All File Changes

v258_preview2 to v258_base (2011-10-04 to 2011-10-10) v258

• src/hg/encode/DAFs/3.0/hg19/wgEncodebuOrchid.daf
  • lines changed 33, context: html, text, full: html, text
    Removing redundant file
• src/hg/encode/DAFs/3.0/mm9/wgEncodeCaltechRnaSeq.daf
  • lines changed 71, context: html, text, full: html, text
    Added newest version of Caltech RNA-seq DAF.
  • lines changed 3, context: html, text, full: html, text
    Updated DAF for new bam validation and compliance of views with cv.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 22, context: html, text, full: html, text
    change the relationship between the trackHub structure and the hubConnectStatus structure to be hierarchical. This fixes #4920. We now *always* fetch the URL contents instead of trusting what's in the hubStatus table *unless* there's an error message in the hubStatus table.
  • lines changed 1, context: html, text, full: html, text
    oops... need to initialize this
  • lines changed 6, context: html, text, full: html, text
    fix a weirdness with the display caused by a pause when the track hubs are collected. The behavior was that the window would paint one way, and then repaint correctly.
  • lines changed 28, context: html, text, full: html, text
    check trackDb.txt files and hub.txt files more closely in hgHubConnect so errors can be discovered ASAP. #4679 and others.
  • lines changed 1, context: html, text, full: html, text
    don't reopen the trackHub's since they get opened when we check the status
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    change the relationship between the trackHub structure and the hubConnectStatus structure to be hierarchical. This fixes #4920. We now *always* fetch the URL contents instead of trusting what's in the hubStatus table *unless* there's an error message in the hubStatus table.
  • lines changed 7, context: html, text, full: html, text
    don't reopen the trackHub since it's already in the hubStatus
• src/hg/hgTables/mainPage.c
  • lines changed 5, context: html, text, full: html, text
    Feature #4773 Add link to hgdownload from the TB page.
  • lines changed 2, context: html, text, full: html, text
    Minor touch up of link to download page in table browser.
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    change the relationship between the trackHub structure and the hubConnectStatus structure to be hierarchical. This fixes #4920. We now *always* fetch the URL contents instead of trusting what's in the hubStatus table *unless* there's an error message in the hubStatus table.
  • lines changed 30, context: html, text, full: html, text
    check trackDb.txt files and hub.txt files more closely in hgHubConnect so errors can be discovered ASAP. #4679 and others.
  • lines changed 4, context: html, text, full: html, text
    don't reopen the trackHub's since they get opened when we check the status
• src/hg/hgTracks/imageV2.c
  • lines changed 2, context: html, text, full: html, text
    Make imgOrd based sort more deterministic. For redmine 5565.
• src/hg/hgTracks/vcfTrack.c
  • lines changed 31, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added filtering by value of FILTER column.
  • lines changed 24, context: html, text, full: html, text
    Filter VCF items at load time so they apply to haplotype sorting mode too (oops).
  • lines changed 37, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added optional filter on min QUAL score.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    In response to Redmine MLQ #5583 and a request from Brooke, reworded the error message to indicate that the problem may be that a sequence not found doesn't exist anymore (which is probably the case), to make it look less like a software bug (which it probably isn't)
• src/hg/hgc/mafClick.c
  • lines changed 2, context: html, text, full: html, text
    fix blue bug #5571
• src/hg/htdocs/ENCODE/antibodies.html
  • lines changed 1, context: html, text, full: html, text
    adjusting the height of the windows for these so that they can show without up and down internal scroll bars on a decently sized screen
• src/hg/htdocs/ENCODE/cellTypes.html
  • lines changed 1, context: html, text, full: html, text
    adjusting the height of the windows for these so that they can show without up and down internal scroll bars on a decently sized screen
• src/hg/htdocs/ENCODE/cellTypesMouse.html
  • lines changed 1, context: html, text, full: html, text
    adjusting the height of the windows for these so that they can show without up and down internal scroll bars on a decently sized screen
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    fixing typo of 'transcripts'
• src/hg/htdocs/ENCODE/otherTerms.html
  • lines changed 3, context: html, text, full: html, text
    adjusting the height of the windows for these so that they can show without up and down internal scroll bars on a decently sized screen
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 8, context: html, text, full: html, text
    Made formatting changes that Greg suggested
• src/hg/htdocs/goldenPath/help/GTF.html
  • lines changed 3, context: html, text, full: html, text
    Made formatting changes that Greg suggested
• src/hg/htdocs/goldenPath/help/hgIndelDisplay.html
  • lines changed 1, context: html, text, full: html, text
    Added missing 'y' to 'nonsynonymous'
• src/hg/htdocs/goldenPath/help/hgVcfTrackHelp.html
  • lines changed 5, context: html, text, full: html, text
    Added description of optional filtering by FILTER column values.
