All File Changes

v258_preview to v258_preview2 (2011-09-27 to 2011-10-04) v258

• python/lib/ucscgenomics/cv.py
  • lines changed 2, context: html, text, full: html, text
    fixed the cv Validator
• python/programs/cvValidate/cvValidate
  • lines changed 2, context: html, text, full: html, text
    fixed the cv Validator
• src/hg/encode/DAFs/3.0/hg19/wgEncodeBuOrchid.daf
  • lines changed 33, context: html, text, full: html, text
    Adding more DAFs to the 3.0 directory
• src/hg/encode/DAFs/3.0/hg19/wgEncodeHaibTfbs.daf
  • lines changed 10, context: html, text, full: html, text
    Adding more DAFs to the 3.0 directory
• src/hg/encode/DAFs/3.0/hg19/wgEncodeOpenChromSynth.daf
  • lines changed 28, context: html, text, full: html, text
    Adding more DAFs to the 3.0 directory
• src/hg/encode/encodeAnnounce/encodeAnnounce.pl
  • lines changed 1, context: html, text, full: html, text
    Minor cleanup (remove double slashes where single can do)
• src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl
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    cleaned up some whitespace stuff
• src/hg/hgCustom/hgCustom.c
  • lines changed 4, context: html, text, full: html, text
    Feature #986 (VCF+tabix): mention VCF in hgCustom's list of supported formats.
• src/hg/hgTracks/hgTracks.c
  • lines changed 32, context: html, text, full: html, text
    moved PS/PDF and Sessions links in topbar to the left of NCBI and Ensembl links so they are onscreen in narrow windows
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    cleanup based on angie's code review comments
• src/hg/hgTracks/makefile.hgRenderTracks
  • lines changed 2, context: html, text, full: html, text
    cleanup based on angie's code review comments
• src/hg/hgc/hgc.c
  • lines changed 7, context: html, text, full: html, text
    Updated logic of omimGene2 for RefSeq to deal with if previous RefSeq no longer available.
  • lines changed 68, context: html, text, full: html, text
    put back logic to handle geneReviews track using the geneReviews table in the database
  • lines changed 11, context: html, text, full: html, text
    Do not do geneReviews for non-human species
• src/hg/hgc/hgc.h
  • lines changed 6, context: html, text, full: html, text
    put back logic to handle geneReviews track using the geneReviews table in the database
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 10, context: html, text, full: html, text
    adding UNC/BSE ProtGeno and its supertrack, redmine 141
• src/hg/htdocs/ENCODE/index.html
  • lines changed 36, context: html, text, full: html, text
    Add Summer human data releases. TODO: retire older ones to news archives. TODO: Add late summer Mouse
  • lines changed 1, context: html, text, full: html, text
    Tweak to title
  • lines changed 6, context: html, text, full: html, text
    removing extraneous '/' from the urls
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 10, context: html, text, full: html, text
    Added lines to the GFF and GenePred sections referring users to the wiki article for converting from GenePred to GTF
  • lines changed 4, context: html, text, full: html, text
    Fixed grammatical error
  • lines changed 52, context: html, text, full: html, text
    Feature #986 (VCF+tabix): Added VCF to FAQformat.
• src/hg/htdocs/contacts.html
  • lines changed 3, context: html, text, full: html, text
    added link to PLoS article on how to get help from scientific communities
• src/hg/htdocs/goldenPath/help/GTF.html
  • lines changed 7, context: html, text, full: html, text
    Added a line referring users to the wiki article for converting from GenePred to GTF
  • lines changed 7, context: html, text, full: html, text
    Changed the order of the last three sentences
  • lines changed 2, context: html, text, full: html, text
    Changed the link to WUStL to a more recent page
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    Feature #986 (VCF+tabix): link to vcf.html from help docs forcustom tracks and track hubs.
  • lines changed 3, context: html, text, full: html, text
    Feature #986 (VCF+tabix): Added VCF to FAQformat.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 22, context: html, text, full: html, text
    Feature #986 (VCF+tabix): link to vcf.html from help docs forcustom tracks and track hubs.
• src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
  • lines changed 89, context: html, text, full: html, text
    Adding help page for VCF track options in hgTrackUi.
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 2, context: html, text, full: html, text
    Updated VCF format spec URL to latest version.
  • lines changed 13, context: html, text, full: html, text
    Feature #986 (VCF+tabix): updated vcf.html w/new example files.
• src/hg/htdocs/images/euFlag.gif
  • lines changed 0, context: html, text, full: html, text
    adding icons to use with euroNode
• src/hg/htdocs/images/phylo/xenTro3_9way.png
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    initial diagram for xenTro3 9-way alignment
• src/hg/htdocs/images/usFlag.gif
  • lines changed 0, context: html, text, full: html, text
    adding icons to use with euroNode
• src/hg/inc/hdb.h
  • lines changed 13, context: html, text, full: html, text
    Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
• src/hg/inc/mdb.h
  • lines changed 8, context: html, text, full: html, text
    Added in '-or' and ' || ' support to mdbPrint/mdbUpdate selections
• src/hg/js/jquery.tablednd.js
  • lines changed 2, context: html, text, full: html, text
    UCSC specific mods to table DnD broke subtrack DnD. Now fixed. Redmine 5494
• src/hg/lib/hdb.c
  • lines changed 38, context: html, text, full: html, text
    Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
  • lines changed 1, context: html, text, full: html, text
    Added a define back in that was accidentally removed.
• src/hg/lib/mdb.c
  • lines changed 10, context: html, text, full: html, text
    Made things a little less awkward for deleting vars
  • lines changed 3, context: html, text, full: html, text
    Added in '-or' and ' || ' support to mdbPrint/mdbUpdate selections
• src/hg/lib/vcfUi.c
  • lines changed 5, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI): make sure link to hgVcfTrackHelp.htmlappears when boxed=TRUE in vcfCfgUi (already there for boxed=FALSE).
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
  • lines changed 184, context: html, text, full: html, text
    updated notes file
  • lines changed 89, context: html, text, full: html, text
    updated notes
  • lines changed 7, context: html, text, full: html, text
    updated notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes
  • lines changed 13, context: html, text, full: html, text
    updated notes files for unc bsu prot
• src/hg/makeDb/doc/hg18.txt
  • lines changed 19, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 107, context: html, text, full: html, text
    new hgPal downloads for new knownGene
  • lines changed 7, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): bi-monthly update.
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 60, context: html, text, full: html, text
    rerun xenTro3 lastz with parameters that produce a bit more coverage
• src/hg/makeDb/doc/proteins/101005.txt
  • lines changed 2, context: html, text, full: html, text
    Updated the documentation in the build script to indicate the tables used only by the proteome browser (thanks, Fan)
• src/hg/makeDb/doc/rn4.txt
  • lines changed 7, context: html, text, full: html, text
    Added a correction step to fixwq rgdGene2Ensembl table.
  • lines changed 51, context: html, text, full: html, text
    add CDS FASTA alignments from rgdGene2 to downloads
• src/hg/makeDb/doc/sacCer3.txt
  • lines changed 2, context: html, text, full: html, text
    note about phyloBoot never finishing
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 34, context: html, text, full: html, text
    Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
• src/hg/makeDb/doc/xenTro3.txt
  • lines changed 243, context: html, text, full: html, text
    repeat the melGal1 alignment and start the 9-way
  • lines changed 206, context: html, text, full: html, text
    have 9-way multiz with gene and gap annotations
  • lines changed 122, context: html, text, full: html, text
    done with 4D site tree estimate
  • lines changed 248, context: html, text, full: html, text
    phastCons done for 9-way
  • lines changed 256, context: html, text, full: html, text
    phyloP done for 9-way and working on downloads
  • lines changed 4, context: html, text, full: html, text
    done with 9-way alignment
  • lines changed 55, context: html, text, full: html, text
    added CDS FASTA alignments for ensGene
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 72, context: html, text, full: html, text
    Added in '-or' and ' || ' support to mdbPrint/mdbUpdate selections
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 1, context: html, text, full: html, text
    Made things a little less awkward for deleting vars
  • lines changed 47, context: html, text, full: html, text
    Added in '-or' and ' || ' support to mdbPrint/mdbUpdate selections
• src/hg/makeDb/schema/all.joiner
  • lines changed 6, context: html, text, full: html, text
    Added a relationship between the tRNAName field in kgXref and the name field in the tRNAs table
  • lines changed 2, context: html, text, full: html, text
    Updated with some rgdGene2 entries.
  • lines changed 1, context: html, text, full: html, text
    Some update for rn4 rgdGene2.
  • lines changed 4, context: html, text, full: html, text
    Updated some entries to cover more rn4 rgdGene2 related IDs.
  • lines changed 8, context: html, text, full: html, text
    Build geneReviews to kgXref.genesymbol relationship
• src/hg/makeDb/trackDb/cow/bosTau2/gold.html
  • lines changed 2, context: html, text, full: html, text
    Re-added removed commas
• src/hg/makeDb/trackDb/cow/bosTau6/gap.html
  • lines changed 2, context: html, text, full: html, text
    Added a period to the end of all bullet points
• src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    add search rules for gold and ctgPos2
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 77, context: html, text, full: html, text
    Adding 5 approved antibodies for Flo
  • lines changed 12, context: html, text, full: html, text
    added 2 new treatments
  • lines changed 6, context: html, text, full: html, text
    There was a term where there should have been a type and adding a label
  • lines changed 15, context: html, text, full: html, text
    Adding new version for mapAlgorithm
  • lines changed 8, context: html, text, full: html, text
    Restored items lots from commit f29e7c395ee0c68912b3b4687a0b49cc3aa6e57a by commit 4df674dc20e935ce620b3c0603fe40008bbddeb3.
  • lines changed 15, context: html, text, full: html, text
    Adding CREB1 antibody
  • lines changed 8, context: html, text, full: html, text
    put back in lines whose deletion broke things, corrected searchable term in dccRep
  • lines changed 167, context: html, text, full: html, text
    Adding Antibodies
  • lines changed 4, context: html, text, full: html, text
    Fixing FOXP2
  • lines changed 9, context: html, text, full: html, text
    corrected incorrect lab name for antibodies registered.
  • lines changed 1, context: html, text, full: html, text
    missed an antibody
  • lines changed 24, context: html, text, full: html, text
    Adding Cell Lines and Antibodies
  • lines changed 8, context: html, text, full: html, text
    Adding Antibody Documents
  • lines changed 5, context: html, text, full: html, text
    added in goat control entry
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 528, context: html, text, full: html, text
    Updates to cv from alpha
• src/hg/makeDb/trackDb/gap.html
  • lines changed 1, context: html, text, full: html, text
    Added a period to the end of all bullet points
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 2, context: html, text, full: html, text
    added missing closing bracket
  • lines changed 1, context: html, text, full: html, text
    Fixed an HTML error that left much of the methods section represented as a hyperlink
  • lines changed 39, context: html, text, full: html, text
    Put back the old content of knownGene.html. Moved the new content to knownGeneNew.html
• src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
  • lines changed 156, context: html, text, full: html, text
    Put back the old content of knownGene.html. Moved the new content to knownGeneNew.html
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 1162, context: html, text, full: html, text
    added new tracks to broad histone metaDb
  • lines changed 259, context: html, text, full: html, text
    loaded 2 new borad tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 682, context: html, text, full: html, text
    See issue 2019, adding in some expIds, some labExpIds, working with the Myocyte issue
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 689, context: html, text, full: html, text
    Changing file names to have Replicate
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
  • lines changed 859, context: html, text, full: html, text
    added new tracks to Haib methyl 450
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 920, context: html, text, full: html, text
    added in 4321 and 4320
  • lines changed 2003, context: html, text, full: html, text
    added a lot of haib tfbs tracks
  • lines changed 1184, context: html, text, full: html, text
    added in new haib tracks
  • lines changed 671, context: html, text, full: html, text
    added in new controls
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 336, context: html, text, full: html, text
    added in new tracks for open chrom chip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 451, context: html, text, full: html, text
    added in new entries for open chrom dnase
  • lines changed 118, context: html, text, full: html, text
    added one track to open chrom dnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 257, context: html, text, full: html, text
    loaded 2 new tracks for sydh Histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    added md5sums
  • lines changed 1409, context: html, text, full: html, text
    loaded new tracks into release 2 sydh TFBS
  • lines changed 7, context: html, text, full: html, text
    last second revoke and replace of an experiment
  • lines changed 31, context: html, text, full: html, text
    corrected controls and long labels for replacement experiment
  • lines changed 23, context: html, text, full: html, text
    added bai's to fileName field.
