.txt
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    removed outdated invirtogen warning
• src/hg/makeDb/genbank/etc/build-mgc
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/etc/build.crontab
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 7, context: html, text, full: html, text
    enabled orfeome for mouse and human. Removed outdated orfeome code
• src/hg/makeDb/genbank/etc/rr-cntl
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/etc/rr-dbload
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/etc/rr.crontab
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/dbload/gbBuildState.c
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    removed outdated invirtogen warning
• src/hg/makeDb/genbank/src/dbload/gbMDParse.c
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    removed outdated invirtogen warning
• src/hg/makeDb/genbank/src/dbload/gbMetaData.c
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    removed outdated invirtogen warning
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
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    include /cluster/bin in genbank path
• src/hg/makeDb/genbank/src/makefile
  • lines changed 1, context: html, text, full: html, text
    enabled orfeome for mouse and human. Removed outdated orfeome code
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/README
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/makefile
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcClone.as
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcClone.c
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcClone.h
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcDbLoad.c
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcDownloadStep
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcFullength.as
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcFullength.c
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcFullength.h
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcImport.c
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcLibrary.as
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcLibrary.c
  • lines changed 313, context: html, text, full: html, text
    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcLibrary.h
  • lines changed 98, context: html, text, full: html, text
    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcStage1.as
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcStage1.c
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/mgc/mgcStage1.h
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    removed outdated MGC stuff
• src/hg/makeDb/genbank/src/orfeome/README
  • lines changed 7, context: html, text, full: html, text
    enabled orfeome for mouse and human. Removed outdated orfeome code
• src/hg/makeDb/genbank/src/orfeome/makefile
  • lines changed 17, context: html, text, full: html, text
    enabled orfeome for mouse and human. Removed outdated orfeome code
• src/hg/makeDb/genbank/src/orfeome/orfeomeDbLoad.c
  • lines changed 274, context: html, text, full: html, text
    enabled orfeome for mouse and human. Removed outdated orfeome code
• src/hg/makeDb/genbank/src/orfeome/orfeomeImageIds.as
  • lines changed 8, context: html, text, full: html, text
    enabled orfeome for mouse and human. Removed outdated orfeome code
• src/hg/makeDb/genbank/src/orfeome/orfeomeImageIds.c
  • lines changed 133, context: html, text, full: html, text
    enabled orfeome for mouse and human. Removed outdated orfeome code
• src/hg/makeDb/genbank/src/orfeome/orfeomeImageIds.h
  • lines changed 64, context: html, text, full: html, text
    enabled orfeome for mouse and human. Removed outdated orfeome code
• src/hg/makeDb/genbank/src/process/gbProcess.c
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    removed outdated invirtogen warning
• src/hg/makeDb/genbank/src/process/keyFields.doc
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    removed outdated invirtogen warning
• src/hg/makeDb/schema/all.joiner
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    renaming all publications tracks tables to pubsXXXX
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
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    Removing CD20 deprecation
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    Fixed incorrect switching of Age and vendor id for ES-E14 cells. Redmine #7199.
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    Adding BMDM cell line
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    Removed duplicate BMDM cell line.
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    Fixes for Redmine #7200 1. Updated term, tag and validation file name to not include Millipore. ATF1_(06-325) 2. Updated term, tag and validation file name to use vendor Id. ATF2_(9221) 3. Update term, tag and validation file name to add dash in vendor id. CBP_(sc-369) 4. Update term, tag and validation file name to add dash in vendor id. COREST_(sc-30189) 7. Updated term, tag and validation file name to use vendor Id. CREB1_(9198) 8. Updated term, tag and validation file name to use vendor Id. CycT1_(sc-10750) 10. Updated term, tag and validation file name to use vendor Id. HMGN1_(ab51212) 11. Update term, tag and validation file name to add dash in vendor id. hSpt5_(sc-28678) 12. Updated term, tag and validation file name to use vendor Id. Med1_(sc-8998) 13. Update term, tag and validation file name to add dash in vendor id. Med26_(sc-48776) 14. Update term, tag and validation file name to add dash in vendor id. TBP_(sc-273)
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    Fixed spacing in SIN3A NB6001263.
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    Fixed links found by weekly link checker.
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    cvDefined is no not off
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    Added tag about validation documents that was missing, found using link checker.
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    Recovered changes lost in merge conflict. Commit recovered: faf9349f5a321c17fef08a65f5170b773e2fb702.
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    added files as a cv typeOfTerm
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    Updates to CV cell line descriptions
  • lines changed 19, context: html, text, full: html, text
    Expanding Ambiguous Labels in CV
  • lines changed 18, context: html, text, full: html, text
    Adding a parent cell for Gingeras:HPIEpC
  • lines changed 39, context: html, text, full: html, text
    Fixing Cell Line vendorIds
  • lines changed 18, context: html, text, full: html, text
    Commented out duplicate term. Found when reviewing cv. Redmine #7283.
  • lines changed 3, context: html, text, full: html, text
    Changes from cv code review. Redmine #7283 1. Term CREB1_(06-863) has antibody validation name that is inconsistent with naming schema. Changed name. 2. Term NFKB. Updated validation name to use vendor Id and be consistent. 3. Removed term nuclearMatrix GO:0016363 duplicate to term nuclearMatrix
  • lines changed 1, context: html, text, full: html, text
    Updated labels to be capatalized.
  • lines changed 18, context: html, text, full: html, text
    Add 10T1/2 cell registration.
  • lines changed 18, context: html, text, full: html, text
    added in parent hpc-l cell line (WIlly)
  • lines changed 19, context: html, text, full: html, text
    trying to resolve merge conflict
  • lines changed 1, context: html, text, full: html, text
    Fixed link for order url found in weekly link checker.
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    Fixed an error in label for Genotype that was removed from a failed merge conflict of commit id: faf9349f5a321c17fef08a65f5170b773e2fb702. Redmine #5149.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Commented out duplicate term. Found when reviewing cv. Redmine #7283.
  • lines changed 223, context: html, text, full: html, text
    Moving alpha cv to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 4, context: html, text, full: html, text
    Fixed links found by weekly link checker.
  • lines changed 1199, context: html, text, full: html, text
    Changes from cv code review. Redmine #7283 1. Term CREB1_(06-863) has antibody validation name that is inconsistent with naming schema. Changed name. 2. Term NFKB. Updated validation name to use vendor Id and be consistent. 3. Removed term nuclearMatrix GO:0016363 duplicate to term nuclearMatrix
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Added 10 of the 19 datasets expected. Redmine #6626.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 2, context: html, text, full: html, text
    added accession for hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1736, context: html, text, full: html, text
    Cleaning out duplicate lines
  • lines changed 42, context: html, text, full: html, text
    fixing the cell lines names caused by the perl hash bug.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 5, context: html, text, full: html, text
    Getting rid of duplicate lines
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliSeq.ra
  • lines changed 386, context: html, text, full: html, text
    Added 10 of the 19 datasets expected. Redmine #6626.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 265, context: html, text, full: html, text
    Willys new ChiaPet.ra
  • lines changed 265, context: html, text, full: html, text
    Changing dates and adding missing objects
  • lines changed 211, context: html, text, full: html, text
    cleaning out old files from metaDb, fixing up html, fixing up defaults
  • lines changed 1813, context: html, text, full: html, text
    trying to resolve merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    added accession for hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 387, context: html, text, full: html, text
    added in replacement tracks and new tracks for open chrom dnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 197, context: html, text, full: html, text
    updated OpenChromFaire to have new geo accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
  • lines changed 2, context: html, text, full: html, text
    added accession for hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 2, context: html, text, full: html, text
    added accession for hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    added accession for hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 3457, context: html, text, full: html, text
    Added 27 submissions. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
  • lines changed 111, context: html, text, full: html, text
    Removed dateUnrestricted for 4 cells: BJ, K562, BG02ES, GM06990 since they have already been published on. Following embargo policy. Redmine #7325.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwRepliSeq.ra
  • lines changed 111, context: html, text, full: html, text
    Venkat made changes to the metadata (redmine #7325)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwRepliSeq.ra
  • lines changed 111, context: html, text, full: html, text
    Venkat made changes to the metadata (redmine #7325)
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 69, context: html, text, full: html, text
    Helping Robert Baertsch get his retroposed genes track up to date.
  • lines changed 14, context: html, text, full: html, text
    Another adjustment for Robert. Note that I am removing tRNAs which I accidentally added, thinking they were Robert's.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Added 10 of the 19 datasets expected. Redmine #6626.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 258, context: html, text, full: html, text
    added in new track (Willy)
  • lines changed 4, context: html, text, full: html, text
    added in defaults
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.html
  • lines changed 149, context: html, text, full: html, text
    Added 10 of the 19 datasets expected. Redmine #6626.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.ra
  • lines changed 103, context: html, text, full: html, text
    Added 10 of the 19 datasets expected. Redmine #6626.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra
  • lines changed 1, context: html, text, full: html, text
    re-ordering the Gencode tracks so that the most recent displays first, will eventually be putting these in their own supertrack, #7329
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
  • lines changed 1, context: html, text, full: html, text
    re-ordering the Gencode tracks so that the most recent displays first, will eventually be putting these in their own supertrack, #7329
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
  • lines changed 1, context: html, text, full: html, text
    re-ordering the Gencode tracks so that the most recent displays first, will eventually be putting these in their own supertrack, #7329
  • lines changed 38, context: html, text, full: html, text
    commenting out search* lines because hgFindSpec isn't aware of release tags yet (and this track was dropped from beta & RR, even though tables were left per revoke policy), redmine #7344
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
  • lines changed 1, context: html, text, full: html, text
    re-ordering the Gencode tracks so that the most recent displays first, will eventually be putting these in their own supertrack, #7329
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 1, context: html, text, full: html, text
    re-ordering the Gencode tracks so that the most recent displays first, will eventually be putting these in their own supertrack, #7329
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 22, context: html, text, full: html, text
    cleaning out old files from metaDb, fixing up html, fixing up defaults
  • lines changed 21, context: html, text, full: html, text
    willy's chia pet fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 4, context: html, text, full: html, text
    cleaning out old files from metaDb, fixing up html, fixing up defaults
  • lines changed 1, context: html, text, full: html, text
    willy's chia pet fixes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html
  • lines changed 11, context: html, text, full: html, text
    added in Terry's release notes for open chrom DNAse
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
  • lines changed 109, context: html, text, full: html, text
    added in replacement tracks and new tracks for open chrom dnase
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra
  • lines changed 491, context: html, text, full: html, text
    Added 27 submissions. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html
  • lines changed 1, context: html, text, full: html, text
    added a period per Steves code review, redmine# 7298
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding speTri2 to the build
  • lines changed 1, context: html, text, full: html, text
    adding rn5 to the build
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 2, context: html, text, full: html, text
    added accession for hg19
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    added mouse accession numbers
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    added mouse accession numbers
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 574, context: html, text, full: html, text
    change controlId of a experiment from cell/Input/std to the dccAccession of its input(control) sample
  • lines changed 142, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    added mouse accession numbers
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 345, context: html, text, full: html, text
    update controlId to the dccAccession number of the corresponding input(control) of the experiments.
  • lines changed 40, context: html, text, full: html, text
    added md5sums
  • lines changed 2, context: html, text, full: html, text
    added mouse accession numbers
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 226, context: html, text, full: html, text
    Replaced Peaks files, to fix error that qa found. Redmine #111.
  • lines changed 2, context: html, text, full: html, text
    added mouse accession numbers
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    added mouse accession numbers
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 439, context: html, text, full: html, text
    Added 3 experiments. Redmine #5397.
  • lines changed 2, context: html, text, full: html, text
    added mouse accession numbers
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrRnaSeq.ra
  • lines changed 2206, context: html, text, full: html, text
    staging LICR RNA-seq release 2 on beta, redmine 6476
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    staging LICR RNA-seq release 2 on beta, redmine 6476
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html
  • lines changed 66, context: html, text, full: html, text
    add new references for new histone modifications submitted
  • lines changed 1, context: html, text, full: html, text
    update release note
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html
  • lines changed 1, context: html, text, full: html, text
    update release note
  • lines changed 55, context: html, text, full: html, text
    add modification based on Katrina's suggestions
  • lines changed 1, context: html, text, full: html, text
    add . in the end of release notes
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra
  • lines changed 0, context: html, text, full: html, text
    changing WholeBrain to Whole Brain in subGroup2 cellType, test to see whether this changes the label in the matrix box on the top of the track setting page
  • lines changed 0, context: html, text, full: html, text
    change Whole Brain back to WholeBrain in subgroup2 cellType as it generated err when doing make
  • lines changed 125, context: html, text, full: html, text
    fixed long labels according to Karina's suggestions
  • lines changed 8, context: html, text, full: html, text
    fix more long labels
  • lines changed 6, context: html, text, full: html, text
    fix matrix labeling, remove rna extrack and localization in subtrack listing, fix shortLabel according to Katrina's suggestions, I also removed RNAextract in the file download list
  • lines changed 1, context: html, text, full: html, text
    capitalize the first letter in immortal cells
  • lines changed 6, context: html, text, full: html, text
    clean up labels
  • lines changed 1, context: html, text, full: html, text
    testing viewLimits setting. see Katrina's question 12 in note #55 in tickiet #6476
  • lines changed 2, context: html, text, full: html, text
    change 0.0 to 3.0 in line starts with type bigWig in BAT rep1 stanza, this is a test to address Katrina's point 12, note #55 in in tickiet #6476
  • lines changed 1, context: html, text, full: html, text
    change 3.0 back to the original value of 0.0 in line starts with type bigWig
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html
  • lines changed 72, context: html, text, full: html, text
    add references for new histone modifications submitted, the description for histone and tfbs are the same as they are related experiments and thus the references
  • lines changed 1, context: html, text, full: html, text
    update release note
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
  • lines changed 101, context: html, text, full: html, text
    Fixes found by Pre-QA Redmine #111 1. Alphabatized Erythoblast in matrix 4. Changed "Because the signal ..." -> "Since, the signal ..." 5. Fixed Data release policy
  • lines changed 6, context: html, text, full: html, text
    6. Added comma's after et .al. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 25, context: html, text, full: html, text
    Replaced Peaks files, to fix error that qa found. Redmine #111.
  • lines changed 1, context: html, text, full: html, text
    Fixes found by Pre-QA Redmine #111 1. Alphabatized Erythoblast in matrix 4. Changed "Because the signal ..." -> "Since, the signal ..." 5. Fixed Data release policy
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
  • lines changed 27, context: html, text, full: html, text
    Replaced Peaks files, to fix error that qa found. Redmine #111.
  • lines changed 1, context: html, text, full: html, text
    Fixes found by Pre-QA Redmine #111 1. Alphabatized Erythoblast in matrix 4. Changed "Because the signal ..." -> "Since, the signal ..." 5. Fixed Data release policy
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
  • lines changed 55, context: html, text, full: html, text
    Added 3 experiments. Redmine #5397.
• src/hg/makeDb/trackDb/pubs.html
  • lines changed 103, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    add a searchSpec for rgdGene2ToDescription (#7155)
• src/hg/makeDb/trackDb/rat/rn5/gap.html
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    updated with new rn5 build original files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rat/rn5/gold.html
  • lines changed 2, context: html, text, full: html, text
    updated with new rn5 build original files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
  • lines changed 25, context: html, text, full: html, text
    updated with new rn5 build original files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/squirrel/speTri2/description.html
  • lines changed 132, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/squirrel/speTri2/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/squirrel/speTri2/gold.html
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    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/t2g.html
  • lines changed 1, context: html, text, full: html, text
    sciencedirect auto activate app
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    renaming all publications tracks tables to pubsXXXX
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 3, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding chainNetMm10
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 35, context: html, text, full: html, text
    renaming all publications tracks tables to pubsXXXX
• src/hg/near/hgNear/hgNearData/columnDb.ra
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    fixing description for yeast column which uses Sac Genome Databse (SGD), not RefSeq
• src/hg/utils/automation/Encode.pm
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    chnged it so that validateFieldList dones't allow ddf's to be processed with fields.ra
  • lines changed 3, context: html, text, full: html, text
    fixed daf version to allow 2.0 and 3.0 for now, will need to remove once all labs are up to date
  • lines changed 3, context: html, text, full: html, text
    changed Encode.pm to allow two daf versions, 2.0 and 3.0, correctly this time, unless is the right conditional
• src/hg/utils/automation/fastaSubseq
  • lines changed 49, context: html, text, full: html, text
    shell script to replace fasta-subseq command
  • lines changed 3, context: html, text, full: html, text
    do not need the test reference to fasta-subseq
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 2, context: html, text, full: html, text
    there are new included trackDb ra files
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 1, context: html, text, full: html, text
    the sort usage message was incorrect
• src/utils/qa/bigPush.csh
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    Added -e tcsh option so that the script will exit on failures (Redmine 4010, note-14) and added an rm of files to the end of the script.
• src/utils/qa/weeklybld/buildEnv.csh
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    v265 preview2
• src/utils/qa/weeklybld/buildZip.csh
  • lines changed 1, context: html, text, full: html, text
    Fixed bug which prevented unzipping and resulted in hung script.

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• files changed: 286