All File Changes

v264_base to v265_preview (2012-03-06 to 2012-03-13) v265

• python/lib/ucscgenomics/qa.py
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    Added qaEncodeTracks2 and qaGbTracks to list of programs known to depend on qa.py.
• python/virtual.txt
  • lines changed 3, context: html, text, full: html, text
    Added in information regarding the python version to use.
• src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrHistone.daf
  • lines changed 4, context: html, text, full: html, text
    rm treatment as variable after renaming bone marrow derived macrophage to BMDM as the treatment was part of the process of making the marcrophage
• src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrRnaSeq.daf
  • lines changed 4, context: html, text, full: html, text
    rm treatment as variable after renaming bone marrow derived macrophage to BMDM as the treatment was part of the process of making the marcrophage
• src/hg/encode/DAFs/3.0/mm9/wgEncodeLicrTfbs.daf
  • lines changed 4, context: html, text, full: html, text
    rm treatment as variable after renaming bone marrow derived macrophage to BMDM as the treatment was part of the process of making the marcrophage
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 3, context: html, text, full: html, text
    added a fatal error message for a missing composite level stanza
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    changes tabs to 4 spaces
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 2, context: html, text, full: html, text
    moved regex into conditional, to prevent uninitialized errors when oldSettings exists, but doesn't have a metaData line
  • lines changed 1, context: html, text, full: html, text
    put check for defined sex variable in the conditional. It was causing errors when the cell was category = tissue and no sex defined in the DDF
  • lines changed 11, context: html, text, full: html, text
    made it so that if the cell is category=tissue, and sex is not defined in the ddf, the program gives an error. Also made it so that identical error lines are collapsed into one line, instead of flooding the screen.
• src/hg/encode/qaAddTrackReferences/makefile
  • lines changed 1, context: html, text, full: html, text
    fixing makefile for python version
• src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
  • lines changed 373, context: html, text, full: html, text
    ported to python, needs a good reviewing before full blown tool usage
• src/hg/encode/validateFiles/validateFilesUsage
  • lines changed 0, context: html, text, full: html, text
    Using git to track proposed changes to validateFiles usage statement
  • lines changed 59, context: html, text, full: html, text
    Using git to track proposed changes to validateFiles usage statement
  • lines changed 9, context: html, text, full: html, text
    First I think we should change the beginning part to all be the same tense and to be the completion of the sentance validateFiles does ...
  • lines changed 13, context: html, text, full: html, text
    Changing the type to have consistent formatting, the links need to be double checked
• src/hg/getRnaPred/getRnaPred.c
  • lines changed 32, context: html, text, full: html, text
    added option to include coordinates in fasta header
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 5, context: html, text, full: html, text
    fix score filtering on bigBed's that are bed9's (#6770)
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    fix score filtering on bigBed's that are bed9's (#6770)
• src/hg/hgc/t2g.c
  • lines changed 1, context: html, text, full: html, text
    publications track description changes and fix for bold text bug see redmine #6833
• src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
  • lines changed 1, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/htdocs/ENCODE/dataMatrix/dataSummary.css
  • lines changed 12, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 2, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
  • lines changed 1, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixMouse.html
  • lines changed 3, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 1, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixMouse.html
  • lines changed 1, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 1, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
  • lines changed 1, context: html, text, full: html, text
    Page header change
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryMouse.html
  • lines changed 1, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
  • lines changed 1, context: html, text, full: html, text
    Tweak page headers to tie in to matrix pages
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    Added line for GENCODE V11 (redmine #6775)
• src/hg/htdocs/ENCODE/otherTerms.html
  • lines changed 32, context: html, text, full: html, text
    adding 'Age' and increasing the height of some of the frames for a better fit, #7100
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    made correction to mm10 release
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    made correction to mm10 credits
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    changed Pat to Pattern in PSL name definition
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 27, context: html, text, full: html, text
    added new mm10 announcement
• src/hg/htdocs/indexIntro.html
  • lines changed 1, context: html, text, full: html, text
    redmine issue 7108
• src/hg/htdocs/indexNews.html
  • lines changed 41, context: html, text, full: html, text
    added mm10 announcement
  • lines changed 1, context: html, text, full: html, text
    fixed date for mm10 announcement
• src/hg/js/encodeDataSummary.js
  • lines changed 21, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/js/encodeMatrix.js
  • lines changed 1, context: html, text, full: html, text
    Colors and labels (from review with Katrina)
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    Changes that pertain to Redmine #7005 1. make tableName searchable: freeText 2. Update label for tableName to be "Table name at UCSC" 3. When choosing dropdown for "Table name at UCSC", change utils.js so this is no link to otherTerms.html page. For example see: "Treatment" 4. Remove subId "Submission ID" as being searchable on dev,beta and public.