  • lines changed 63, context: html, text, full: html, text
    updated md5sums
  • lines changed 27, context: html, text, full: html, text
    cleanup SydhTfbs track
  • lines changed 54, context: html, text, full: html, text
    renamed K562/SetDb1/UCD to be consistent with the other objects in the experiment
  • lines changed 65, context: html, text, full: html, text
    added new control to sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 70, context: html, text, full: html, text
    adding geoAccessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 75, context: html, text, full: html, text
    Adding submissions 4771-4775 into a release2
  • lines changed 13, context: html, text, full: html, text
    Adding accessions
  • lines changed 5, context: html, text, full: html, text
    removed erroneous origAsembly hg19 term
  • lines changed 4, context: html, text, full: html, text
    Remove origAssembly
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtFasp.ra
  • lines changed 40, context: html, text, full: html, text
    Adding the metaData for UncBsuProtFasp
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 1277, context: html, text, full: html, text
    added a lot of uw tracks
  • lines changed 813, context: html, text, full: html, text
    added a lot of DGF tracks
  • lines changed 108, context: html, text, full: html, text
    removed random accession=hg19 fields
  • lines changed 108, context: html, text, full: html, text
    removed origAssembly from DGF
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 115, context: html, text, full: html, text
    restored lost metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 70, context: html, text, full: html, text
    restored missing metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging GIS RNA PET, redmine# 42
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
  • lines changed 3550, context: html, text, full: html, text
    staging GIS RNA PET, redmine# 42
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
  • lines changed 3975, context: html, text, full: html, text
    moving the updated metaDb for SYDH TFBS, redmine# 69
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUncBsuProt.ra
  • lines changed 83, context: html, text, full: html, text
    staging metadata for two new subtracks on beta, redmine 141
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing to release UNC/BSU ProtGeno, redmine 141
  • lines changed 1, context: html, text, full: html, text
    Releasing HAIB Methyl RRBS (release 2), redmine# 2254
  • lines changed 2, context: html, text, full: html, text
    fixed merge conflict
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethylRrbs.ra
  • lines changed 9884, context: html, text, full: html, text
    Releasing HAIB Methyl RRBS (release 2), redmine# 2254
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUncBsuProt.ra
  • lines changed 306, context: html, text, full: html, text
    preparing to release UNC/BSU ProtGeno, redmine 141
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    add python to this skunkworks alignment
  • lines changed 50, context: html, text, full: html, text
    Setting out to support two versions of the UCSC Genes details page: the old one on beta and RR, and a new one on alpha only. Trying to achieve this with two new trackDb.ra stanzas for knownGene (one for beta and RR, one for alpha), which should override the stanza in trackDb/trackDb.ra for hg19 only
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    Just learned that when you use the html qualifier, you shouldn't list your html filename with the html suffix
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Adding submissions 4771-4775 into a release2
  • lines changed 1, context: html, text, full: html, text
    changed alpha to .new.ra for sydh tfbs
  • lines changed 1, context: html, text, full: html, text
    put it back to the .ra for sydh tfbs
  • lines changed 1, context: html, text, full: html, text
    Adding UncBsuProt
  • lines changed 2, context: html, text, full: html, text
    enabling .ra to work on beta and alpha since it now contains the changes (2 new subtracks) that the .new.ra file had, redmine 141
  • lines changed 2, context: html, text, full: html, text
    Releasing HAIB Methyl RRBS (release 2), redmine# 2254
  • lines changed 1, context: html, text, full: html, text
    staging GIS RNA PET, redmine# 42
  • lines changed 2, context: html, text, full: html, text
    alpha, beta, public on sydh TFBS trackDb
  • lines changed 2, context: html, text, full: html, text
    Adding the release 2 structure and taking out the view level
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    inserted new antibody terms
  • lines changed 180, context: html, text, full: html, text
    added new tracks
  • lines changed 41, context: html, text, full: html, text
    loaded 2 new borad tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 1, context: html, text, full: html, text
    See issue 2019, adding in some expIds, some labExpIds, working with the Myocyte issue
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 9, context: html, text, full: html, text
    See issue 2019, adding in some expIds, some labExpIds, working with the Myocyte issue
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 33, context: html, text, full: html, text
    Adding Rep 3 and 4
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.html
  • lines changed 28, context: html, text, full: html, text
    fixed html errors for GIS RNA PET, redmine# 42
  • lines changed 17, context: html, text, full: html, text
    Issue 42, adding the multiview instructions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    Many small changes for issue 42 for Vanessa
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 353, context: html, text, full: html, text
    added new tracks to Haib methyl 450
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 122, context: html, text, full: html, text
    Releasing HAIB Methyl RRBS (release 2), redmine# 2254
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
  • lines changed 65, context: html, text, full: html, text
    Fixed typos, fixed html errors and rephrased sentences to avoid the use of the word we for HAIB Methyl RRBS, redmine# 2254
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 1246, context: html, text, full: html, text
    Releasing HAIB Methyl RRBS (release 2), redmine# 2254
