All File Changes

v271_preview2 to v271_base (2012-07-31 to 2012-08-07) v271

• python/programs/cvValidate/makefile
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    Forgot to commit makefile for cvValidate.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 4, context: html, text, full: html, text
    adding in bed cluster
• src/hg/hgGateway/hgGateway.c
  • lines changed 8, context: html, text, full: html, text
    remove "clear position" button and wordsmithing
• src/hg/hgGene/domains.c
  • lines changed 3, context: html, text, full: html, text
    stop building the proteome browser binaries and the protein library. This required a small change to hgGene which had a little bit of code supporting the SAM T-02 links that were only present in sacCer1 #5740
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 10, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/hgGene/hgGeneData/Mouse/links.ra
  • lines changed 10, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/hgGene/hgGeneData/Mouse/mm6/links.ra
  • lines changed 1, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/hgGene/hgGeneData/Rat/rn2/links.ra
  • lines changed 12, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/hgGene/links.c
  • lines changed 18, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/hgGene/makefile
  • lines changed 1, context: html, text, full: html, text
    stop building the proteome browser binaries and the protein library. This required a small change to hgGene which had a little bit of code supporting the SAM T-02 links that were only present in sacCer1 #5740
• src/hg/hgLogin/hgLogin.c
  • lines changed 2, context: html, text, full: html, text
    Bug #8693 eed to url encode space character in the activation link in confirmation mail send to new user.
• src/hg/hgTrackUi/hgTrackUi.c
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    Got rid of the serif font declaration to match rest of site.
  • lines changed 9, context: html, text, full: html, text
    Code Review #8673 - thanks Tim!
• src/hg/hgTracks/hgTracks.c
  • lines changed 0, context: html, text, full: html, text
    handle edge case of user zeroing out the positionInput box
  • lines changed 1, context: html, text, full: html, text
    remove "clear position" button and wordsmithing
• src/hg/hgTracks/vcfTrack.c
  • lines changed 39, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1): added recently-released chrY.Fixed bugs with display of haploid genotype data.
    1000 Genomes' chrY has tons of missing calls, and it turns out that clustering
    results are much better if missing info is completely omitted from distance
    measure -- although the tree calls things identical that clearly aren't.
    
  • lines changed 15, context: html, text, full: html, text
    Fix to haplotype clustering in VCF display: was still giving too much weight to missing data.
• src/hg/hgc/ccdsClick.c
  • lines changed 8, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/hgc/hgc.c
  • lines changed 28, context: html, text, full: html, text
    hgc - cleaned up code with simpler, more reliable approach.
  • lines changed 1, context: html, text, full: html, text
    test for table altSeqLiftOverPsl* should be startsWith not sameString
  • lines changed 29, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Adding splice_region_variant, defined by SO as "A sequence variant in
    which a change has occurred within the region of the splice site,
    either within 1-3 bases of the exon or 3-8 bases of the intron."
    
  • lines changed 34, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
  • lines changed 2, context: html, text, full: html, text
    Code Review #8673 - thanks Tim!
• src/hg/hgc/vcfClick.c
  • lines changed 27, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1): added recently-released chrY.Fixed bugs with display of haploid genotype data.
    1000 Genomes' chrY has tons of missing calls, and it turns out that clustering
    results are much better if missing info is completely omitted from distance
    measure -- although the tree calls things identical that clearly aren't.
    
• src/hg/htdocs/ENCODE/index.html
  • lines changed 3, context: html, text, full: html, text
    A change in HGStyle.css turned the bg color of this page yellow. Hard coded it back to white.
  • lines changed 1, context: html, text, full: html, text
    Adding link to new google groups on ENCODE portal page as per Pauline and Gmail move
• src/hg/htdocs/ENCODE/search.html
  • lines changed 3, context: html, text, full: html, text
    according to redmine #7887, I changed the '&' in URLs to '%26', but this was causing the links not to work; changed back to '&';
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 58, context: html, text, full: html, text
    Updated section on mysql to point to our new mysql help page.
  • lines changed 30, context: html, text, full: html, text
    Corrected comments so they don't mess up syntax highlighting in editors.
  • lines changed 27, context: html, text, full: html, text
    Shortedned Downloading seq/anno section and pointed to our new FTP page.
• src/hg/htdocs/FAQ/index.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to new mailing list google groups.
  • lines changed 1, context: html, text, full: html, text
    Updating links to google groups with more compact urls.
• src/hg/htdocs/Neandertal/index.html
  • lines changed 2, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/admin/mirror.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to new mailing list google groups.
  • lines changed 1, context: html, text, full: html, text
    Updating links to google groups with more compact urls.
• src/hg/htdocs/cite.html
  • lines changed 11, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/contacts.html
  • lines changed 3, context: html, text, full: html, text
    Updating links to new mailing list google groups.
  • lines changed 3, context: html, text, full: html, text
    Updating links to google groups with more compact urls.
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    edited reference to 'position or search term' to 'search term' will be going out with v271 changes
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 55, context: html, text, full: html, text
    Initial new ftp help page.
  • lines changed 39, context: html, text, full: html, text
    Made several edits for format and clarity. Hard wrapped doc to 100 chars.