  • lines changed 4, context: html, text, full: html, text
    Changes for Redmine #7100 1. Added info link for "Experiment (Assay) type" 2. Suppressed info link for: - "GEO sample accession" - "Obtained by" - "UCSC Accession" - "Experimet ID" *NOTE: Only suppressed on DEV
• src/hg/lib/grcIncidentDb.as
  • lines changed 9, context: html, text, full: html, text
    change description comment due to new printout of extra bigBed fields change
• src/hg/lib/ncbiIncidentDb.as
  • lines changed 1, context: html, text, full: html, text
    change description comment due to new printout of extra bigBed fields change
• src/hg/lib/t2g.sql
  • lines changed 2, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/lib/t2gArticle.sql
  • lines changed 13, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/lib/t2gBlat.sql
  • lines changed 19, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/lib/t2gMarkerAnnot.sql
  • lines changed 14, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/lib/t2gMarkerBand.sql
  • lines changed 11, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/lib/t2gMarkerGene.sql
  • lines changed 11, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/lib/t2gMarkerSnp.sql
  • lines changed 11, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/lib/t2gSequenceAnnot.sql
  • lines changed 13, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    add pgSnp to packableType (#7055)
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeDukeAffyExon.release3.notes
  • lines changed 590, context: html, text, full: html, text
    notes for duke affy exon
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrRnaSeq.release2.notes
  • lines changed 437, context: html, text, full: html, text
    create notes file
  • lines changed 418, context: html, text, full: html, text
    Adding notes file that is compared to release1
• src/hg/makeDb/doc/hg19.txt
  • lines changed 55, context: html, text, full: html, text
    running mm10 lastz and removed some spaces at the ends of lines
  • lines changed 10, context: html, text, full: html, text
    swap mm10 lastz done
  • lines changed 1, context: html, text, full: html, text
    running lastz for panTro3 ponAbe2
• src/hg/makeDb/doc/mm10.txt
  • lines changed 21, context: html, text, full: html, text
    swap mm10 to hg19 lastz done
  • lines changed 279, context: html, text, full: html, text
    running lastz for rn4 gorGor3 nomLeu1 and rheMac3
  • lines changed 139, context: html, text, full: html, text
    completed several lastz runs on mm10
  • lines changed 223, context: html, text, full: html, text
    running papHam1 saiBol1 calJac3 panTro4 tarSyr1 lastz
  • lines changed 7, context: html, text, full: html, text
    lastz runs to mm10 coming to completion
• src/hg/makeDb/doc/otoGar3.txt
  • lines changed 371, context: html, text, full: html, text
    initial browser built and masking started
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 49, context: html, text, full: html, text
    running lastz for panTro3 ponAbe2
  • lines changed 8, context: html, text, full: html, text
    lastz runs to mm10 coming to completion
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 66, context: html, text, full: html, text
    construct UCSC to Ensembl name translation and load v65 Ensembl genes
• src/hg/makeDb/doc/papHam1.txt
  • lines changed 22, context: html, text, full: html, text
    lastz runs to mm10 coming to completion
• src/hg/makeDb/doc/ponAbe2.txt
  • lines changed 49, context: html, text, full: html, text
    running lastz for panTro3 ponAbe2
  • lines changed 14, context: html, text, full: html, text
    completed several lastz runs on mm10
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Added fr3 assembly. New assembly to go out soon.