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.new.ra
  • lines changed 122, context: html, text, full: html, text
    added in 4321 and 4320
  • lines changed 381, context: html, text, full: html, text
    added a lot of haib tfbs tracks
  • lines changed 1, context: html, text, full: html, text
    changed alpha to html character code
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    revamped long labels
  • lines changed 231, context: html, text, full: html, text
    added in new haib tracks
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    added in new controls
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
  • lines changed 57, context: html, text, full: html, text
    added in new tracks for open chrom chip
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
  • lines changed 98, context: html, text, full: html, text
    added in new entries for open chrom dnase
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    added in missing no treatments
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    added one track to open chrom dnase
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    added in missing non treatment
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
  • lines changed 4, context: html, text, full: html, text
    Trying to add the pValue filters
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    Getting rid of minGreyLevel as it is not working properly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
  • lines changed 44, context: html, text, full: html, text
    loaded 2 new tracks for sydh Histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 17, context: html, text, full: html, text
    long labels for sydh tfbs
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    short labels sydh tfbs
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    added time to EtOH 36Hr treatment. We should consider adding this to the cv, as that term is inconsistent with the others.
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    objects that needed to be pushed got pushed to release2, uncomment this later
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    loaded new tracks into release 2 sydh TFBS
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    updated the info on a replaced track
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    added new control to sydh tfbs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 184, context: html, text, full: html, text
    merged non-released release1 with the WIP release2 to be the new release 1
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    removed bad experiments after once-over
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    last second revoke and replace of an experiment
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    corrected controls and long labels for replacement experiment
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    cleanup SydhTfbs track
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    cleaned up more trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
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    Adding submissions 4771-4775 into a release2
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    changing 'nuclear' in a long label to 'nucleus' to be consistent with its shortLabel and other nucleus localization subtrack longLabel, redmine 141
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 20, context: html, text, full: html, text
    copying .new.ra version over .ra to incorporate new subtracks, redmine #141
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.ra
  • lines changed 32, context: html, text, full: html, text
    Adding UncBsuProt
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html
  • lines changed 71, context: html, text, full: html, text
    Adding the release 2 structure and taking out the view level
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra
  • lines changed 1255, context: html, text, full: html, text
    Adding the release 2 structure and taking out the view level
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 441, context: html, text, full: html, text
    added a lot of uw tracks
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    added a lot of DGF tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
  • lines changed 14, context: html, text, full: html, text
    changed html for uw histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 263, context: html, text, full: html, text
    fixed long labels UwHistone
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    fixed short labels
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    fixed longlabels in uwtfbs, added in treatments in uw histone tfbs and cleanup
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
  • lines changed 328, context: html, text, full: html, text
    fixed longlabels in uwtfbs, added in treatments in uw histone tfbs and cleanup
  • lines changed 236, context: html, text, full: html, text
    short labels for uw tfbs
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    put back logic to handle geneReviews track using the geneReviews table in the database
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    Remove geneReviewsBB which is using wiki for update
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 452, context: html, text, full: html, text
    Added 3 submissions, one of which replaced an old submission 3039.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 845, context: html, text, full: html, text
    Added 3 more submissions.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 804, context: html, text, full: html, text
    Added 6 new submissions for new release 3. Updated new.ra and trackDb.wgEncode.ra to have release 3 data showing on dev.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Added 6 new submissions for new release 3. Updated new.ra and trackDb.wgEncode.ra to have release 3 data showing on dev.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 87, context: html, text, full: html, text
    Added 3 submissions, one of which replaced an old submission 3039.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 55, context: html, text, full: html, text
    Added 3 more submissions.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.ra
  • lines changed 888, context: html, text, full: html, text
    Updated name of file to be in line with other new.ra files.