  • lines changed 17, context: html, text, full: html, text
    Added section on FTP'ing from a web browser, and updated some styling and grammar for clarity.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
  • lines changed 6, context: html, text, full: html, text
    edited reference to 'position or search term' to 'search term' will be going out with v271 changes
• src/hg/htdocs/goldenPath/help/multiView.html
  • lines changed 1, context: html, text, full: html, text
    fixed doc errors with highlighting
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 62, context: html, text, full: html, text
    Initial new mysql help page.
  • lines changed 47, context: html, text, full: html, text
    Made many edits to format, clear up text for easier reading, etc. Hard wrapped doc to 100 chars.
  • lines changed 2, context: html, text, full: html, text
    Added a section heading for clarity.
  • lines changed 2, context: html, text, full: html, text
    Shortened sentence for clarity.
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 1, context: html, text, full: html, text
    changed name of search box to reflect changes in v271
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 3, context: html, text, full: html, text
    Doc #5088 (clean up trackDb/README): fixing a couple bugs in 272ef2ef59 found by Tim.
• src/hg/htdocs/images/phylo/geoFor1_7way.png
  • lines changed 0, context: html, text, full: html, text
    7-way phylo tree for Darwin Finch
  • lines changed 0, context: html, text, full: html, text
    correct tree diagram for geoFor1
• src/hg/htdocs/inc/FAQ.topbar.html
  • lines changed 1, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/inc/download.topbar.html
  • lines changed 1, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 2, context: html, text, full: html, text
    Broke out ftp and mysql into their own links - for obvious reasons.
  • lines changed 1, context: html, text, full: html, text
    Changed ftp link to something more informational since not all browsers support browsing files on an ftp server (notably Safari).
  • lines changed 2, context: html, text, full: html, text
    Changed 2 links to point to newly created ftp and mysql pages.
• src/hg/htdocs/inc/help.topbar.html
  • lines changed 1, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/inc/home.topbar.html
  • lines changed 1, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/inc/neandertal.topbar.html
  • lines changed 1, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/inc/topbar.html
  • lines changed 1, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/index.html
  • lines changed 2, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to new mailing list google groups.
  • lines changed 1, context: html, text, full: html, text
    Updating links to google groups with more compact urls.
• src/hg/htdocs/mirror.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to new mailing list google groups.
  • lines changed 1, context: html, text, full: html, text
    Updating links to google groups with more compact urls.
• src/hg/htdocs/staff.html
  • lines changed 21, context: html, text, full: html, text
    updating: adding Brian Lee, moving Mary, Vanessa, and Fan to alumni section, adding Venkat to alumni section.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 12, context: html, text, full: html, text
    Added new style for displaying code in <pre> tags. Can see this used in goldenPath/help/ftp.html
  • lines changed 9, context: html, text, full: html, text
    remove the gray background for the positionDisplay on hgTracks
  • lines changed 7, context: html, text, full: html, text
    Fixed display issue; Redmine #8685.
  • lines changed 3, context: html, text, full: html, text
    Fixed IE bug where dashes between the links in the top blue bar were v-aligned at the bottom. Also pulled out a style that was not needed.
• src/hg/htdocs/style/encodeProject.css
  • lines changed 1, context: html, text, full: html, text
    Added background color to white, since the change in HGStyle.css changed it to yellow.
• src/hg/htdocs/style/nice_menu.css
  • lines changed 2, context: html, text, full: html, text
    Fixed a missing closing to a comment and deleted some extra *s
• src/hg/htdocs/training.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to new mailing list google groups.
  • lines changed 1, context: html, text, full: html, text
    Updating links to google groups with more compact urls.
  • lines changed 1, context: html, text, full: html, text
    remove Proteome Browser for top bar, side bar, citations, and help. (#5740)
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v271
• src/hg/js/autocomplete.js
  • lines changed 9, context: html, text, full: html, text
    handle edge case of user zeroing out the positionInput box
  • lines changed 1, context: html, text, full: html, text
    encodeURIComponent key in case it has punctuation in it (e.g. "RH18061;RH80175")
• src/hg/lib/cart.c
  • lines changed 5, context: html, text, full: html, text
    hgc - cleaned up code with simpler, more reliable approach.
• src/hg/lib/hdb.c
  • lines changed 31, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    change "known genes" to "UCSC Genes"
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    fixed doc errors with highlighting
• src/hg/lib/snp125Ui.c
  • lines changed 1, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Adding splice_region_variant, defined by SO as "A sequence variant in
    which a change has occurred within the region of the splice site,
    either within 1-3 bases of the exon or 3-8 bases of the intron."
    
• src/hg/lib/web.c
  • lines changed 5, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/hg/makeDb/doc/chiLan1.txt
  • lines changed 5, context: html, text, full: html, text
    done with genbank run and loading
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHistone.release3.notes
  • lines changed 3322, context: html, text, full: html, text
    adding in Broad Histone notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release4.notes
  • lines changed 1402, context: html, text, full: html, text
    Adding notes file
  • lines changed 11, context: html, text, full: html, text
    Adding the name changed file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaPet.release2.notes
  • lines changed 16, context: html, text, full: html, text
    fixed notes
  • lines changed 18, context: html, text, full: html, text
    Adding supplemental dir to the notes file
  • lines changed 54, context: html, text, full: html, text
    Removing the Hela Rep 2 from the notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProtGenc.release1.notes
  • lines changed 89, context: html, text, full: html, text
    creating the notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDgf.release4.notes
  • lines changed 189, context: html, text, full: html, text
    updating notes for uw dgf
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuHistone.release2.notes
  • lines changed 516, context: html, text, full: html, text
    Added release 2 notes of track. Redmine #6703.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuRnaSeq.release1.notes
  • lines changed 443, context: html, text, full: html, text
    Added release 1 notes for track. Redmine #107
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuTfbs.release2.notes
  • lines changed 566, context: html, text, full: html, text
    Added releases 2 notes for track. Redmine #7516.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhRnaSeq.release2.notes
  • lines changed 168, context: html, text, full: html, text
    Adding notes file and structure for a release2 with a relase notes to explain replaced file
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 7, context: html, text, full: html, text
    completed galGal4 geoFor1 lastz chain net
• src/hg/makeDb/doc/geoFor1.txt
  • lines changed 22, context: html, text, full: html, text
    completed galGal4 geoFor1 lastz chain net
  • lines changed 194, context: html, text, full: html, text
    done with chicken galGal4 and finch taeGut1 lastz chain net and starting 7-way
  • lines changed 82, context: html, text, full: html, text
    looking at recipbest and synNets for all alignments
  • lines changed 207, context: html, text, full: html, text
    featureBits on all syntenic nets and reciprocal best nets and starting 7-way alignment
  • lines changed 44, context: html, text, full: html, text
    reset default position to FOXP2 and loading the 7-way multiz
  • lines changed 434, context: html, text, full: html, text
    7-way annotations and frames and 4d estimation done
  • lines changed 20, context: html, text, full: html, text
    the calculated 4d tree indicates fixing the original tree to start the 7-way
  • lines changed 27, context: html, text, full: html, text
    restarted multiz with better tree
  • lines changed 92, context: html, text, full: html, text
    reloaded the 7-way with the better phylo tree
• src/hg/makeDb/doc/hg18.txt
  • lines changed 10, context: html, text, full: html, text
    fixed broken net file
  • lines changed 4, context: html, text, full: html, text
    Track #1656 (GWAS catalog): bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
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    Track #1656 (GWAS catalog): bi-monthly update.
  • lines changed 18, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1): added recently-released chrY.Fixed bugs with display of haploid genotype data.
    1000 Genomes' chrY has tons of missing calls, and it turns out that clustering
    results are much better if missing info is completely omitted from distance
    measure -- although the tree calls things identical that clearly aren't.
    
• src/hg/makeDb/doc/taeGut1.txt
  • lines changed 8, context: html, text, full: html, text
    done with geoFor1 chain net
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added chiLan1.
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Added geoFor1 as I'm staging on beta now.
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added chiLan1.
  • lines changed 1, context: html, text, full: html, text
    add strPur4 for Kord
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra
  • lines changed 193, context: html, text, full: html, text
    adding 7-way conservation for geoFor1
  • lines changed 2, context: html, text, full: html, text
    fixup phylo image reference
  • lines changed 1, context: html, text, full: html, text
    setting default track visibilities
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    correct order of species to display
  • lines changed 17, context: html, text, full: html, text
    all phastCons and phyloP tracks now on
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.chainNet.ra
  • lines changed 17, context: html, text, full: html, text
    readjust budgie above mouse
  • lines changed 13, context: html, text, full: html, text
    adding overrides for minScore linearGap and matrix
  • lines changed 24, context: html, text, full: html, text
    setting default track visibilities
• src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding the chainNet overrides
  • lines changed 2, context: html, text, full: html, text
    adding 7-way for geoFor1
  • lines changed 6, context: html, text, full: html, text
    setting default track visibilities
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.chainNet.ra
  • lines changed 10, context: html, text, full: html, text
    adding overrides for geoFor1 and mm10
  • lines changed 1, context: html, text, full: html, text
    default pack for geoFor1 chain net
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding overrides for geoFor1 and mm10
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.chainNet.ra
  • lines changed 8, context: html, text, full: html, text
    adding geoFor1 chainNet and overrides for mm10
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    adding geoFor1 chainNet and overrides for mm10
• src/hg/makeDb/trackDb/chimp/panTro1/snp125.html
  • lines changed 52, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/cow/bosTau3/snp127.html
  • lines changed 52, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed sex of G1E and G1E-ER4 cell line to be M. Redmine #6703, #107.
  • lines changed 101, context: html, text, full: html, text
    Adding provisional antibodies, Jeff needs to look these over
  • lines changed 1, context: html, text, full: html, text
    This primary cell can come from either male or female..
  • lines changed 2, context: html, text, full: html, text
    Redmine #7663
    Q6. Fixed spelling of Facility
    Q7. Made VendorId lowercase for iPS_hFib2_IPS5
    
  • lines changed 2, context: html, text, full: html, text
    Fixed two spelling errors in the iPS lines
  • lines changed 2, context: html, text, full: html, text
    Redmine #7663. Fixed Description to include line information.
  • lines changed 177, context: html, text, full: html, text
    Fixing up new antibodies in CV
  • lines changed 3, context: html, text, full: html, text
    Adding iPS cell line details to CV
  • lines changed 2, context: html, text, full: html, text
    fixed a small issue in cv
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in the Description of FV-progenitor cells.
  • lines changed 14, context: html, text, full: html, text
    Fixing broken html links
  • lines changed 1, context: html, text, full: html, text
    Fixing missing protocol in CV
  • lines changed 3, context: html, text, full: html, text
    Changing the labels of insert length
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 634, context: html, text, full: html, text
    Copying alpha cv to beta
• src/hg/makeDb/trackDb/dog/canFam1/snp125.html
  • lines changed 52, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra
  • lines changed 33, context: html, text, full: html, text
    this version ages out as patch9 replaces it, preserve at P5 for hgwdev viewing
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite9.ra
  • lines changed 1, context: html, text, full: html, text
    Changed track short label (redmine #7195)
  • lines changed 1, context: html, text, full: html, text
    Made change suggested by Hiram to fix problems with the Alignment subtrack (redmine #7195)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 380, context: html, text, full: html, text
    added in md5sums and added treatment as a expVar
  • lines changed 877, context: html, text, full: html, text
    adding in Broad Histone tracks
  • lines changed 56, context: html, text, full: html, text
    added in dateUnrestricted dates
  • lines changed 1406, context: html, text, full: html, text
    fixes for QA for broad histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 25, context: html, text, full: html, text
    Adding md5sums
  • lines changed 76, context: html, text, full: html, text
    Adding the release 4 structure and cleaning up the replacement fastq metadata, including a rename object
  • lines changed 432, context: html, text, full: html, text
    added new GSMs to Caltech. This is post-fix (#8537) so it should be completely up to date
  • lines changed 2, context: html, text, full: html, text
    Fixing objectStatus
  • lines changed 8, context: html, text, full: html, text
    fixed md5sums for double-compressed Caltech data. See tickets 8537 & 8537
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 32, context: html, text, full: html, text
    Adding expIds
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 569, context: html, text, full: html, text
    added accessions for CSHL short hg19 back into mdb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 134, context: html, text, full: html, text
    Added release notes, dccAccessions, and the dimChecked on the filerComposite
  • lines changed 13, context: html, text, full: html, text
    Removing labProtocolId
  • lines changed 7, context: html, text, full: html, text
    Revoking replicate 2 of the Hela whole cell sample, changing the date of the release, setting the replicates to all
  • lines changed 37, context: html, text, full: html, text
    updating the dates
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 47, context: html, text, full: html, text
    added accessions into Riken and Haib RRBS
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 641, context: html, text, full: html, text
    added in md5sums
  • lines changed 4722, context: html, text, full: html, text
    spacing issues in the text
  • lines changed 216, context: html, text, full: html, text
    added in mdt5sums and some expIds
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 47, context: html, text, full: html, text
    added in md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 172, context: html, text, full: html, text
    added in md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 220, context: html, text, full: html, text
    added accessions into Riken and Haib RRBS
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProtGenc.ra
  • lines changed 25, context: html, text, full: html, text
    added md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 265, context: html, text, full: html, text
    added in expIds for uw dgf
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 7332, context: html, text, full: html, text
    Staging Broad Histone (Release 3) on beta (redmine #6919)
  • lines changed 1461, context: html, text, full: html, text
    Matt made some metadata changes (redmine #6919)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 8, context: html, text, full: html, text
    fixed md5sums for double-compressed Caltech data. See tickets 8537 & 8537
  • lines changed 1446, context: html, text, full: html, text
    Staging Caltech RNA-seq (Release 4) on beta (redmine #8537)
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
  • lines changed 4480, context: html, text, full: html, text
    Staging on beta GIS RNA PET (Release 2) RM#5942
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 458, context: html, text, full: html, text
    Staging on beta UW Affy Exon Array (Release 4) RM#8650
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 2654, context: html, text, full: html, text
    Staging UW DNaseI DGF (Release 4) on beta (redmine #6806)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 8774, context: html, text, full: html, text
    Releasing Broad Histone (Release 3) to the RR (redmine #6919)
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeFsuRepliChip.ra
  • lines changed 293, context: html, text, full: html, text
    Staging FSU Replication Timing (Release 2) RM7663 on public
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwAffyExonArray.ra
  • lines changed 458, context: html, text, full: html, text
    Staging on Public for UW Affy Exon Array (Release 4) RM#8650
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 2654, context: html, text, full: html, text
    Releasing UW DNaseI DGF (Release 4) to the RR (redmine #6806)
• src/hg/makeDb/trackDb/human/hg19/snp130.html
  • lines changed 54, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
  • lines changed 9, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
  • lines changed 14, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):"internal term" --> "dbSNP term" as suggested by Brooke in note 12.
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Modified release tags (redmine #7195)
  • lines changed 1, context: html, text, full: html, text
    Had to remove the GRC Patch 5 line for the changes for Patch 9 to work (redmine #7195)
  • lines changed 2, context: html, text, full: html, text
    Track #7964 (1000 Genomes Phase 1): added recently-released chrY.Fixed bugs with display of haploid genotype data.
    1000 Genomes' chrY has tons of missing calls, and it turns out that clustering
    results are much better if missing info is completely omitted from distance
    measure -- although the tree calls things identical that clearly aren't.