  • lines changed 6, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added optional filter on min QUAL score.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    Change text alignment to left rather than justified. Added just a tab bit more space between lines so they're less crowded/easier to read.
• src/hg/inc/hubConnect.h
  • lines changed 8, context: html, text, full: html, text
    change the relationship between the trackHub structure and the hubConnectStatus structure to be hierarchical. This fixes #4920. We now *always* fetch the URL contents instead of trusting what's in the hubStatus table *unless* there's an error message in the hubStatus table.
  • lines changed 5, context: html, text, full: html, text
    don't reopen the trackHub's since they get opened when we check the status
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    check trackDb.txt files and hub.txt files more closely in hgHubConnect so errors can be discovered ASAP. #4679 and others.
  • lines changed 3, context: html, text, full: html, text
    don't reopen the trackHub's since they get opened when we check the status
• src/hg/inc/vcfUi.h
  • lines changed 8, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added optional filter on min QUAL score.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v258
• src/hg/lib/genes_rat.as
  • lines changed 42, context: html, text, full: html, text
    Created .as file for genes_rat table.
• src/hg/lib/hubConnect.c
  • lines changed 207, context: html, text, full: html, text
    change the relationship between the trackHub structure and the hubConnectStatus structure to be hierarchical. This fixes #4920. We now *always* fetch the URL contents instead of trusting what's in the hubStatus table *unless* there's an error message in the hubStatus table.
  • lines changed 29, context: html, text, full: html, text
    don't reopen the trackHub's since they get opened when we check the status
• src/hg/lib/mafGene.c
  • lines changed 3, context: html, text, full: html, text
    fix a bug that only showed up in building the CDS FASTA alignments for rn4 RGD genes
• src/hg/lib/rgdGene2KeggPathway.as
  • lines changed 7, context: html, text, full: html, text
    Created rgdGene2KeggPathway.as.
• src/hg/lib/trackHub.c
  • lines changed 29, context: html, text, full: html, text
    check trackDb.txt files and hub.txt files more closely in hgHubConnect so errors can be discovered ASAP. #4679 and others.
  • lines changed 25, context: html, text, full: html, text
    don't reopen the trackHub's since they get opened when we check the status
• src/hg/lib/vcfUi.c
  • lines changed 44, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added filtering by value of FILTER column.
  • lines changed 24, context: html, text, full: html, text
    Feature #3710 (vcfTabix UI options): added optional filter on min QUAL score.
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 32, context: html, text, full: html, text
    adding upstream mafs to 8-way business
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeUwDnaseSeq.release5.notes
  • lines changed 743, context: html, text, full: html, text
    Changing name to fit with new standard
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeUwDnaseSeq.release5.notes.txt
  • lines changed 743, context: html, text, full: html, text
    Changing name to fit with new standard
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBuOrchid.release1.notes
  • lines changed 2, context: html, text, full: html, text
    updated for testing purposes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyGeneSt.release2.notes
  • lines changed 24, context: html, text, full: html, text
    adding full path to download files for easy copying, redmine 4834
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhHistone.release2.notes
  • lines changed 362, context: html, text, full: html, text
    Updated Release Notes for track. This includes adding old files and tables that were removed. Redmine #4018.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUw5C.release1.notes
  • lines changed 3, context: html, text, full: html, text
    Fixes issues in Redmine #222 1. Added the dummy table, wgEncodeUw5C to composite level metaData and added table 'by hand' to notes file 2. There is no whole-chromosome analysis as of yet. So I will commented that section for now and highlight the two other projects. 3. Updated the setnece "(Neuroblastoma cell line differentiated with retinoic acid, aka SKNSH)." -> "Updated sentence to be (neuroblastoma cell line differentiated, SKNSH, with retinoic acid)." 4. Fixed indenting to be the same for description of each view. 5. Moved the following waring to matrix view "In order to understand the Matrix data, you must download the associated primer data file." 6. Added link to cell growth protocols 7. Reordered the following sentence:"The interaction files provided map all the reads in the output sequence without a mismatch threshold." 8. Changed 2 -> Two in the following sentence: "2 replicates were performed ..." 9. Added space after greater than symbol for 'extending > 2 Mb' 10. Added space after greater than symbol for 'displaying correlation coefficient > 0.9' 11. No need for release notes for the first release. Removed this section 12. Removed extra <p> and paired up <p> with </p>