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    added new mm10 assembly
• src/hg/makeDb/schema/all.joiner
  • lines changed 27, context: html, text, full: html, text
    trying to make necessary changes to all.joiner and .sql files for qa
• src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html
  • lines changed 132, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/bushbaby/otoGar3/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/bushbaby/otoGar3/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl
• src/hg/makeDb/trackDb/chimp/panTro2/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing metaDb from panTro2
• src/hg/makeDb/trackDb/chimp/panTro2/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Removing metaDb from panTro2
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Removing metaDb from panTro2
• src/hg/makeDb/trackDb/cow/bosTau4/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing metaData on bosTau4
• src/hg/makeDb/trackDb/cow/bosTau4/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Removing metaData on bosTau4
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Removing metaData on bosTau4
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Found broken links on public. Correct stanzas with correct protocol document on alpha. Replaced lines with missing on beta and public to ensure links aren't broken and allow changes to propagate through cv review process.
  • lines changed 2, context: html, text, full: html, text
    Fixed broken links found by cron job. Fixed typo in RAD21 link for validation document in all cv's. Updated link for RFX5_(200-401-194).
  • lines changed 1, context: html, text, full: html, text
    Reset the tag for IMMORTAL from IMMOR to IMMORTAL.
  • lines changed 3, context: html, text, full: html, text
    provisional insertLength labels
  • lines changed 11, context: html, text, full: html, text
    provisional labels for fragSize
  • lines changed 10, context: html, text, full: html, text
    provisional labels for localizations
  • lines changed 31, context: html, text, full: html, text
    provisional labels for control
  • lines changed 8, context: html, text, full: html, text
    completing provisional labels
  • lines changed 3, context: html, text, full: html, text
    Changes that pertain to Redmine #7005 1. make tableName searchable: freeText 2. Update label for tableName to be "Table name at UCSC" 3. When choosing dropdown for "Table name at UCSC", change utils.js so this is no link to otherTerms.html page. For example see: "Treatment" 4. Remove subId "Submission ID" as being searchable on dev,beta and public.
  • lines changed 35, context: html, text, full: html, text
    Change descriptions for clarity and consistency (input from David H.)
  • lines changed 238, context: html, text, full: html, text
    Reverting my changes (to 44e3e62d724dc1e4b62ea72d18c2b7e263a43c09) so they can be merged in more coordinated fashion
  • lines changed 24, context: html, text, full: html, text
    Added back reigstration for BMDM cells after talking with lab to determine this was the correct registration and removed differentiation treatment as this is not needed now.
  • lines changed 2, context: html, text, full: html, text
    Fixed tags misspelling Provisional.
  • lines changed 1, context: html, text, full: html, text
    Removed term type as searchable as only a few datasets on hg18 have this metaData term. Redmine #7100.
  • lines changed 280, context: html, text, full: html, text
    Adding merged cell types, this is likely to cause a merge conflict with Willy's cv changes
  • lines changed 373, context: html, text, full: html, text
    Willy's changes to the urls and terms
  • lines changed 317, context: html, text, full: html, text
    Adding changes the Willy did to merge the donor cell types into one
  • lines changed 6, context: html, text, full: html, text
    A few updates from code review 7199
  • lines changed 4, context: html, text, full: html, text
    new labels for EtOH treatments, see ticket 4537
  • lines changed 36, context: html, text, full: html, text
    Fixing restriction enzymes, seq platform labels and adding BMDM cell line details
  • lines changed 2, context: html, text, full: html, text
    Making shRNA treatment generalizable to all cell lines
  • lines changed 91, context: html, text, full: html, text
    fixed gingeras slashes in tissues
  • lines changed 15, context: html, text, full: html, text
    Adding donorId
  • lines changed 99, context: html, text, full: html, text
    Fixing up PCR description, tissue definitions and removing provisional tags
  • lines changed 13, context: html, text, full: html, text
    Removing remaining provisional tags
  • lines changed 9, context: html, text, full: html, text
    Fixing blood tissue designations to match
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Found broken links on public. Correct stanzas with correct protocol document on alpha. Replaced lines with missing on beta and public to ensure links aren't broken and allow changes to propagate through cv review process.