    
  • lines changed 19, context: html, text, full: html, text
    adding geoFor1 chain and net
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Adding the release 4 structure and cleaning up the replacement fastq metadata, including a rename object
  • lines changed 2, context: html, text, full: html, text
    Staging FSU Replication Timing (Release 2) RM7663 on public
  • lines changed 2, context: html, text, full: html, text
    Staging on beta UW Affy Exon Array (Release 4) RM#8650
  • lines changed 2, context: html, text, full: html, text
    Staging on Public for UW Affy Exon Array (Release 4) RM#8650
  • lines changed 2, context: html, text, full: html, text
    Staging on beta GIS RNA PET (Release 2) RM#5942
  • lines changed 2, context: html, text, full: html, text
    Staging UW DNaseI DGF (Release 4) on beta (redmine #6806)
  • lines changed 2, context: html, text, full: html, text
    Staging Broad Histone (Release 3) on beta (redmine #6919)
  • lines changed 2, context: html, text, full: html, text
    Staging Caltech RNA-seq (Release 4) on beta (redmine #8537)
  • lines changed 2, context: html, text, full: html, text
    Releasing UW DNaseI DGF (Release 4) to the RR (redmine #6806)
  • lines changed 2, context: html, text, full: html, text
    Releasing Broad Histone (Release 3) to the RR (redmine #6919)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html
  • lines changed 14, context: html, text, full: html, text
    html fixes
  • lines changed 2, context: html, text, full: html, text
    html fixes for broad
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 813, context: html, text, full: html, text
    fixed labels
  • lines changed 1, context: html, text, full: html, text
    Fixing the shortLabelnal issue that was breaking the build
  • lines changed 1, context: html, text, full: html, text
    removing default peak options box
  • lines changed 111, context: html, text, full: html, text
    fixes for QA for broad histone
  • lines changed 319, context: html, text, full: html, text
    more qa fixes for broad histone
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release4.html
  • lines changed 206, context: html, text, full: html, text
    Adding the release 4 structure and cleaning up the replacement fastq metadata, including a rename object
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release4.ra
  • lines changed 1494, context: html, text, full: html, text
    Adding the release 4 structure and cleaning up the replacement fastq metadata, including a rename object
  • lines changed 5, context: html, text, full: html, text
    Fixing issues in ticket #8537
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.html
  • lines changed 49, context: html, text, full: html, text
    Description and Method edits for FSU Replication Timing (Release 2) RM#7663
  • lines changed 6, context: html, text, full: html, text
    Minor edit to description of FSU Replication Timing (Release 2) RM#7663
  • lines changed 6, context: html, text, full: html, text
    Adding Release Notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
  • lines changed 5, context: html, text, full: html, text
    Added release notes, dccAccessions, and the dimChecked on the filerComposite
  • lines changed 1, context: html, text, full: html, text
    Revoking replicate 2 of the Hela whole cell sample, changing the date of the release, setting the replicates to all
  • lines changed 7, context: html, text, full: html, text
    Html Changes in ticket 5942
  • lines changed 111, context: html, text, full: html, text
    Adding changes to description html for GIS RNA PET (Release 2) 5942
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
  • lines changed 3, context: html, text, full: html, text
    Added release notes, dccAccessions, and the dimChecked on the filerComposite
  • lines changed 36, context: html, text, full: html, text
    Revoking replicate 2 of the Hela whole cell sample, changing the date of the release, setting the replicates to all
  • lines changed 2, context: html, text, full: html, text
    shortening 2 long labels
  • lines changed 181, context: html, text, full: html, text
    Changing the sort order for views
  • lines changed 5, context: html, text, full: html, text
    Trying again to reorder the views
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
  • lines changed 747, context: html, text, full: html, text
    added in new tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html
  • lines changed 35, context: html, text, full: html, text
    updates description and references based on lab's input
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html
  • lines changed 18, context: html, text, full: html, text
    Checking-in change for Updating html for UNC BSU Prot to have release notes (Release 2) RM#6805
  • lines changed 6, context: html, text, full: html, text
    add release note which was accidently placed in the old html
  • lines changed 7, context: html, text, full: html, text
    try to resolve merge conflict
  • lines changed 6, context: html, text, full: html, text
    add release note back
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.html
  • lines changed 43, context: html, text, full: html, text
    update edits from John
  • lines changed 1, context: html, text, full: html, text
    updates description and references based on lab's input
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
  • lines changed 1, context: html, text, full: html, text
    fix long label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.html
  • lines changed 1, context: html, text, full: html, text
    added in new release date
  • lines changed 11, context: html, text, full: html, text
    fixed for qa dgf html
  • lines changed 1, context: html, text, full: html, text
    fixing html link
  • lines changed 2, context: html, text, full: html, text
    added version number to bowtie
  • lines changed 1, context: html, text, full: html, text
    added version number to bowtie perperly this time
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.ra
  • lines changed 71, context: html, text, full: html, text
    first attempt at labels for uw dgf
  • lines changed 208, context: html, text, full: html, text
    removing unnecessary lines
  • lines changed 4, context: html, text, full: html, text
    last of the labels
  • lines changed 4, context: html, text, full: html, text
    adding rep tags for uw dgf
  • lines changed 5, context: html, text, full: html, text
    more shortlabels for uw dgf
  • lines changed 43, context: html, text, full: html, text
    removed filter composite
  • lines changed 0, context: html, text, full: html, text
    spacing issues in the text
  • lines changed 1, context: html, text, full: html, text
    added proper link, made draw window 100m
  • lines changed 1, context: html, text, full: html, text
    max window to 250M to encompass chr1
  • lines changed 1, context: html, text, full: html, text
    fixed window again
• src/hg/makeDb/trackDb/human/snp131Clinical.html
  • lines changed 261, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/human/snp131NonClinical.html
  • lines changed 265, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    adding allMis0 and geoFor1 overrides
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 1, context: html, text, full: html, text
    Changed default species to what Jim recommended in http://redmine.soe.ucsc.edu/issues/7038#note-28.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 137, context: html, text, full: html, text
    added in known expIds
  • lines changed 469, context: html, text, full: html, text
    added in the rest of the expIds
  • lines changed 729, context: html, text, full: html, text
    added in the last of the missing cshl long mouse tracks
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 209, context: html, text, full: html, text
    add new expId
  • lines changed 194, context: html, text, full: html, text
    add controlId
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Removed extra rnaExtract information at the composite stanza.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 15, context: html, text, full: html, text
    add revoked status to those datasets with input (control) only but no corresponding Tfbs datasets
  • lines changed 3, context: html, text, full: html, text
    add revoked status
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 8, context: html, text, full: html, text
    Fixed the MEL Cell line to be referenced as M rather than U. Redmine #7516, #6703.