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release3.notes
  • lines changed 383, context: html, text, full: html, text
    some last second uw dnase name chages to add donor id's
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes
  • lines changed 503, context: html, text, full: html, text
    updated notes file for uw tfbs and histone
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes
  • lines changed 367, context: html, text, full: html, text
    updated notes file for uw tfbs and histone
• src/hg/makeDb/doc/hg19.txt
  • lines changed 20, context: html, text, full: html, text
    (1) Rebuilt the swissprot and proteins databases with new versions of the build scripts, (2) Rebuilt the Rfam alignments and updated the build process in hg19, (3) Modified the UCSC Genes build script to add the Rfam and tRNA transcripts to the txWalk transcripts (along with the antibodies) rather than using them as input to txWalk, (4) updated the new track details page based on feedback from Brooke
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 6, context: html, text, full: html, text
    Re-load melGal's genbank tables
  • lines changed 3, context: html, text, full: html, text
    Re-load genbank tables for melGal1 and myoLuc2
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 4, context: html, text, full: html, text
    Re-load genbank tables for melGal1 and myoLuc2
• src/hg/makeDb/doc/proteins/111004.txt
  • lines changed 641, context: html, text, full: html, text
    (1) Rebuilt the swissprot and proteins databases with new versions of the build scripts, (2) Rebuilt the Rfam alignments and updated the build process in hg19, (3) Modified the UCSC Genes build script to add the Rfam and tRNA transcripts to the txWalk transcripts (along with the antibodies) rather than using them as input to txWalk, (4) updated the new track details page based on feedback from Brooke
• src/hg/makeDb/doc/sacCer3.txt
  • lines changed 21, context: html, text, full: html, text
    add the self sgd blast tab
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 41, context: html, text, full: html, text
    (1) Rebuilt the swissprot and proteins databases with new versions of the build scripts, (2) Rebuilt the Rfam alignments and updated the build process in hg19, (3) Modified the UCSC Genes build script to add the Rfam and tRNA transcripts to the txWalk transcripts (along with the antibodies) rather than using them as input to txWalk, (4) updated the new track details page based on feedback from Brooke
• src/hg/makeDb/doc/uniProt/sp111004.txt
  • lines changed 50, context: html, text, full: html, text
    (1) Rebuilt the swissprot and proteins databases with new versions of the build scripts, (2) Rebuilt the Rfam alignments and updated the build process in hg19, (3) Modified the UCSC Genes build script to add the Rfam and tRNA transcripts to the txWalk transcripts (along with the antibodies) rather than using them as input to txWalk, (4) updated the new track details page based on feedback from Brooke
• src/hg/makeDb/doc/xenTro3.txt
  • lines changed 32, context: html, text, full: html, text
    add upstream maf files
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    turn on upstreamGeneTbl for xenTro3
  • lines changed 2, context: html, text, full: html, text
    nativ refseq disabled, Xeno refseqs enabled.
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    added sacCer3 to list to start genbank updates for it on the RR
• src/hg/makeDb/schema/all.joiner
  • lines changed 5, context: html, text, full: html, text
    Added definition of rgdGene2IdRaw for genes_rat table.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 26, context: html, text, full: html, text
    Fixing the Myocyte and Diff_7d issue
  • lines changed 1, context: html, text, full: html, text
    Reverting term back
  • lines changed 14, context: html, text, full: html, text
    Updating Antibody Docs
  • lines changed 20, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 19, context: html, text, full: html, text
    Adding Antibody
  • lines changed 2, context: html, text, full: html, text
    Adding Validation Type
  • lines changed 10, context: html, text, full: html, text
    Updated metadata to used region as an experiment defining variable. Restoring CV terms that were previously deperated in Redmine #222. There will be 11 experiments. Redmine #222.
  • lines changed 12, context: html, text, full: html, text
    Fixing a few details from the code review
  • lines changed 1, context: html, text, full: html, text
    These changes are related to QA fixes of this track. