All File Changes

v249_preview to v249_preview2 (2011-03-15 to 2011-03-22) v249

• python/ucscgenomics/rafile/OrderedDict.py
  • lines changed 49, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/RaFile.py
  • lines changed 125, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
  • lines changed 4, context: html, text, full: html, text
    Small update to previous commit, fixed a few errors
• python/ucscgenomics/rafile/RaFileTest
  • lines changed 110, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
  • lines changed 110, context: html, text, full: html, text
    Small update to previous commit, fixed a few errors
• python/ucscgenomics/rafile/RaFileTest.py
  • lines changed 110, context: html, text, full: html, text
    Small update to previous commit, fixed a few errors
• python/ucscgenomics/rafile/orderedDict.py
  • lines changed 49, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/raFile.py
  • lines changed 91, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/testoutput/BasicDiff.out
  • lines changed 27, context: html, text, full: html, text
    Small update to previous commit, fixed a few errors
• python/ucscgenomics/rafile/testoutput/CommentsDiff.out
  • lines changed 32, context: html, text, full: html, text
    Small update to previous commit, fixed a few errors
• python/ucscgenomics/rafile/testoutput/ExtraneousWhitespace.out
  • lines changed 27, context: html, text, full: html, text
    Small update to previous commit, fixed a few errors
  • lines changed 11, context: html, text, full: html, text
    build of ra suite to be submitted to Jim for grade
• python/ucscgenomics/rafile/tests/BasicDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/tests/CommentsDiff.ra
  • lines changed 12, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/tests/DuplicateKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/tests/ExtraneousWhitespace.ra
  • lines changed 27, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/tests/ExtraneousWhitespaceExpected.ra
  • lines changed 12, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
  • lines changed 2, context: html, text, full: html, text
    build of ra suite to be submitted to Jim for grade
• python/ucscgenomics/rafile/tests/InvalidComments.ra
  • lines changed 9, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/tests/MisplacedKeys.ra
  • lines changed 8, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• python/ucscgenomics/rafile/tests/NonNewlineFile.ra
  • lines changed 5, context: html, text, full: html, text
    Added testing suite for RaFile. Will have to edit slightly in the future once comment implementation is finished.
• src/hg/encode/DAFs/2.0/gisChiaPet.daf
  • lines changed 29, context: html, text, full: html, text
    update to current usage
• src/hg/encode/DAFs/2.0/stanfordMm9RnaSeq.daf
  • lines changed 60, context: html, text, full: html, text
    First pass of SYDH Mouse RNA-seq DAF.
  • lines changed 1, context: html, text, full: html, text
    Added replicates required at Peak level. Need to confirm with lab if this is correct.
• src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
  • lines changed 12, context: html, text, full: html, text
    Updated DAF settings. Alignments will be download only. Lab will be submitting csfasta and csqual files instead of fastqs. Updated long label for Signal to say Signal instead of Peaks.
• src/hg/encode/DAFs/2.0/uw5cSample.ddf
  • lines changed 3, context: html, text, full: html, text
    Wrangling UW 5C
• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 151, context: html, text, full: html, text
    Beginnings of ENCODE experiment table
  • lines changed 63, context: html, text, full: html, text
    Incremental change
  • lines changed 210, context: html, text, full: html, text
    Major update: 1. Add metaFind option 2. Add table-driven ra conversion to remove repetitive field refs (a step toward 'once-and-only-once') 3. Add test
  • lines changed 108, context: html, text, full: html, text
    Add -composite to encodeExp. Extract modules to lib.
  • lines changed 83, context: html, text, full: html, text
    Finish up API for encodeExp lib. Cleanup utility. Still needs testing
  • lines changed 22, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
  • lines changed 8, context: html, text, full: html, text
    Field rename and accession format change, by request of JK
• src/hg/encode/encodeExp/makefile
  • lines changed 12, context: html, text, full: html, text
    Beginnings of ENCODE experiment table
  • lines changed 3, context: html, text, full: html, text
    Major update: 1. Add metaFind option 2. Add table-driven ra conversion to remove repetitive field refs (a step toward 'once-and-only-once') 3. Add test
• src/hg/encode/encodeExp/tests/expected/addTest.out.ra
  • lines changed 16, context: html, text, full: html, text
    Major update: 1. Add metaFind option 2. Add table-driven ra conversion to remove repetitive field refs (a step toward 'once-and-only-once') 3. Add test
  • lines changed 4, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
  • lines changed 4, context: html, text, full: html, text
    Field rename and accession format change, by request of JK
• src/hg/encode/encodeExp/tests/input/addTest.in.ra
  • lines changed 16, context: html, text, full: html, text
    Major update: 1. Add metaFind option 2. Add table-driven ra conversion to remove repetitive field refs (a step toward 'once-and-only-once') 3. Add test
  • lines changed 2, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
  • lines changed 2, context: html, text, full: html, text
    Field rename and accession format change, by request of JK
• src/hg/encode/encodeExp/tests/makefile
  • lines changed 22, context: html, text, full: html, text
    Major update: 1. Add metaFind option 2. Add table-driven ra conversion to remove repetitive field refs (a step toward 'once-and-only-once') 3. Add test
  • lines changed 3, context: html, text, full: html, text
    Add -composite to encodeExp. Extract modules to lib.
  • lines changed 3, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 3, context: html, text, full: html, text
    Improving usage comment
  • lines changed 3, context: html, text, full: html, text
    Added strain and age information for know Mouse cell lines.
  • lines changed 3, context: html, text, full: html, text
    Accidently checked in some changes I was playing with. Restoring commig 4888a0b7264461d213f0e0970d4a9fd9b074d983.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 2, context: html, text, full: html, text
    removed the release tag line and added H1hESC to Tier 1 list
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 3, context: html, text, full: html, text
    Fixed bug resulting from 'control' being both a type and a term. Solution: exclude typeOfTerms lookup.
• src/hg/encode/metaCheck/metaCheck.c
  • lines changed 22, context: html, text, full: html, text
    added a -help option.
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 123, context: html, text, full: html, text
    Added search for composites by name, desc and group.
  • lines changed 1, context: html, text, full: html, text
    Fix bug where search was done before the button was pressed.
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 8, context: html, text, full: html, text
    Fix floating link to description
• src/hg/hgTables/filterFields.c
  • lines changed 21, context: html, text, full: html, text
    Bug #2908 (hgTables retains the same "selected fields from primary andrelated tables" when switching between tracks): refactoring in bdb1a185 (4/12/10) mistakenly replaced the removal of field select variables with the removal of filter variables. Fix: restored removal of field select variables (when field select db.table changes).
  • lines changed 7, context: html, text, full: html, text
    add support for "select fields" in custom bam tracks, output message if the output is being maxed out. #27
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    remove the --executability from the rsync opts
• src/hg/hgTracks/bamTrack.c
  • lines changed 11, context: html, text, full: html, text
    fix #3224 . Custom track hgc clicks expect to have an extra field with the table name which isn't used by the bam click handler, but not having anything there breaks hgc.
• src/hg/hgTracks/config.c
  • lines changed 65, context: html, text, full: html, text
    Support for downloads only tracks in the config list even when they are not in a supertrack
• src/hg/hgTracks/factorSource.c
  • lines changed 17, context: html, text, full: html, text
    Improving packing of factorSource tracks.
• src/hg/hgTracks/hgTracks.h
  • lines changed 5, context: html, text, full: html, text
    Support for downloads only tracks in the config list even when they are not in a supertrack
• src/hg/hgTracks/netTrack.c
  • lines changed 3, context: html, text, full: html, text
    fixing spelling error in static function
• src/hg/hgTracks/searchTracks.c
  • lines changed 4, context: html, text, full: html, text
    Fixed radiobuttons for IE (redmine 3189)
• src/hg/hgTracks/simpleTracks.c
  • lines changed 28, context: html, text, full: html, text
    pgSnp track: move labels over if run out of room on left, fix bug that lost labels on following tracks. Redmine 3225, 3207
  • lines changed 61, context: html, text, full: html, text
    Move OMIM entry class filtering to omimLoadBed.
  • lines changed 9, context: html, text, full: html, text
    Changed if else style of omimGene2Color() to Jim's liking.
  • lines changed 0, context: html, text, full: html, text
    Changed indentations of a few lines.
  • lines changed 7, context: html, text, full: html, text
    adding tweak code to chain and net draw color to distinguish chr2B from chr2A, as requested by b0b
• src/hg/hgc/peakClusters.c
  • lines changed 114, context: html, text, full: html, text
    Making it so factorSource tracks can list hits and misses based on the table of inputs rather than relying on the trackDb system. Needed now that integrated regulatory TFBS track is based on data not in other tracks yet.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 8, context: html, text, full: html, text
    Add links to test downloads ('preview')
  • lines changed 15, context: html, text, full: html, text
    adding new group with link to superTrack desc and UTA TFBS and UW CTCF Binding
  • lines changed 6, context: html, text, full: html, text
    added UNC FAIRE, redmine # 64
• src/hg/htdocs/images/phylo/panTro3_12way.png
  • lines changed 0, context: html, text, full: html, text
    image for panTro3 12-way
• src/hg/htdocs/inc/FAQ.topbar.html
  • lines changed 10, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/download.topbar.html
  • lines changed 9, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/encode.custTracks.topbar.html
  • lines changed 7, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/encode.home.topbar.html
  • lines changed 6, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/encode.terms.topbar.html
  • lines changed 4, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/encode.topbar.html
  • lines changed 5, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/encode.topbar_pilot.html
  • lines changed 7, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/help.topbar.html
  • lines changed 10, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/home.topbar.html
  • lines changed 10, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/neandertal.topbar.html
  • lines changed 11, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/inc/topbar.html
  • lines changed 10, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    remove the --executability from the rsync opts
  • lines changed 2, context: html, text, full: html, text
    never update the style directory from this directory
  • lines changed 1, context: html, text, full: html, text
    fix... hopefully... to fix the pernicious make beta style bug on hgwbeta
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    add padding for topbar
• src/hg/inc/encode/encodeExp.h
  • lines changed 100, context: html, text, full: html, text
    Beginnings of ENCODE experiment table
  • lines changed 18, context: html, text, full: html, text
    Incremental change
  • lines changed 22, context: html, text, full: html, text
    Major update: 1. Add metaFind option 2. Add table-driven ra conversion to remove repetitive field refs (a step toward 'once-and-only-once') 3. Add test
  • lines changed 17, context: html, text, full: html, text
    Add -composite to encodeExp. Extract modules to lib.
  • lines changed 24, context: html, text, full: html, text
    Finish up API for encodeExp lib. Cleanup utility. Still needs testing
  • lines changed 17, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
  • lines changed 8, context: html, text, full: html, text
    Support required for mdbPrint/mdbUpdate -encodeExp
  • lines changed 8, context: html, text, full: html, text
    Field rename and accession format change, by request of JK
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    Exposing controlledVocabLink, now used outside of module.
• src/hg/inc/mdb.h
  • lines changed 10, context: html, text, full: html, text
    Add -composite to encodeExp. Extract modules to lib.
  • lines changed 3, context: html, text, full: html, text
    Finish up API for encodeExp lib. Cleanup utility. Still needs testing
  • lines changed 7, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
  • lines changed 44, context: html, text, full: html, text
    Integrated mdbPrint/mdbUpdate -encodeExp with the encodeExp APIs.
• src/hg/inc/samAlignment.h
  • lines changed 2, context: html, text, full: html, text
    need this for #27
• src/hg/js/hgTracks.js
  • lines changed 26, context: html, text, full: html, text
    remove some experimental code; don't bother to retreive an updated track image if user hasn't change anything in configuration dialog
• src/hg/js/hui.js
  • lines changed 9, context: html, text, full: html, text
    Minor code cleanup due to debuging nav link problem on hgFileUi.
• src/hg/lib/clusterInputTrackTable3.as
  • lines changed 9, context: html, text, full: html, text
    Adding some more varients of clusterInput tracks, with more fields. Hmm, not wild about this proliferation.
• src/hg/lib/clusterInputTrackTable3.sql
  • lines changed 17, context: html, text, full: html, text
    Adding some more varients of clusterInput tracks, with more fields. Hmm, not wild about this proliferation.
• src/hg/lib/clusterInputTrackTable4.as
  • lines changed 10, context: html, text, full: html, text
    Adding some more varients of clusterInput tracks, with more fields. Hmm, not wild about this proliferation.
  • lines changed 1, context: html, text, full: html, text
    Changing cell field to cellType to better connect with Encode controlled vocab.
  • lines changed 1, context: html, text, full: html, text
    Updating 3's to 4's to be consistent and make buildTableDescriptions happy.
• src/hg/lib/clusterInputTrackTable4.sql
  • lines changed 18, context: html, text, full: html, text
    Adding some more varients of clusterInput tracks, with more fields. Hmm, not wild about this proliferation.
  • lines changed 1, context: html, text, full: html, text
    Changing cell field to cellType to better connect with Encode controlled vocab.
  • lines changed 3, context: html, text, full: html, text
    Updating 3's to 4's to be consistent and make buildTableDescriptions happy.
• src/hg/lib/customFactory.c
  • lines changed 1, context: html, text, full: html, text
    add support for "select fields" in custom bam tracks, output message if the output is being maxed out. #27
• src/hg/lib/encode/encodeExp.as
  • lines changed 10, context: html, text, full: html, text
    Beginnings of ENCODE experiment table
  • lines changed 2, context: html, text, full: html, text
    Incremental change
  • lines changed 2, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
  • lines changed 1, context: html, text, full: html, text
    Field rename and accession format change, by request of JK
• src/hg/lib/encode/encodeExp.c
  • lines changed 290, context: html, text, full: html, text
    Beginnings of ENCODE experiment table
  • lines changed 99, context: html, text, full: html, text
    Incremental change
  • lines changed 131, context: html, text, full: html, text
    Major update: 1. Add metaFind option 2. Add table-driven ra conversion to remove repetitive field refs (a step toward 'once-and-only-once') 3. Add test
  • lines changed 94, context: html, text, full: html, text
    Add -composite to encodeExp. Extract modules to lib.
  • lines changed 101, context: html, text, full: html, text
    Finish up API for encodeExp lib. Cleanup utility. Still needs testing
  • lines changed 128, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
  • lines changed 12, context: html, text, full: html, text
    Some cleanup
  • lines changed 127, context: html, text, full: html, text
    Support required for mdbPrint/mdbUpdate -encodeExp
  • lines changed 7, context: html, text, full: html, text
    Fixing a couple compiler warnings on Ubuntu: "(char) NULL" gives'cast to different size', and comparison of strings using != is not safe. Also replaced #define BUF_SIZE with sizeof, because BUF_SIZE is a very general name, and sizeof avoids the need to type the number twice. If there is a meaningful limit to impose, the constant should have a meaningful name.
  • lines changed 58, context: html, text, full: html, text
    Field rename and accession format change, by request of JK
• src/hg/lib/encode/encodeExp.sql
  • lines changed 16, context: html, text, full: html, text
    Beginnings of ENCODE experiment table
  • lines changed 2, context: html, text, full: html, text
    Incremental change
  • lines changed 1, context: html, text, full: html, text
    Major update: 1. Add metaFind option 2. Add table-driven ra conversion to remove repetitive field refs (a step toward 'once-and-only-once') 3. Add test
  • lines changed 4, context: html, text, full: html, text
    Schema changes: add lastUpdate time, rename vars to factors to distinguish from mdbVars. Change accession format to be clearer to end-users. Extend 'find' and 'add' to check if already experiment is already present. Add lib routines to update entries in a limited fashion.
• src/hg/lib/fileUi.c
  • lines changed 7, context: html, text, full: html, text
    Special case for beta is not an rsync or an htdocs-downloads solution.
  • lines changed 3, context: html, text, full: html, text
    Fixed bug with fileFilter link to hgEncodeVocab.
  • lines changed 6, context: html, text, full: html, text
    hwdev does rsync now.
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    make hHostHasPrefix work when CGIs are run from the command line
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Beginnings of ENCODE experiment table
• src/hg/lib/mdb.c
  • lines changed 2, context: html, text, full: html, text
    Needed special case of searchability for composite, since it is not directly searchable but IS indirectly
  • lines changed 18, context: html, text, full: html, text
    Add -composite to encodeExp. Extract modules to lib.