  • lines changed 11, context: html, text, full: html, text
    Fixed sex of G1E and G1E-ER4 cell line to be M. Redmine #6703, #107.
  • lines changed 49, context: html, text, full: html, text
    Fixed control's that stated None when they should state Input. Redmine #6703.
  • lines changed 190, context: html, text, full: html, text
    Revoked MEL input not used. Updated Sort Order. Redmine #6703."
  • lines changed 226, context: html, text, full: html, text
    added accessions to PsuHistone to coincide with release 2
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuRnaSeq.ra
  • lines changed 253, context: html, text, full: html, text
    Fixed sex of G1E and G1E-ER4 cell line to be M. Redmine #6703, #107.
  • lines changed 73, context: html, text, full: html, text
    Fixed cell line designations from Megakaryocyte and Erythroblast from U to B. Redmine #107.
  • lines changed 2, context: html, text, full: html, text
    Updated expVars to add readType. Redmone #107.
  • lines changed 3, context: html, text, full: html, text
    Removed the localization and rnaExtract added to the composite level. Redmine #8659.
  • lines changed 152, context: html, text, full: html, text
    Fixed long label for 1 experiment. Added labExpId for experimetns to be an expVar. Redmine #107.
  • lines changed 301, context: html, text, full: html, text
    Added UCSC accession numbers. Redmine #107.
  • lines changed 133, context: html, text, full: html, text
    Added md5sum to metadata. Redmine #107.
  • lines changed 2, context: html, text, full: html, text
    Fixed md5sum error for file. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 28, context: html, text, full: html, text
    Fixed the MEL Cell line to be referenced as M rather than U. Redmine #7516, #6703.
  • lines changed 140, context: html, text, full: html, text
    Fixed typo in DDF that had control as None instead of Input. Redmine #7516.
  • lines changed 913, context: html, text, full: html, text
    Added 6 time course datasets. Redmine #7516.
  • lines changed 157, context: html, text, full: html, text
    Added last input controls for time course datasets. Redmin #7516.
  • lines changed 2, context: html, text, full: html, text
    Added treatment as an experimental var. Redmine #7516.
  • lines changed 44, context: html, text, full: html, text
    Added labExpId to fileSortOrder, metaDb and expVars. Redmine #7516.
  • lines changed 205, context: html, text, full: html, text
    Added ucsc accession numbers and md5sum. Redmine #7516.
  • lines changed 78, context: html, text, full: html, text
    Added controlId's for new experiments. Redmine #7516
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 26, context: html, text, full: html, text
    added GEO accessions for mm9 SYDH RNA with bigwig fix, ticket #8653
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Removed extra rnaExtract information at the composite stanza.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuHistone.ra
  • lines changed 474, context: html, text, full: html, text
    Staging on beta PSU Histone (Release 2) RM#6703
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhRnaSeq.ra
  • lines changed 58, context: html, text, full: html, text
    Staging on beta SYDH RNA-seq mm9 (Release 2) RM#8653
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuHistone.ra
  • lines changed 474, context: html, text, full: html, text
    staging on public PSU Histone mm9 (Release2) RM#6703
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhRnaSeq.ra
  • lines changed 58, context: html, text, full: html, text
    Staging on public mm9, Stanford Yale RNA-Seq (Release 2) RM#8653
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Adding notes file and structure for a release2 with a relase notes to explain replaced file
  • lines changed 2, context: html, text, full: html, text
    Staging on beta SYDH RNA-seq mm9 (Release 2) RM#8653
  • lines changed 2, context: html, text, full: html, text
    Staging on public mm9, Stanford Yale RNA-Seq (Release 2) RM#8653
  • lines changed 2, context: html, text, full: html, text
    Staging on beta PSU Histone (Release 2) RM#6703
  • lines changed 2, context: html, text, full: html, text
    staging on public PSU Histone mm9 (Release2) RM#6703
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.html
  • lines changed 1, context: html, text, full: html, text
    update release note
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra
  • lines changed 2, context: html, text, full: html, text
    fix double entries of celltype B-cell
  • lines changed 88, context: html, text, full: html, text
    fix long labels
  • lines changed 27, context: html, text, full: html, text
    fix long labels
  • lines changed 2, context: html, text, full: html, text
    clean up longlabels
  • lines changed 1, context: html, text, full: html, text
    clean up long labels
  • lines changed 20, context: html, text, full: html, text
    correct subGroup name starts with digit
  • lines changed 154, context: html, text, full: html, text
    correct age name starts with digit
  • lines changed 53, context: html, text, full: html, text
    set, modify viewLimits based on lab's request, note 25, #7501
  • lines changed 5, context: html, text, full: html, text
    set viewLimits of other tracks