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links found by cron job. Fixed typo in RAD21 link for validation document in all cv's. Updated link for RFX5_(200-401-194).
  • lines changed 733, context: html, text, full: html, text
    Moving CV updates from alpha to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 3, context: html, text, full: html, text
    Found broken links on public. Correct stanzas with correct protocol document on alpha. Replaced lines with missing on beta and public to ensure links aren't broken and allow changes to propagate through cv review process.
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links found by cron job. Fixed typo in RAD21 link for validation document in all cv's. Updated link for RFX5_(200-401-194).
  • lines changed 1264, context: html, text, full: html, text
    Changes approved from cv.ra review. Redmine #7200.
• src/hg/makeDb/trackDb/dog/canFam2/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing metaData from canFam2
• src/hg/makeDb/trackDb/dog/canFam2/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Removing metaData from canFam2
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Removing metaData from canFam2
• src/hg/makeDb/trackDb/human/hg18/knownGene.html
  • lines changed 13, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 8, context: html, text, full: html, text
    fixed dataVersions in hg18 tracks
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 7, context: html, text, full: html, text
    fixed dataVersions in hg18 tracks
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 22, context: html, text, full: html, text
    fixed dataVersions in hg18 tracks
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 2, context: html, text, full: html, text
    Fixing up NHGRI Bip hg18 metaData
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 32, context: html, text, full: html, text
    fixed dataVersions in hg18 tracks
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 902, context: html, text, full: html, text
    Matt made changes to hg18 metadata (redmine #6581)
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeChromatinMap.ra
  • lines changed 1534, context: html, text, full: html, text
    Matt made changes to hg18 metadata (redmine #6581)
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 5483, context: html, text, full: html, text
    Matt made changes to hg18 metadata (redmine #6581)
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeNhgriBip.ra
  • lines changed 4, context: html, text, full: html, text
    Moving Cricket's metadata updates to beta and public (redmine #7117)
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeYaleChIPseq.ra
  • lines changed 32, context: html, text, full: html, text
    Matt made changes to hg18 metadata (redmine #6581)
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 902, context: html, text, full: html, text
    Matt made changes to hg18 metadata (redmine #6581)
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeChromatinMap.ra
  • lines changed 1534, context: html, text, full: html, text
    Matt made changes to hg18 metadata (redmine #6581)
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 5483, context: html, text, full: html, text
    Matt made changes to hg18 metadata (redmine #6581)
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeNhgriBip.ra
  • lines changed 4, context: html, text, full: html, text
    Moving Cricket's metadata updates to beta and public (redmine #7117)
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeYaleChIPseq.ra
  • lines changed 32, context: html, text, full: html, text
    Matt made changes to hg18 metadata (redmine #6581)
• src/hg/makeDb/trackDb/human/hg18/wgRna.html
  • lines changed 4, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 10, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 5054, context: html, text, full: html, text
    Added many cell lines and tried to get the labels looking good
  • lines changed 51, context: html, text, full: html, text
    Adding the new metaData for sub 5768 which replaced 5120
  • lines changed 2495, context: html, text, full: html, text
    Adding a lot of data for Short and Long, fixing up the labels and the metaData
  • lines changed 1736, context: html, text, full: html, text
    Fixing the merge
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 3713, context: html, text, full: html, text
    Added many cell lines and tried to get the labels looking good
  • lines changed 162, context: html, text, full: html, text
    Adding a lot of data for Short and Long, fixing up the labels and the metaData
  • lines changed 6, context: html, text, full: html, text
    Fixing the merge
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 108, context: html, text, full: html, text
    revokoing entire Duke Affy Exon track
  • lines changed 1983, context: html, text, full: html, text
    replaced old submissions with V2's
  • lines changed 1008, context: html, text, full: html, text
    added in new submissions for duke affy exon
  • lines changed 153, context: html, text, full: html, text
    added md5sums
  • lines changed 215, context: html, text, full: html, text
    expIds and dccAccession for known ones
