All File Changes

v274_preview to v274_preview2 (2012-09-25 to 2012-10-02) v274

• python/lib/ucscGb/qa/tables/factory.py
  • lines changed 1, context: html, text, full: html, text
    Added vcfTabix to pointer track types.
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 16, context: html, text, full: html, text
    Changed formatting of count/megabase numbers in countPerChrom to shorten output. Also sent featureBits commands and output to reporter (requested by QAers). Redmine 9075#note-13 and 7224#note-17.
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 2, context: html, text, full: html, text
    Pulled the serif style declaration out of the code so the font style is left up to the css.
• src/hg/hgGene/domains.c
  • lines changed 1, context: html, text, full: html, text
    change link to Interpro graphical view of domains in hgGene. This really shouldn't be in the source, but it is! (#9206)
• src/hg/hgLogin/hgLogin.c
  • lines changed 4, context: html, text, full: html, text
    Found consistent cookie dates that safari likes. Do not go beyond end of 2037 yet for signed 32-bit integer. Added semi-colon to the end of the path just to be sure.
  • lines changed 51, context: html, text, full: html, text
    Bug #9151 Missing username information in hgLogin forgot password confirmation message.
• src/hg/hgTables/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    hgTables schema page was using hub (sub)trackDb's without ->html;refactored html-fetching code out of hubConnectAddHubForTrackAndFindTdb
    and into new hubConnectAddDescription. Also fixed the code to work
    for subtracks (instead of assigning tdb->html to parents, if tdb->html
    is empty, recurse up parents until we find a non-empty ->html and assign
    that to tdb).
    
• src/hg/hgTables/schema.c
  • lines changed 12, context: html, text, full: html, text
    hgTables schema page was using hub (sub)trackDb's without ->html;refactored html-fetching code out of hubConnectAddHubForTrackAndFindTdb
    and into new hubConnectAddDescription. Also fixed the code to work
    for subtracks (instead of assigning tdb->html to parents, if tdb->html
    is empty, recurse up parents until we find a non-empty ->html and assign
    that to tdb).
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    setting the track limits to be more liberal as advised by Jim Kent
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    setting the track limits to be more liberal as advised by Jim Kent
  • lines changed 1, context: html, text, full: html, text
    use proteome.spXref3 instead of depricated proteom.spXref2 to decide what color to make known genes on assemblies that don't have kgColor table. (#8694)
• src/hg/htdocs/ENCODE/index.html
  • lines changed 72, context: html, text, full: html, text
    Update ENCODE News to include Sept. data releases
  • lines changed 26, context: html, text, full: html, text
    reviewing Kate's Spet 20 & 25 news updates: made use of : consistent, added in line breaks at 100 characters for easier editing
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    Update ENCODE News to include Sept. data releases
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    hgTables schema page was using hub (sub)trackDb's without ->html;refactored html-fetching code out of hubConnectAddHubForTrackAndFindTdb
    and into new hubConnectAddDescription. Also fixed the code to work
    for subtracks (instead of assigning tdb->html to parents, if tdb->html
    is empty, recurse up parents until we find a non-empty ->html and assign
    that to tdb).
    
• src/hg/lib/dhcHumDerDenAnc.as
  • lines changed 27, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Added composite track from Denisovaanalysis: sites where humans have a derived allele relative to chimp,
    gorilla, and/or orangutan, and Denisova had the ancestral allele;
    plus VEP annotations of predicted functional consequence.
    
• src/hg/lib/hubConnect.c
  • lines changed 47, context: html, text, full: html, text
    hgTables schema page was using hub (sub)trackDb's without ->html;refactored html-fetching code out of hubConnectAddHubForTrackAndFindTdb
    and into new hubConnectAddDescription. Also fixed the code to work
    for subtracks (instead of assigning tdb->html to parents, if tdb->html
    is empty, recurse up parents until we find a non-empty ->html and assign
    that to tdb).
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 59, context: html, text, full: html, text
    patch 10 for hg19/GRCh37
  • lines changed 191, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Added composite track from Denisovaanalysis: sites where humans have a derived allele relative to chimp,
    gorilla, and/or orangutan, and Denisova had the ancestral allele;
    plus VEP annotations of predicted functional consequence.
    
• src/hg/makeDb/doc/hg19Patch10.txt
  • lines changed 501, context: html, text, full: html, text
    patch 10 for hg19/GRCh37
• src/hg/makeDb/doc/mm10Patch1.txt
  • lines changed 480, context: html, text, full: html, text
    constructed mm10Patch1 browser and tracks on mm10
• src/hg/makeDb/doc/mm10Strains1.txt
  • lines changed 181, context: html, text, full: html, text
    initial database build for mouse strain sequences
• src/hg/makeDb/doc/saiBol1.txt
  • lines changed 2, context: html, text, full: html, text
    fixup assembly ID redmine issue 8887 question 47
• src/hg/makeDb/genbank/src/dbload/gbBuildState.c
  • lines changed 1, context: html, text, full: html, text
    fix typo
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 9, context: html, text, full: html, text
    Removed temporary restriction from validating tags on 'strict' which had been added as n ugly work around because the RR already had bad tags released. The RR has now been cleaned up. This should be the final stone in redmine 6813.
• src/hg/makeDb/schema/all.joiner
  • lines changed 7, context: html, text, full: html, text
    fixup xenoRefGene and ensembl database listings, and a couple of new chains, redmine 8887
• src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 5, context: html, text, full: html, text
    fixed term names to not have commas
  • lines changed 0, context: html, text, full: html, text
    removing trailing white spaces
  • lines changed 8, context: html, text, full: html, text
    Changing link, updating vendorId, and adding accents to vendorName for Dr. Lazlo Tora's antibodies
  • lines changed 1, context: html, text, full: html, text
    removing colon to make link work for H3K9Ac_(39137)(Dot_blot,Western_blot)
  • lines changed 1, context: html, text, full: html, text
    Fixing link in cv
  • lines changed 9, context: html, text, full: html, text
    Adding as many of the document names for Tenebaum again, ticket 9159
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 5, context: html, text, full: html, text
    Patching the fix to take out the commas in the term names
  • lines changed 0, context: html, text, full: html, text
    removing trailing white spaces
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 573, context: html, text, full: html, text
    releasing reviewed cv.ra changes to public
• src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/gadMor/gadMor1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/hedgehog/eriEur1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    Fixing the defualts
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Fixing the default tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 4002, context: html, text, full: html, text
    fixing broad histone metadata
  • lines changed 808, context: html, text, full: html, text
    Changed the seqPlatform to have the terms instead of the labels. This brought up and issue for ones that had multiple platforms. See ticket 9210.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 74, context: html, text, full: html, text
    accessioned CSHL long & short, and riken, finishing the files for these tracks
  • lines changed 17, context: html, text, full: html, text
    Adding in seqPlatform info
  • lines changed 261, context: html, text, full: html, text
    Adding in the protocol docs
  • lines changed 11, context: html, text, full: html, text
    Getting the file name extensions correct
  • lines changed 11, context: html, text, full: html, text
    Adding md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 14, context: html, text, full: html, text
    accessioned CSHL long & short, and riken, finishing the files for these tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 3, context: html, text, full: html, text
    revoked bad experiment 599
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 24, context: html, text, full: html, text
    accessioned CSHL long & short, and riken, finishing the files for these tracks
  • lines changed 2, context: html, text, full: html, text
    Something happened with an md5sum. I think someone must have unzipped the file
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 4002, context: html, text, full: html, text
    Updating metaData for platforms on Broad Histon RM#9210
  • lines changed 808, context: html, text, full: html, text
    ReUpdating metaDB for Broad Histone RM#9210, earlier commit 02f8b1a0065f090fe80c988816676c363a71c7c1
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 350, context: html, text, full: html, text
    Staging on public,updating beta metaDb, CSHL Long RNA-seq (Release 3) RM7907
  • lines changed 11, context: html, text, full: html, text
    Restaging metaDb for public/beta CSHL Long RNA-seq (Release 3) RM#7907
  • lines changed 11, context: html, text, full: html, text
    Staging public/beta metaData md5sums for protocols for CSHL Long RNA-seq (Release 3) RM#7907
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlShortRnaSeq.ra
  • lines changed 14, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
  • lines changed 3, context: html, text, full: html, text
    release updated metadata (expId=599 were revoked because they were bad data and were already replaced under a different name), redmine #9157
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 25, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyTiling.ra
  • lines changed 10, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUchicagoTfbs.ra