  • lines changed 4, context: html, text, full: html, text
    clean up longLabels
  • lines changed 33, context: html, text, full: html, text
    fix short labels
  • lines changed 38, context: html, text, full: html, text
    fix short labels
  • lines changed 20, context: html, text, full: html, text
    fix age and strain error for ES-E14 cells
  • lines changed 1, context: html, text, full: html, text
    fix a typo in color setting
  • lines changed 1, context: html, text, full: html, text
    fix a typo in color setting
  • lines changed 1, context: html, text, full: html, text
    clean up short labels
  • lines changed 1, context: html, text, full: html, text
    clean up shortlabels
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release3.ra
  • lines changed 3, context: html, text, full: html, text
    clean up long labels
  • lines changed 1, context: html, text, full: html, text
    change geoSeriesAccession to geoSampleAccession
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuDnase.html
  • lines changed 44, context: html, text, full: html, text
    Added skeleton of Description Page. Redmine #109.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuDnase.ra
  • lines changed 3, context: html, text, full: html, text
    Fixed default track height and sort order. Redmine #109.
  • lines changed 5, context: html, text, full: html, text
    Fixed sorting order of Treatment Column for blank to be first. Redmine #109.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.html
  • lines changed 24, context: html, text, full: html, text
    Updated track defaults and track description. Redmine #6703.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed the MEL Cell line to be referenced as M rather than U. Redmine #7516, #6703.
  • lines changed 2, context: html, text, full: html, text
    Fixed sex of G1E and G1E-ER4 cell line to be M. Redmine #6703, #107.
  • lines changed 52, context: html, text, full: html, text
    Added reference to release2 html file and updated short labels. Redmine #6703.
  • lines changed 70, context: html, text, full: html, text
    Revoked MEL input not used. Updated Sort Order. Redmine #6703."
  • lines changed 1, context: html, text, full: html, text
    Added in control id column. Redmine # 6703.
  • lines changed 20, context: html, text, full: html, text
    Updated track defaults and track description. Redmine #6703.
  • lines changed 1, context: html, text, full: html, text
    Added GEO Sample Accession in file sort order.
  • lines changed 1, context: html, text, full: html, text
    Accidently removked a k for an Pk in an object name. Redmine #6703.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.html
  • lines changed 65, context: html, text, full: html, text
    Updated track Description. Redmine #107.
  • lines changed 5, context: html, text, full: html, text
    Updated Credits section for track. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.ra
  • lines changed 126, context: html, text, full: html, text
    Fixed sex of G1E and G1E-ER4 cell line to be M. Redmine #6703, #107.
  • lines changed 36, context: html, text, full: html, text
    Fixed cell line designations from Megakaryocyte and Erythroblast from U to B. Redmine #107.
  • lines changed 114, context: html, text, full: html, text
    Updated defaults and seperated time course datasets. Redmine #107.
  • lines changed 76, context: html, text, full: html, text
    Updated long and short labels. Redmine #107.
  • lines changed 57, context: html, text, full: html, text
    Updated sortOrder of view, Short labels for Plus and Minus Signal and added geoSampleAccession for fileSortOrder. Also updated default view ranges for Signal data. Redmine #107.
  • lines changed 4, context: html, text, full: html, text
    Fixed long label for 1 experiment. Added labExpId for experimetns to be an expVar. Redmine #107.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in fileSortOrder for replicate. Redmine #107.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html
  • lines changed 5, context: html, text, full: html, text
    Updated credits section. Redmine #7516.
  • lines changed 17, context: html, text, full: html, text
    Added release notes. Redmine #7516.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.ra
  • lines changed 5, context: html, text, full: html, text
    Fixed the MEL Cell line to be referenced as M rather than U. Redmine #7516, #6703.
  • lines changed 166, context: html, text, full: html, text
    Added 6 time course datasets. Redmine #7516.
  • lines changed 54, context: html, text, full: html, text
    Added last input controls for time course datasets. Redmin #7516.
  • lines changed 89, context: html, text, full: html, text
    Updated track defaults and seperated time course data out. Redmine #7516.
  • lines changed 1, context: html, text, full: html, text
    Added controlId into the fileSortOrder. Redmine #7516.
  • lines changed 6, context: html, text, full: html, text
    Moved Time-Course Inputs under the Time-Course G1E-ER4 column. Redmine #7516.
  • lines changed 64, context: html, text, full: html, text
    Fixed long and short labels. Redmine #7516.
  • lines changed 37, context: html, text, full: html, text
    Fixed long and short labels. Also updated signal to be at height 50. Redmine #7516.