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
  • lines changed 8, context: html, text, full: html, text
    V4 has been replaced by V11
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylWgbs.ra
  • lines changed 10, context: html, text, full: html, text
    added md5sums and composite level metaData
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 7, context: html, text, full: html, text
    Removed sentence for object, on request by lab. Redmine #3794.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging GENCODE V11 on beta (redmine #6775)
  • lines changed 1, context: html, text, full: html, text
    Releasing GENCODE V11 to RR. Also unstaging GENCODE V4. (redmine #6775)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV11.ra
  • lines changed 295, context: html, text, full: html, text
    Staging GENCODE V11 on beta (redmine #6775)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV4.ra
  • lines changed 24, context: html, text, full: html, text
    V4 has been replaced by V11
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhHistone.ra
  • lines changed 58, context: html, text, full: html, text
    Matt made some metadata changes (redmine #6581)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 2, context: html, text, full: html, text
    Releasing GENCODE V11 to RR. Also unstaging GENCODE V4. (redmine #6775)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencodeV11.ra
  • lines changed 295, context: html, text, full: html, text
    Releasing GENCODE V11 to RR. Also unstaging GENCODE V4. (redmine #6775)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencodeV4.ra
  • lines changed 24, context: html, text, full: html, text
    V4 has been replaced by V11
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhHistone.ra
  • lines changed 58, context: html, text, full: html, text
    Matt made some metadata changes (redmine #6581)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging GENCODE V11 on beta (redmine #6775)
  • lines changed 2, context: html, text, full: html, text
    removed extra includes for dead RRBS track
  • lines changed 6, context: html, text, full: html, text
    addin in patch files for matrix and other corrections in uw tracks
  • lines changed 6, context: html, text, full: html, text
    Applied Matt's patches (redmine #7183)
  • lines changed 2, context: html, text, full: html, text
    Releasing GENCODE V11 to RR. Also unstaging GENCODE V4. (redmine #6775)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
  • lines changed 885, context: html, text, full: html, text
    Added many cell lines and tried to get the labels looking good
  • lines changed 605, context: html, text, full: html, text
    Adding a lot of data for Short and Long, fixing up the labels and the metaData
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 865, context: html, text, full: html, text
    Added many cell lines and tried to get the labels looking good
  • lines changed 896, context: html, text, full: html, text
    Adding a lot of data for Short and Long, fixing up the labels and the metaData
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra
  • lines changed 869, context: html, text, full: html, text
    revokoing entire Duke Affy Exon track
  • lines changed 830, context: html, text, full: html, text
    replaced old submissions with V2's
  • lines changed 441, context: html, text, full: html, text
    added in new submissions for duke affy exon
  • lines changed 1, context: html, text, full: html, text
    changed html tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
  • lines changed 4, context: html, text, full: html, text
    Corrected a spelling error. Added a link to the PubMed article that Mark D referenced for Exonerate. (redmine #6775)
  • lines changed 1, context: html, text, full: html, text
    Changed the text in the link to The GENCODE Project page in the Release Notes section (redmine #6775)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
  • lines changed 1, context: html, text, full: html, text
    changed to ascii apostrophe
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
  • lines changed 38, context: html, text, full: html, text
    trackDb fixes for track functionality
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
  • lines changed 3, context: html, text, full: html, text
    removing k562/NaBut from defaults
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 2, context: html, text, full: html, text
    Changing the track name to the table name to deal with the issue in ticket 7222
  • lines changed 2, context: html, text, full: html, text
    Changing for H3K4Me3 according to ticket #7222
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.release2.ra
  • lines changed 2, context: html, text, full: html, text
    Changing the track name to the table name since no other composite is using this table, see ticket 7083
  • lines changed 2, context: html, text, full: html, text
    Changing for H3K4Me3 according to ticket #7222
• src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
  • lines changed 16, context: html, text, full: html, text
    reformed refereces properly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html