  • lines changed 2856, context: html, text, full: html, text
    Unstaging the metaData for the rejected track
  • lines changed 166, context: html, text, full: html, text
    Adding the md5sums, the geoAccessions, and the bai filenames to the metadata since we are not having a release2
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 4002, context: html, text, full: html, text
    Updating metaData for platforms on Broad Histon RM#9210
  • lines changed 808, context: html, text, full: html, text
    ReUpdating metaDB for Broad Histone RM#9210, earlier commit 02f8b1a0065f090fe80c988816676c363a71c7c1
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 8931, context: html, text, full: html, text
    Staging on public,updating beta metaDb, CSHL Long RNA-seq (Release 3) RM7907
  • lines changed 11, context: html, text, full: html, text
    Restaging metaDb for public/beta CSHL Long RNA-seq (Release 3) RM#7907
  • lines changed 11, context: html, text, full: html, text
    Staging public/beta metaData md5sums for protocols for CSHL Long RNA-seq (Release 3) RM#7907
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlShortRnaSeq.ra
  • lines changed 14, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromChip.ra
  • lines changed 3, context: html, text, full: html, text
    release updated metadata (expId=599 were revoked because they were bad data and were already replaced under a different name), redmine #9157
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
  • lines changed 25, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyAlbanyTiling.ra
  • lines changed 10, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUchicagoTfbs.ra
  • lines changed 166, context: html, text, full: html, text
    releasing metadata fixes, redmine #5697, note 59
• src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
  • lines changed 394, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): Added composite track from Denisovaanalysis: sites where humans have a derived allele relative to chimp,
    gorilla, and/or orangutan, and Denisova had the ancestral allele;
    plus VEP annotations of predicted functional consequence.
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging on public,updating beta metaDb, CSHL Long RNA-seq (Release 3) RM7907
  • lines changed 2, context: html, text, full: html, text
    Not releasing Release 2 of UChicago TFBS. Copied updated Release 2 html file back to Release 1 and edited release tags (redmine #5697)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.html
  • lines changed 35, context: html, text, full: html, text
    inserting pubmed publications 2012 Gingeras for CSHL Long RNA-seq (Release#3) RM#7907
  • lines changed 28, context: html, text, full: html, text
    Fixes from ticket 7907 note 52
  • lines changed 3, context: html, text, full: html, text
    fixing the gingeras email
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.ra
  • lines changed 38, context: html, text, full: html, text
    Short label and defualts
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 1, context: html, text, full: html, text
    Adding the geo accession column
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
  • lines changed 158, context: html, text, full: html, text
    Not releasing Release 2 of UChicago TFBS. Copied updated Release 2 html file back to Release 1 and edited release tags (redmine #5697)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 33, context: html, text, full: html, text
    Making the changes from release2 that we would like to leak. See http://redmine.soe.ucsc.edu/issues/5697#note-56
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra
  • lines changed 4, context: html, text, full: html, text
    Changing small typos to clean up a diff for release1 and release2
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.html
  • lines changed 21, context: html, text, full: html, text
    grouping the more general config info together and other small edits, redmine 8419 note 139
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.html
  • lines changed 1, context: html, text, full: html, text
    added supplemental link
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding mm10Strains1 to the build
• src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Alterning trackvisibilities per redmine 8887#note-30
• src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/mouse/altSeqComposite.html
  • lines changed 236, context: html, text, full: html, text
    adding GRC patch release html
  • lines changed 9, context: html, text, full: html, text
    fixup chrom 14 color key and FTP site at NCBI
  • lines changed 19, context: html, text, full: html, text
    remove references to haplotypes
• src/hg/makeDb/trackDb/mouse/mm10/altSeqComposite1.ra
  • lines changed 104, context: html, text, full: html, text
    adding the altSeqComposite1 tracks
  • lines changed 14, context: html, text, full: html, text
    remove all references to haplotypes
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 31, context: html, text, full: html, text
    Small grammar/punctuation changes, removed no-longer-relevant remarks, made text reflect change from 5 to 4 groups (glires, euarchontoglires, placental mammals, all vertebrates), alphabetized tree shrew in table 1, changed gene track names to their shortLabels in table 2, updated a publication date.