  • lines changed 16, context: html, text, full: html, text
    Finish up API for encodeExp lib. Cleanup utility. Still needs testing
  • lines changed 154, context: html, text, full: html, text
    Integrated mdbPrint/mdbUpdate -encodeExp with the encodeExp APIs.
• src/hg/lib/samAlignment.c
  • lines changed 17, context: html, text, full: html, text
    add support for "select fields" in custom bam tracks, output message if the output is being maxed out. #27
• src/hg/lib/web.c
  • lines changed 17, context: html, text, full: html, text
    remove unneccssary nbsp from topbar to fix problems with IE
  • lines changed 47, context: html, text, full: html, text
    changed webTimeStampedLinkToResource as follows: (a) stop trying to create softlink as this usually didn't work and violates the fact that we are now imposing version checking in production sites (see redmine 3170); (b) improve/update code comments; (c) improve error message shown to user when appropriate version isn't found
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • lines changed 550, context: html, text, full: html, text
    Cheking in wrangling docs from past work. Moved some hg18 stuff to the hg18 doc
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeYaleChIPseq.release4.notes.txt
  • lines changed 1466, context: html, text, full: html, text
    Release notes of release 4 of track.
  • lines changed 1110, context: html, text, full: html, text
    Updated release notes to have path for files.
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • lines changed 244, context: html, text, full: html, text
    Cheking in wrangling docs from past work. Moved some hg18 stuff to the hg18 doc
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 486, context: html, text, full: html, text
    Cheking in wrangling docs from past work. Moved some hg18 stuff to the hg18 doc
  • lines changed 183, context: html, text, full: html, text
    Getting impatient on Jason's liftOver.
  • lines changed 365, context: html, text, full: html, text
    Late changing stuses from 'reviewing' to 'released'
• src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
  • lines changed 664, context: html, text, full: html, text
    Cheking in wrangling docs from past work. Moved some hg18 stuff to the hg18 doc
  • lines changed 51, context: html, text, full: html, text
    Late changing stuses from 'reviewing' to 'released'
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisChiaPet.release1.notes
  • lines changed 62, context: html, text, full: html, text
    Removed bam files from release notes
• src/hg/makeDb/doc/hg19.txt
  • lines changed 57, context: html, text, full: html, text
    Working on figuring out colors for wgEncodeReg rainbow fringe graphs based on clustering cell expression patterns
  • lines changed 72, context: html, text, full: html, text
    Updated hg19 IKMC track.
  • lines changed 107, context: html, text, full: html, text
    AceView Gene track for hg19
  • lines changed 10, context: html, text, full: html, text
    Further work on wgEncodeReg
  • lines changed 7, context: html, text, full: html, text
    Refined omimGene2 build process by picking only one RefSeq for each LocusLink ID.
  • lines changed 19, context: html, text, full: html, text
    Doing more wgEncodeReg work. This is version put on pushQ initially.
• src/hg/makeDb/doc/mm9.txt
  • lines changed 99, context: html, text, full: html, text
    Updated mm9 IKMC track.
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 11, context: html, text, full: html, text
    done with Mm9 chain net swap and running swap on MonDom5
  • lines changed 5, context: html, text, full: html, text
    done with monDom5 lastz
  • lines changed 18, context: html, text, full: html, text
    finished rn4 lastz
  • lines changed 89, context: html, text, full: html, text
    beginning of 12-way multiz
  • lines changed 137, context: html, text, full: html, text
    12-alignment multiz run done
• src/hg/makeDb/doc/proteins/090821.txt
  • lines changed 58, context: html, text, full: html, text
    Updated Reactome V36.
• src/hg/makeDb/doc/uniProt/sp110315.txt
  • lines changed 50, context: html, text, full: html, text
    Downloading a new version of UniProt so we can figure out what's going on with the version number. There's a discrepancy between the current database, sp101005, which gives no version number to the canonical isoform, and the data that's on the web, which gives the canonical isoform a version number of 1. For example, on the web UniProt shows that P46108 has two isoforms, canonical isoform P46108-1 and alternative isoform P46108-2, while sp101005 shows isoforms P46108 and P46108-2. To track this down, markd and I are starting out by loading a fresh copy of UniProt
• src/hg/makeDb/genbank/makefile
  • lines changed 11, context: html, text, full: html, text
    add program to remote stray MGC and ORFeome entries
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • lines changed 10, context: html, text, full: html, text
    removed code moved to library
• src/hg/makeDb/genbank/src/align/gbPython
  • lines changed 6, context: html, text, full: html, text
    support use of genbank copy of python on RR
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • lines changed 7, context: html, text, full: html, text
    perl fork returns undef on error, just check for that
• src/hg/makeDb/genbank/src/lib/py/genbank/Config.py
  • lines changed 12, context: html, text, full: html, text
    add program to remote stray MGC and ORFeome entries
• src/hg/makeDb/genbank/src/lib/py/genbank/__init__.py
  • lines changed 16, context: html, text, full: html, text
    add program to remote stray MGC and ORFeome entries
  • lines changed 13, context: html, text, full: html, text
    check for database actually existing before trying to repair. Make sure HGDB_CONF is set when needed
• src/hg/makeDb/genbank/src/lib/py/genbank/procOps.py
  • lines changed 3, context: html, text, full: html, text
    add program to remote stray MGC and ORFeome entries
• src/hg/makeDb/genbank/src/repair/makefile
  • lines changed 6, context: html, text, full: html, text
    add program to remote stray MGC and ORFeome entries
• src/hg/makeDb/genbank/src/repair/repairMgcOrfeome
  • lines changed 152, context: html, text, full: html, text
    add program to remote stray MGC and ORFeome entries
  • lines changed 2, context: html, text, full: html, text
    check for database actually existing before trying to repair. Make sure HGDB_CONF is set when needed
  • lines changed 9, context: html, text, full: html, text
    Check for database existing and the database actually having genbank files. A skelton database might exist on the RR for something that was archived
• src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
  • lines changed 25, context: html, text, full: html, text
    Adding in a check for each source + factor combination being unique.
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 1, context: html, text, full: html, text
    Integrated mdbPrint/mdbUpdate -encodeExp with the encodeExp APIs.
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 8, context: html, text, full: html, text
    Integrated mdbPrint/mdbUpdate -encodeExp with the encodeExp APIs.
• src/hg/makeDb/trackDb/README
  • lines changed 7, context: html, text, full: html, text
    Adding a new tag so can select fields to display from input table instead of groups to display from trackDb in factorSource type tracks such as wgEncodeRegTfbs
  • lines changed 16, context: html, text, full: html, text
    update bam file information with hgBbiDbLink loader
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 18, context: html, text, full: html, text
    Added strain and age information for know Mouse cell lines.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 302, context: html, text, full: html, text
    Updating beta
• src/hg/makeDb/trackDb/human/affyExonArray.html
  • lines changed 1, context: html, text, full: html, text
    fixing ending tag for <I> for affy exon array track
• src/hg/makeDb/trackDb/human/affyHuEx1.html
  • lines changed 2, context: html, text, full: html, text
    Fixed product link for Affy's Human Exon 1.0 ST Genechip
• src/hg/makeDb/trackDb/human/affyHumanExon.html
  • lines changed 1, context: html, text, full: html, text
    Fixed product link for Affy's Human Exon 1.0 Genechip
• src/hg/makeDb/trackDb/human/encodeStanfordMeth.html
  • lines changed 3, context: html, text, full: html, text
    Fixed link to Myer Lab homepage
• src/hg/makeDb/trackDb/human/encodeStanfordMethSmoothed.html
  • lines changed 4, context: html, text, full: html, text
    Fixed link to Myer Lab homepage
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo
• src/hg/makeDb/trackDb/human/encodeUvaDnaRep.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link to Dutta Lab homepage
• src/hg/makeDb/trackDb/human/encodeUvaDnaRepSuper.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link to Dutta Lab homepage
• src/hg/makeDb/trackDb/human/encodeYaleChIPSTAT1Pval.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link for ScienceDirect Cawly article
• src/hg/makeDb/trackDb/human/encodeYaleChIPSTAT1Sig.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link for ScienceDirect Cawley article
• src/hg/makeDb/trackDb/human/encodeYaleChIPSTAT1Sites.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link for ScienceDirect Cawley article
• src/hg/makeDb/trackDb/human/hg16/encodeGencodeGene.html
  • lines changed 1, context: html, text, full: html, text
    Fixed ScienceDirect link for Reymond article
• src/hg/makeDb/trackDb/human/hg16/encodeGencodeIntron.html
  • lines changed 1, context: html, text, full: html, text
    Fixed ScienceDirect link to Reymond article
• src/hg/makeDb/trackDb/human/hg16/encodeNhgriDnaseHs.html
  • lines changed 1, context: html, text, full: html, text
    Fixed ScienceDirect link for McArthur article
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 1527, context: html, text, full: html, text
    Removed some obsolete objects (which were replaced by V2s)
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 66, context: html, text, full: html, text
    Removed obsolete objs which were replaced by V2s
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 130, context: html, text, full: html, text
    Removed obsolete objects. There is no H3K4me1 in UW Histone hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 312, context: html, text, full: html, text
    Removed obsolete objs which were replaced by V2s
  • lines changed 108, context: html, text, full: html, text
    Removed obsolete objects. cell=HIPEpiC and phase=G1 don't exist for hg18 UW Dnase
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 3730, context: html, text, full: html, text
    Removed 2 experiments as they used the wrong lanes (K562: NF-YA and NF-YB). Advised by lab to revoke data from hg18.
  • lines changed 723, context: html, text, full: html, text
    Finally got around to loading ancient Yale TFBS submissions
  • lines changed 460, context: html, text, full: html, text
    Added release notes to new html file and removed meta-data of replaced files.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Removed 2 experiments as they used the wrong lanes (K562: NF-YA and NF-YB). Advised by lab to revoke data from hg18.
  • lines changed 1, context: html, text, full: html, text
    Removed accession number for wgEncodeUwAffyExonArray track. Accession number has been migrated to metaDb as var=dccInternalNotes. Redmine issue 1492 note 17.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.html
  • lines changed 6, context: html, text, full: html, text
    Minor changes in anticipation of hg19 lift over.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
  • lines changed 17, context: html, text, full: html, text
    Minor changes in anticipation of hg19 lift over.
  • lines changed 1, context: html, text, full: html, text
    Sorry. Had wgEncode setting twice. Thanks Angie for finding this.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.html
  • lines changed 178, context: html, text, full: html, text
    Added release notes to new html file and removed meta-data of replaced files.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra
  • lines changed 2349, context: html, text, full: html, text
    Removed 2 experiments as they used the wrong lanes (K562: NF-YA and NF-YB). Advised by lab to revoke data from hg18.