  • lines changed 18, context: html, text, full: html, text
    Modified "Time Course" -> "TC" to be consistent with RNA-seq data set. Redmine #7516.
  • lines changed 7, context: html, text, full: html, text
    Fixed the default Signal Range for TimeCourse datasets. Redmine #7516.
  • lines changed 1, context: html, text, full: html, text
    Added labExpId to fileSortOrder, metaDb and expVars. Redmine #7516.
  • lines changed 1, context: html, text, full: html, text
    Added geoSample in fileSortOrder. Redmine #7516.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.release2.html
  • lines changed 69, context: html, text, full: html, text
    Adding notes file and structure for a release2 with a relase notes to explain replaced file
  • lines changed 12, context: html, text, full: html, text
    Adding the changes from ticket 8653
  • lines changed 1, context: html, text, full: html, text
    Round 2 of fixing the html errors in ticket 8653
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.release2.ra
  • lines changed 123, context: html, text, full: html, text
    Adding notes file and structure for a release2 with a relase notes to explain replaced file
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 125, context: html, text, full: html, text
    adding overrides for Rn5 DipOrd1 HetGla2 HetGla1 SpeTri2 OchPri2 OtoGar3 MicMur1 TarSyr1 SaiBol1 PapHam1 RheMac3 NomLeu1 NomLeu2 GorGor3 PteVam1 MyoLuc2 CanFam3 FelCat5 FelCat4 OviAri1 TurTru1 TurTru2 VicPac1 SusScr1 ChoHof1 DasNov3 DasNov2 TriMan1 ProCap1 MacEug2 SarHar1 ChrPic1 MelUnd1 TaeGut1 GeoFor1 GalGal4 MelGal1 LatCha1 OreNil1 OreNil2 Fr3
• src/hg/makeDb/trackDb/rat/rn4/snp125.html
  • lines changed 52, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp125.html
  • lines changed 52, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp126.html
  • lines changed 52, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp127.html
  • lines changed 52, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp128.html
  • lines changed 64, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp129.html
  • lines changed 57, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp130.html
  • lines changed 54, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp131.html
  • lines changed 57, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp132.shared.html
  • lines changed 57, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp134.html
  • lines changed 36, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp134.shared.html
  • lines changed 360, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp134Common.html
  • lines changed 28, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp134Flagged.html
  • lines changed 29, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp134Mult.html
  • lines changed 25, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/snp135.shared.html
  • lines changed 56, context: html, text, full: html, text
    Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Brooke pointed out that the change in hgc affects all SNPs tracks for versions 125 onward,
    so track details should make clear the relationship of dbSNP terms used in the table (and by
    dbSNP) to Sequence Ontology terms shown on the details page.
    I also cleaned up some miscellany as encountered, and removed track HTML for SNP tracks that
    never were released.
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    adding 7-way conservation for geoFor1
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding chainNet definitions for galGal4
• src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra
  • lines changed 11, context: html, text, full: html, text
    adding geoFor1 and mm10 overrides
• src/hg/makeDb/trackDb/uniGene_3.html
  • lines changed 39, context: html, text, full: html, text
    Made changes to the description page (redmine #2904)
• src/hg/makeDb/trackDb/zebraFinch/trackDb.chainNet.ra
  • lines changed 14, context: html, text, full: html, text
    adding overrides for geoFor1 melGal1 and mm10
• src/hg/makefile
  • lines changed 3, context: html, text, full: html, text
    stop building the proteome browser binaries and the protein library. This required a small change to hgGene which had a little bit of code supporting the SAM T-02 links that were only present in sacCer1 #5740
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 193, context: html, text, full: html, text
    Initial db list set up for ensGene V68.
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 3, context: html, text, full: html, text
    Documentation #8708 edit makeGenomeDb.pl script.
• src/hg/utils/mkPhotoGateway.pl
  • lines changed 1, context: html, text, full: html, text
    remove links out of the source code to the proteome browser (#5740)
• src/inc/dsPrint.h
  • lines changed 100, context: html, text, full: html, text
    Adding dsPrint module for printing into a dyString based stack of buffers and then optionally printing to stdout.
  • lines changed 16, context: html, text, full: html, text
    By redefining printf, puts and putc in the header file and including that header in select c files, hgTrackUi can decide to add a box around the cfg dialog after it is written. This is useful since it is not clear whether a cfg will be written until it is tried. Openning the box beforehand can leave an empty box. This minor check-in does not include changes to any cgis, only the ability to do so.
• src/lib/dsPrint.c
  • lines changed 328, context: html, text, full: html, text
    Adding dsPrint module for printing into a dyString based stack of buffers and then optionally printing to stdout.
  • lines changed 3, context: html, text, full: html, text
    By redefining printf, puts and putc in the header file and including that header in select c files, hgTrackUi can decide to add a box around the cfg dialog after it is written. This is useful since it is not clear whether a cfg will be written until it is tried. Openning the box beforehand can leave an empty box. This minor check-in does not include changes to any cgis, only the ability to do so.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding dsPrint module for printing into a dyString based stack of buffers and then optionally printing to stdout.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    stop building the proteome browser binaries and the protein library. This required a small change to hgGene which had a little bit of code supporting the SAM T-02 links that were only present in sacCer1 #5740
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v271 final build

• lines changed: 65504
• files changed: 389