  • lines changed 2, context: html, text, full: html, text
    Small wording changes for consistency.
  • lines changed 21, context: html, text, full: html, text
    Moved links to downloads to top of description page to make them easier to find.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 5, context: html, text, full: html, text
    Changed Placental to Placental Mammal in multiz track controls and in longLabels.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding the altSeqComposite1 tracks
• src/hg/makeDb/trackDb/mouse/mm10Patch1/trackDb.ra
  • lines changed 30, context: html, text, full: html, text
    add the altSequence and chain to mm10 tracks
• src/hg/makeDb/trackDb/mouse/mm10Strains1/description.html
  • lines changed 63, context: html, text, full: html, text
    mm10 haplotypes (other mouse strains)
• src/hg/makeDb/trackDb/mouse/mm10Strains1/gap.html
  • lines changed 31, context: html, text, full: html, text
    mm10 haplotypes (other mouse strains)
• src/hg/makeDb/trackDb/mouse/mm10Strains1/gold.html
  • lines changed 34, context: html, text, full: html, text
    mm10 haplotypes (other mouse strains)
• src/hg/makeDb/trackDb/mouse/mm10Strains1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    mm10 haplotypes (other mouse strains)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 24, context: html, text, full: html, text
    updated md5sums
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 21, context: html, text, full: html, text
    changed values to not have commas
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrHistone.ra
  • lines changed 6, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added (mm9)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrTfbs.ra
  • lines changed 15, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added (mm9)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added (mm9)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 24, context: html, text, full: html, text
    Staging metaDb for mm9 UwDgf for double compression md5sum RM#8477
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 21, context: html, text, full: html, text
    releasing update to metadata fixing the EPC tissues to remove , and put in _ instead because the commas were breaking hgEncodeVocab, redmine 4468, note 79
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrHistone.ra
  • lines changed 6, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added (mm9)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrTfbs.ra
  • lines changed 15, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added (mm9)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    releasing more GEO numbers that Morgan added (mm9)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 24, context: html, text, full: html, text
    Staging metaDb for mm9 UwDgf for double compression md5sum RM#8477
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 10508, context: html, text, full: html, text
    Releasing UW DNaseI HS (Release 2) to the RR (redmine #4468)
  • lines changed 21, context: html, text, full: html, text
    releasing update to metadata fixing the EPC tissues to remove , and put in _ instead because the commas were breaking hgEncodeVocab, redmine 4468, note 79
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Releasing UW DNaseI HS (Release 2) to the RR (redmine #4468)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.html
  • lines changed 1, context: html, text, full: html, text
    added in more release notes
  • lines changed 1, context: html, text, full: html, text
    Corrected a typo (redmine #4468)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
  • lines changed 222, context: html, text, full: html, text
    Edited long and short labels (redmine #4468)
• src/hg/makeDb/trackDb/mouseLemur/micMur1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/oreNil/oreNil2/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/pika/ochPri2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/rhesus/rheMac3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Set so names/short labels would appear correct: ex. Rat rather than rn4.
• src/hg/makeDb/trackDb/rockHyrax/proCap1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/saiBol/saiBol1/description.html
  • lines changed 2, context: html, text, full: html, text
    fixup assembly ID redmine issue 8887 question 47
• src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/shrew/sorAra1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/sloth/choHof1/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/tarsier/tarSyr1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Made track visibility changes per redmine 8887#note-30, and making sure the display is appealing.
• src/hg/utils/automation/configFiles/saiBol1.config.ra
  • lines changed 1, context: html, text, full: html, text
    fixup assembly ID redmine issue 8887 question 47
• src/hg/utils/twoBitMask/twoBitMask.c
  • lines changed 2, context: html, text, full: html, text
    took out bogus check to see if output file was a 2bit file. This check used to just make sure that the name ended in .2bit, but now it actually opens the file to look for a signature. I don't think we should have twoBitMask enforce filenames ending in .2bit
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v274 preview1
  • lines changed 2, context: html, text, full: html, text
    v274 preview2

• lines changed: 42211
• files changed: 148