  • lines changed 48, context: html, text, full: html, text
    Finally got around to loading 5 ancient submissions.
  • lines changed 1, context: html, text, full: html, text
    Added release notes to new html file and removed meta-data of replaced files.
• src/hg/makeDb/trackDb/human/hg19/acembly.html
  • lines changed 191, context: html, text, full: html, text
    Specific hg19 details description of aceView track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Broad HMM has been lifted over from hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 163, context: html, text, full: html, text
    Broad HMM has been lifted over from hg18
  • lines changed 10, context: html, text, full: html, text
    Fime names are bed not bed9
  • lines changed 27, context: html, text, full: html, text
    Jason's liftover of HMM from hg18 is finally here.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 4800, context: html, text, full: html, text
    sorting out files, lots of adding and subtracting of objects
  • lines changed 208, context: html, text, full: html, text
    Great file sort continues with adding and subtracting objects
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 16, context: html, text, full: html, text
    Swapped HsmmRep2 for HsmmtRep2
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 199, context: html, text, full: html, text
    changed fileNames to match the new ones Brian loaded
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1256, context: html, text, full: html, text
    Undid load of 3 submissions due to meta-data errors: 3752,3751,3749.
  • lines changed 283, context: html, text, full: html, text
    Removed 12 files and meta-data as advised by lab. Redmine issue 3057 note 6.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 115, context: html, text, full: html, text
    And validation docs for 2 cell lines in Open Chrom Chip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 33, context: html, text, full: html, text
    First submission of 1 percent verification data submitted as 'attic by exp' archives
  • lines changed 5, context: html, text, full: html, text
    Files are tgz, not doc.gz
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 33, context: html, text, full: html, text
    And 1 percent verification for 2 of FAIRE's
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 617, context: html, text, full: html, text
    Reloaded data with normal table and file naming schema, removed docId naming strategy. Also removed fastq files, as these are not the correct RawData format that will be provided by the lab.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 231, context: html, text, full: html, text
    Removed 2 experiments K562 NF-YA and NF-YB the were submitted using incorrect lanes.
  • lines changed 129, context: html, text, full: html, text
    Added submission 3755.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metaDb for UNC FAIRE, redmine# 64
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
  • lines changed 6, context: html, text, full: html, text
    getting beta metaDb up to date for before releasing the track; incorporates Cricket's changes of adding experimental variables to all composite tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromFaire.ra
  • lines changed 3548, context: html, text, full: html, text
    staging metaDb for UNC FAIRE, redmine# 64
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwTfbs.ra
  • lines changed 144, context: html, text, full: html, text
    staging cricket's change experimental variables to all compositesand Venkat's change of removing metaDb for removed fastqs
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing for release of UTA TFBS: removing release tags, preparing metaDb
  • lines changed 1, context: html, text, full: html, text
    preparing for release of UW CTCF TFBS to RR: removed release tags, prepared metadata, Redmine #1604
  • lines changed 1, context: html, text, full: html, text
    released UNC FAIRE, redmine #64
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromChip.ra
  • lines changed 5902, context: html, text, full: html, text
    preparing for release of UTA TFBS: removing release tags, preparing metaDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromFaire.ra
  • lines changed 3548, context: html, text, full: html, text
    released UNC FAIRE, redmine #64
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwTfbs.ra
  • lines changed 11509, context: html, text, full: html, text
    preparing for release of UW CTCF TFBS to RR: removed release tags, prepared metadata, Redmine #1604
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    staging UNC FAIRE on hgwbeta, redmine # 64
  • lines changed 3, context: html, text, full: html, text
    First cut of ENCODE regulation super track for hg19.
  • lines changed 1, context: html, text, full: html, text
    Updated wgEncodeSydhNsome to use global tag's rather than local tags.
  • lines changed 1, context: html, text, full: html, text
    preparing for release of UTA TFBS: removing release tags, preparing metaDb
  • lines changed 2, context: html, text, full: html, text
    preparing for release of UW CTCF TFBS to RR: removed release tags, prepared metadata, Redmine #1604
  • lines changed 1, context: html, text, full: html, text
    released UNC FAIRE, redmine #64
  • lines changed 5, context: html, text, full: html, text
    Jason's liftover of HMM from hg18 is finally here.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
  • lines changed 132, context: html, text, full: html, text
    Jason's liftover of HMM from hg18 is finally here.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 117, context: html, text, full: html, text
    Jason's liftover of HMM from hg18 is finally here.
  • lines changed 1, context: html, text, full: html, text
    Fixed filterBy for '_'s.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 482, context: html, text, full: html, text
    Trying to sort out which tracks to display for Caltech
  • lines changed 200, context: html, text, full: html, text
    sorting out files, lots of adding and subtracting of objects
  • lines changed 84, context: html, text, full: html, text
    Great file sort continues with adding and subtracting objects
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed fileSort to show the run
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 6, context: html, text, full: html, text
    Swapped HsmmRep2 for HsmmtRep2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 334, context: html, text, full: html, text
    Undid load of 3 submissions due to meta-data errors: 3752,3751,3749.