  • lines changed 189, context: html, text, full: html, text
    Added 6 new submissions for new release 3. Updated new.ra and trackDb.wgEncode.ra to have release 3 data showing on dev.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 888, context: html, text, full: html, text
    Updated name of file to be in line with other new.ra files.
• src/hg/makeDb/trackDb/oreganno.html
  • lines changed 13, context: html, text, full: html, text
    Redid the Display Conventions section to make it much easier to see what the colors mean ... as before they were buried in a paragraph with no color cues. I put a white backgound on it because the light green was almost impossible to read on the yellow background. It'sstill faint on the whote, but much better.
  • lines changed 3, context: html, text, full: html, text
    Added a little hack so that the box would expand/contract with font size and also work in IE7
• src/hg/makeDb/trackDb/sacCer/sacCer3/sgdGene.html
  • lines changed 14, context: html, text, full: html, text
    Cleaned up the html and rearranged text to make more sense and increase readability.
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    Added the word accessed for clarity and match the other sgd track.
• src/hg/makeDb/trackDb/sacCer/sacCer3/sgdOther.html
  • lines changed 2, context: html, text, full: html, text
    Fixe dtwo errors per code review #5470: corrected end p tag missing / and sentence missing a period.
• src/hg/makeDb/trackDb/turkey/melGal1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Added a period to the end of all bullet points
• src/hg/makeDb/trackDb/windowmaskerSdust.html
  • lines changed 1, context: html, text, full: html, text
    Removed the 's' from 'sequence'
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 400, context: html, text, full: html, text
    initial contents copied from anoCar2 and updated for xenTro3
• src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra
  • lines changed 104, context: html, text, full: html, text
    adding cons9way
• src/hg/rnaStructure/utrFa/utrFa.c
  • lines changed 13, context: html, text, full: html, text
    Adding back some changes that were previously lost ina failed effort to neatly go back, review the commits, and write a better commit message. With that said, (1) hdb.h, hdb.c, and utrFa.c were all revised to allow utrFa to take a user-specified path to the nib files rather than looking up the path in dbDb. This allowed me to run utrFa on the transcripts in the temporary staging directory for the new UCSC Genes build, before those transcripts were in hg19 (the temporary directory was not in dbDb, and probably shouldn't be). (2) Copied some code from hg19.txt (thanks, Fan) to generate the keggPathway table. The previous code missed a lot of associations: since making this change, keggPathway has grown from about 9K to 60K lines
• src/hg/utils/refSeqGet/refSeqGet.c
  • lines changed 4, context: html, text, full: html, text
    data status to metadata TSV
• src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
  • lines changed 6, context: html, text, full: html, text
    data status to metadata TSV
• src/hg/utils/refSeqGet/tests/expected/versionedListTest.meta
  • lines changed 4, context: html, text, full: html, text
    data status to metadata TSV
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 1, context: html, text, full: html, text
    fix per Jim.. a more clear usage message
• src/utils/qa/checkGbdbDiffs.csh
  • lines changed 3, context: html, text, full: html, text
    Got rid of annoying rm error with a hacky redirect to /dev/null.
• src/utils/qa/doGenbankTests
  • lines changed 2, context: html, text, full: html, text
    Implicating Brian in addition to Mark for gbSanity problems.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v258 preview2

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• files changed: 231