  • lines changed 24, context: html, text, full: html, text
    First round of fixes for U Mass 5C, fixed grammar issues, did some rewording, removed references to shading since this track is unable to have this capability, and fixed credits, redmine# 225
  • lines changed 3, context: html, text, full: html, text
    Second round of fixes for U Mass 5C, added ascii character, rearranaged and fixed more typos, redmine# 225
  • lines changed 1, context: html, text, full: html, text
    forgot to save my previous change before committing, this commit adds the ascii character for UMass 5C, redmine# 225
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassTfbsValid.html
  • lines changed 69, context: html, text, full: html, text
    This is my first draft at making a TFBSValid track, it is not a functional track but a place holder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassTfbsValid.ra
  • lines changed 11, context: html, text, full: html, text
    This is my first draft at making a TFBSValid track, it is not a functional track but a place holder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.patch.ra
  • lines changed 1488, context: html, text, full: html, text
    addin in patch files for matrix and other corrections in uw tracks
  • lines changed 1488, context: html, text, full: html, text
    Applied Matt's patches (redmine #7183)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.ra
  • lines changed 13, context: html, text, full: html, text
    Applied Matt's patches (redmine #7183)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
  • lines changed 1383, context: html, text, full: html, text
    addin in patch files for matrix and other corrections in uw tracks
  • lines changed 5953, context: html, text, full: html, text
    Applied Matt's patches (redmine #7183)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
  • lines changed 27, context: html, text, full: html, text
    Applied Matt's patches (redmine #7183)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.patch.ra
  • lines changed 3582, context: html, text, full: html, text
    addin in patch files for matrix and other corrections in uw tracks
  • lines changed 3582, context: html, text, full: html, text
    Applied Matt's patches (redmine #7183)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.ra
  • lines changed 10, context: html, text, full: html, text
    Applied Matt's patches (redmine #7183)
• src/hg/makeDb/trackDb/human/hg19/wgRna.html
  • lines changed 4, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/human/hgIkmc.html
  • lines changed 4, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/human/kiddEichlerDisc.html
  • lines changed 11, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/human/kiddEichlerValid.html
  • lines changed 3, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding otoGar3 to the build
• src/hg/makeDb/trackDb/mouse/ikmc.html
  • lines changed 4, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/mouse/komp.html
  • lines changed 4, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/mouse/mm10/description.html
  • lines changed 5, context: html, text, full: html, text
    made correction to assembly details section
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.chainNet.ra
  • lines changed 226, context: html, text, full: html, text
    grouping primate chain net tracks into one control
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    grouping primate chain net tracks into one control
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 8, context: html, text, full: html, text
    alphabetizing
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 1847, context: html, text, full: html, text
    update metaDb with new submissions
  • lines changed 1223, context: html, text, full: html, text
    add new MEL submission data
  • lines changed 599, context: html, text, full: html, text
    update new submission of BMDM cells
  • lines changed 283, context: html, text, full: html, text
    add expId for the new submissions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    update metaDb with new submissions
  • lines changed 155, context: html, text, full: html, text
    add new MEL submission data
  • lines changed 155, context: html, text, full: html, text
    update with new submission, clean up short, long label
  • lines changed 155, context: html, text, full: html, text
    update new submission of BMDM cells
  • lines changed 37, context: html, text, full: html, text
    add expId for the new submissions
  • lines changed 19, context: html, text, full: html, text
    added md5sums with encodeMkFilesList
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 131, context: html, text, full: html, text
    update metaDb with new submissions
  • lines changed 443, context: html, text, full: html, text
    add new MEL submission data
  • lines changed 443, context: html, text, full: html, text
    update new submission of BMDM cells
  • lines changed 79, context: html, text, full: html, text
    add expId for the new submissions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 3, context: html, text, full: html, text
    Swapped grant and lab
  • lines changed 1, context: html, text, full: html, text