  • lines changed 1, context: html, text, full: html, text
    Fixed missing underscore(_) in GATA2SC267=GATA2(SC-267)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 5, context: html, text, full: html, text
    since UNC FAIRE was released, changed link from genome-preview; changed links to other open chrom so they open new tab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 11, context: html, text, full: html, text
    Zinba is some mythical character that is trapped in hg18 land. No sign of Zinba in hg19
  • lines changed 5, context: html, text, full: html, text
    fixed typos and formatting, redmine issue #64
  • lines changed 11, context: html, text, full: html, text
    Missed some Zinba voodoo
  • lines changed 1, context: html, text, full: html, text
    changing link to point to its own supplemental directory, redmine# 64
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.html
  • lines changed 63, context: html, text, full: html, text
    Adding description html pages for wgEncodeReg tracks for hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 328, context: html, text, full: html, text
    First cut of ENCODE regulation super track for hg19.
  • lines changed 8, context: html, text, full: html, text
    Moving to V2 Caltech RNA tables.
  • lines changed 6, context: html, text, full: html, text
    Adding a new tag so can select fields to display from input table instead of groups to display from trackDb in factorSource type tracks such as wgEncodeRegTfbs
  • lines changed 1, context: html, text, full: html, text
    Improving scale on wgEncodeRegTxn.
  • lines changed 1, context: html, text, full: html, text
    Making HSMM color green in transcription like it is in the histones.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.html
  • lines changed 28, context: html, text, full: html, text
    Adding description html pages for wgEncodeReg tracks for hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k27ac.html
  • lines changed 38, context: html, text, full: html, text
    Adding description html pages for wgEncodeReg tracks for hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k4me1.html
  • lines changed 37, context: html, text, full: html, text
    Adding description html pages for wgEncodeReg tracks for hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegMarkH3k4me3.html
  • lines changed 37, context: html, text, full: html, text
    Adding description html pages for wgEncodeReg tracks for hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.html
  • lines changed 57, context: html, text, full: html, text
    Adding description html pages for wgEncodeReg tracks for hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTxn.html
  • lines changed 33, context: html, text, full: html, text
    Adding description html pages for wgEncodeReg tracks for hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
  • lines changed 4, context: html, text, full: html, text
    Changed the labels for conflicting replicates and explained in the release notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 78, context: html, text, full: html, text
    Changed the labels for conflicting replicates and explained in the release notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 90, context: html, text, full: html, text
    Added track description as provided by Peggy Farnham.
  • lines changed 1, context: html, text, full: html, text
    Removed specificiation of human protocols in protocols link.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 5, context: html, text, full: html, text
    Updated default tracks on to be all cell lines and Histone marks. Updated default signal windowing function to be mean+whiskers.
  • lines changed 4, context: html, text, full: html, text
    Updated spacing of trackDb enteries.
  • lines changed 8, context: html, text, full: html, text
    Updated spacing and removed some extra comment lines.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
  • lines changed 27, context: html, text, full: html, text
    Reloaded data with normal table and file naming schema, removed docId naming strategy. Also removed fastq files, as these are not the correct RawData format that will be provided by the lab.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 20, context: html, text, full: html, text
    Removed 2 experiments K562 NF-YA and NF-YB the were submitted using incorrect lanes.
  • lines changed 21, context: html, text, full: html, text
    Added submission 3755.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
  • lines changed 288, context: html, text, full: html, text
    Completely re-worked Description Page for U Chicago TFBS
  • lines changed 5, context: html, text, full: html, text
    White Space Edit for Description Page for U Chicago TFBS
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 12, context: html, text, full: html, text
    Revised the text of the peptide rank description, based on feedback from Jainab
• src/hg/makeDb/trackDb/human/nhgriDnaseHs.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link for ScienceDirect McArthur article
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    AceView Gene track for hg19
• src/hg/makeDb/trackDb/human/vegaGene.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link to new Genome Institute at Washington University site
• src/hg/makeDb/trackDb/human/vegaPseudoGene.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link to new Genome Institute at Washington University site
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 157, context: html, text, full: html, text
    Added 1 submission, subId 3812.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 157, context: html, text, full: html, text
    Added 1 submission, subId 3811.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 1059, context: html, text, full: html, text
    Added 7 new submissions mouse data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 120, context: html, text, full: html, text
    Renamed 7 replicates as provided by Lab. Redmine issue: 2985.
  • lines changed 51, context: html, text, full: html, text
    Updated UW display with initial attic design for supplemental experiments.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 20, context: html, text, full: html, text
    Added 1 submission, subId 3812.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 20, context: html, text, full: html, text
    Added 1 submission, subId 3811.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 127, context: html, text, full: html, text
    Added 7 new submissions mouse data.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 85, context: html, text, full: html, text
    Renamed 7 replicates as provided by Lab. Redmine issue: 2985.
  • lines changed 287, context: html, text, full: html, text
    Updated UW display with initial attic design for supplemental experiments.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    AceView Gene track for hg19
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    Adding a new tag so can select fields to display from input table instead of groups to display from trackDb in factorSource type tracks such as wgEncodeRegTfbs
• src/hg/makeDb/trackDb/trackDb.ra
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    Track #1684 (SNPs 132 (dbSNP)): Brooke pointed out that the maxWindowToDrawsetting is not necessary for the very sparse Patient SNPs subset -- removed.
• src/hg/near/hgNear/hgNearData/columnDb.ra
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    Updated UniProt KB and UniProtKB Acc column definitions to avoid IE problem.
• src/hg/oneShot/doOmimGene2/doOmimGene2.c
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    Added one shot program doOmimGene2 for OMIM Genes build.
• src/hg/oneShot/doOmimGene2/makefile
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    Added one shot program doOmimGene2 for OMIM Genes build.
• src/hg/oneShot/freen/freen.c
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    Making freen make a web page with rainbows derived from Autodesk Animator color map.
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    Adding rainbow generating routines.