    Adding composite line in the metaDb to hopefully be able to make on beta
  • lines changed 4, context: html, text, full: html, text
    Trying to add magic number to see if that helps beta
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Added wgEncodeNhgriBip.ra to beta and modified beta makefile (redmine #7117)
  • lines changed 1, context: html, text, full: html, text
    Removed blank line from top of makefile
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeNhgriBip.ra
  • lines changed 12, context: html, text, full: html, text
    Added wgEncodeNhgriBip.ra to beta and modified beta makefile (redmine #7117)
  • lines changed 1, context: html, text, full: html, text
    Adding composite line in the metaDb to hopefully be able to make on beta
  • lines changed 4, context: html, text, full: html, text
    Trying to add magic number to see if that helps beta
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
  • lines changed 2, context: html, text, full: html, text
    Moved .ra file from beta to public and added to public makefile (redmine #7117)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeNhgriBip.ra
  • lines changed 15, context: html, text, full: html, text
    Moved .ra file from beta to public and added to public makefile (redmine #7117)
• src/hg/makeDb/trackDb/mouse/mm9/rest.html
  • lines changed 6, context: html, text, full: html, text
    Changed old font tags to span to fix display issues in some browser/os combos per redmine 6850. Fixed a couple minor html formatting issues while I was at it. Made a few tags lowercase.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removing the metaDb line from trackDb
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html
  • lines changed 189, context: html, text, full: html, text
    made release2 html by copying release1 html
  • lines changed 36, context: html, text, full: html, text
    added information of new sample, new experiments for the new submission, added release note to Histone and Tfbs
  • lines changed 4, context: html, text, full: html, text
    update release note to inlcude newly submitted experiments
  • lines changed 3, context: html, text, full: html, text
    update release notes
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra
  • lines changed 219, context: html, text, full: html, text
    remove stanz of macrophages derived from bone marrow and related entries: stanzas, treatment subgroups, age=IMMORT, treatment=None
  • lines changed 177, context: html, text, full: html, text
    clean up short, long labels
  • lines changed 1, context: html, text, full: html, text
    added IMMORTAL=immortalized in age subgroup
  • lines changed 135, context: html, text, full: html, text
    add new MEL submission data
  • lines changed 31, context: html, text, full: html, text
    clean up short and long labels
  • lines changed 1, context: html, text, full: html, text
    add age as selected dimensions
  • lines changed 1, context: html, text, full: html, text
    add filterComposite dimensionA=multi
  • lines changed 1, context: html, text, full: html, text
    made release2 html by copying release1 html
  • lines changed 55, context: html, text, full: html, text
    update viewLimits
  • lines changed 75, context: html, text, full: html, text
    set default displaying subtracks
  • lines changed 2, context: html, text, full: html, text
    changed peak visibility default to dense
  • lines changed 64, context: html, text, full: html, text
    update new submission of BMDM cells
  • lines changed 17, context: html, text, full: html, text
    clean up short, long labels for new submission of BMDM cells
  • lines changed 1, context: html, text, full: html, text
    change visibility from defaults setting of dense to pack
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html
  • lines changed 9, context: html, text, full: html, text
    added information of new sample, new experiments for the new submission, added release note to Histone and Tfbs
  • lines changed 4, context: html, text, full: html, text
    update release note to inlcude newly submitted experiments
  • lines changed 3, context: html, text, full: html, text
    update release notes
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra
  • lines changed 40, context: html, text, full: html, text
    remove stanza submitted in 03/12 and relevant changes
  • lines changed 76, context: html, text, full: html, text
    remove treatment=None from all the stanza after removing treatment from the parent treatment subgroup
  • lines changed 1, context: html, text, full: html, text
    added IMMORTAL=immortalized in age subgroup
  • lines changed 38, context: html, text, full: html, text
    add new MEL submission data
  • lines changed 9, context: html, text, full: html, text
    clean up short and long labels
  • lines changed 36, context: html, text, full: html, text
    update with new submission, clean up short, long label
  • lines changed 1, context: html, text, full: html, text
    update viewLimits
  • lines changed 18, context: html, text, full: html, text
    set default displaying subtracks
  • lines changed 37, context: html, text, full: html, text
    update new submission of BMDM cells
  • lines changed 8, context: html, text, full: html, text
    clean up short, long labels for new submission of BMDM cells
  • lines changed 1, context: html, text, full: html, text
    clean up long label in title
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html
  • lines changed 189, context: html, text, full: html, text
    made release2 html by copying release1 html
  • lines changed 40, context: html, text, full: html, text
    added information of new sample, new experiments for the new submission, added release note to Histone and Tfbs
  • lines changed 4, context: html, text, full: html, text
    update release note to inlcude newly submitted experiments
  • lines changed 3, context: html, text, full: html, text
    update release note
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra
  • lines changed 133, context: html, text, full: html, text
    remove entries related with macrophages derived from bone marrow: stanzas, treatment subgroup, age=IMMORT, treatment=None
  • lines changed 2, context: html, text, full: html, text
    clean up long label
  • lines changed 1, context: html, text, full: html, text
    added IMMORTAL=immortalized in age subgroup
  • lines changed 45, context: html, text, full: html, text
    add new MEL submission data
  • lines changed 98, context: html, text, full: html, text
    clean up short and long labels
  • lines changed 5, context: html, text, full: html, text
    clean up shorlabels
  • lines changed 2, context: html, text, full: html, text
    add age as multi-selectable dimension
  • lines changed 1, context: html, text, full: html, text
    made release2 html by copying release1 html
  • lines changed 24, context: html, text, full: html, text
    update viewLimits
  • lines changed 43, context: html, text, full: html, text
    set default displaying subtracks
  • lines changed 1, context: html, text, full: html, text
    change defult peak display from dense to pack
  • lines changed 1, context: html, text, full: html, text
    changed peak visibility default to dense
  • lines changed 46, context: html, text, full: html, text
    update new submission of BMDM cells
  • lines changed 12, context: html, text, full: html, text
    clean up short, long labels for new submission of BMDM cells
  • lines changed 1, context: html, text, full: html, text
    change visibility from defaults setting of dense to pack
• src/hg/makeDb/trackDb/rat/rn4/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing metaData from rn4
• src/hg/makeDb/trackDb/rat/rn4/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Removing metaData from rn4
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Removing metaData from rn4
• src/hg/makeDb/trackDb/rhesus/rheMac2/metaDb/alpha/makefile
  • lines changed 4, context: html, text, full: html, text
    Removing metaDb from panTro2
• src/hg/makeDb/trackDb/rhesus/rheMac2/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 14, context: html, text, full: html, text
    Removing metaDb from panTro2
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Removing metaDb from panTro2
• src/hg/makeDb/trackDb/t2g.html
  • lines changed 54, context: html, text, full: html, text
    publications track description changes and fix for bold text bug see redmine #6833
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fixing stupid trackDb that crashed build
• src/hg/utils/automation/grcIncidentDb.pl
  • lines changed 303, context: html, text, full: html, text
    updated to new XML schema from NCBI
• src/hg/utils/automation/ncbiIncidentDb.pl
  • lines changed 174, context: html, text, full: html, text
    updated to new NCBI XML schema
• src/hg/utils/omim/omimWrapper.sh
  • lines changed 2, context: html, text, full: html, text
    some small fixes to run out of my crontab (#6943)
• src/hg/utils/omim/validateOmim.sh
  • lines changed 2, context: html, text, full: html, text
    fix typo and put difference ratio back to 10% (#6943)
• src/utils/qa/makeUniProtFile.csh
  • lines changed 15, context: html, text, full: html, text
    Added a new special case for rn4 (it now uses RGD Genes instead of a UCSC Genes build) and got rid of the checking the gdbPdb table to determine whether an assembly is a UCSC Genes assembly. Added a comment to the usage that the script should be checked to see if it is using up-to-date tables.
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    Added runCheckHgFindSpec to makefile.
• src/utils/qa/qaGbTracks
  • lines changed 82, context: html, text, full: html, text
    Starting qaGbTracks, which will take a database and a list of tables and run applicable QA tests. It is intended to be a fast starting point for Genome Browser project track QA. So far, this is just a copy of qaEncodeTracks2 with some style adjustments. (Redmine #7224)
• src/utils/qa/runCheckHgFindSpec
  • lines changed 29, context: html, text, full: html, text
    Checking in runCheckHgFindSpec, which is running on the qateam crontab. Redmine #5880.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v265 preview1
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    Ann requested this change so that she can keep her thumb on her victims.

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• files changed: 306