• src/hg/oneShot/wgEncodeRegGenRa/makefile
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    A little program to generate parts of trackDb.ra file for wgEncodeReg.
• src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
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    A little program to generate parts of trackDb.ra file for wgEncodeReg.
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    Tweaking and debugging.
• src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c
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    Adding lab column
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    Fixing bug Fan found reading my code. Yea!
• src/hg/regulate/regClusterTreeCells/makefile
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c
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    Making it use a standard tree output format. Changing to be a binary tree rather than general hierarchy.
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    Adding -short and -rename options
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    Adding distances output
• src/hg/regulate/regClusterTreeCells/tests/expected.tree
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in.lst
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/1.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/10.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/2.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/3.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/4.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/5.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/6.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/7.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/8.bed
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    Adding test set.
• src/hg/regulate/regClusterTreeCells/tests/in/9.bed
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    Adding test set.
• src/hg/regulate/wgEncodeReg/picksFromDupes.tab
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    Saving away input to cleanup program.
• src/hg/txCds/txCdsEvFromBed/txCdsEvFromBed.c
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    To clear up a problem in the UCSC Genes pipeline, changed the code so that instead of first addressing the longest CDS in each cluster, we address the CDS that has the fewest number of compatible transcripts. In testing against previous output, this cleared up the one strange error condition that was stopping the pipeline. Other than that, it had no effect, aside from changing the order of output slightly for a few lines
• src/hg/txCds/txCdsToGene/txCdsToGene.c
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    Changed the code to issue a warning and continue when finding a CDS with a premature stop codon, rather than doing an errAbort. This comes from Rachel and Mark, and their perspective that CCDS contains some transcripts that appear to have PTCs, but don't due to genetic variation. This also follows the growing acceptance that NMD doesn't stop protein translation so much as it turns it down. And the growing acceptance that we don't fully understand NMD.
• src/hg/utils/cpAndLinkToResourceFiles.pl
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    improve usage message
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
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    Fixing compiler warning from gcc 4.1.2 20080704 (Red Hat 4.1.2-48) --casting system()'s return to void is not enough, have to assign it to something, and then we have to do something else to that variable to avoid the unused-var warning, annoying.
• src/hg/utils/refreshNamedSessionCustomTracks/rr.trashCleaner.csh
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    update to include the sed of the quote mark in a file name
• src/hg/utils/wigBedToStep/wigBedToStep.c
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    Added a -forceSpanOne option and also fixed a fixedStep bug that was not outputting headers at discontinuities in the data... a pretty bad bug.
• src/inc/common.h
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    Added useful function used by text search alogrithm
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    Added support for turning slPairs list back into string
• src/inc/common.mk
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    add -lz if we're using tabix. This only matters if you're not linking with SSL or mySql.
• src/inc/rainbow.h
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    Adding rainbow generating routines.
• src/lib/common.c
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    Added useful function used by text search alogrithm
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    Added support for turning slPairs list back into string
• src/lib/hash.c
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    Indulging in a little paranoia about void pointer arithmetic.
• src/lib/makefile
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    Adding rainbow generating routines.
• src/lib/rainbow.c
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    Adding rainbow generating routines.
• src/product/scripts/browserEnvironment.txt
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    indicate potential PNG definitions and a new error message cleaner from the kent src build
• src/product/scripts/kentSrcUpdate.sh
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    indicate potential PNG definitions and a new error message cleaner from the kent src build
• src/utils/bedCommonRegions/bedCommonRegions.c
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    Making a little utility to extract common regions from bed files. Not bulletproof, but should abort on input it can't handle 99% of the time, and limitations are stated in usage.
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    Adding -removeOverlap flag.
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    Removing removeOverlaps flag since under larger scale testing didn't work, and it looked to be a scary pipeline mode problem.
• src/utils/bedCommonRegions/makefile
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    Making a little utility to extract common regions from bed files. Not bulletproof, but should abort on input it can't handle 99% of the time, and limitations are stated in usage.
• src/utils/bedCommonRegions/tests/expected.bed
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    Making a little utility to extract common regions from bed files. Not bulletproof, but should abort on input it can't handle 99% of the time, and limitations are stated in usage.
• src/utils/bedCommonRegions/tests/in/1.bed
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    Making a little utility to extract common regions from bed files. Not bulletproof, but should abort on input it can't handle 99% of the time, and limitations are stated in usage.
• src/utils/bedCommonRegions/tests/in/2.bed
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    Making a little utility to extract common regions from bed files. Not bulletproof, but should abort on input it can't handle 99% of the time, and limitations are stated in usage.
• src/utils/bedCommonRegions/tests/in/3.bed
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    Making a little utility to extract common regions from bed files. Not bulletproof, but should abort on input it can't handle 99% of the time, and limitations are stated in usage.
• src/utils/bedRestrictToPositions/bedRestrictToPositions.c
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    Adding another bed cleanup utility.
• src/utils/bedRestrictToPositions/makefile
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    Adding another bed cleanup utility.
• src/utils/qa/weeklybld/buildCgi32.csh
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    ignore bigWarn since it's a file, not a warning. Also fix some day numbers in email notifications
• src/utils/qa/weeklybld/buildEnv.csh
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    v249 preview
• src/utils/qa/weeklybld/buildZip.csh
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    ignore bigWarn since it's a file, not a warning. Also fix some day numbers in email notifications
• src/utils/qa/weeklybld/doNewBranch.csh
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    ignore bigWarn since it's a file, not a warning. Also fix some day numbers in email notifications

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• files changed: 366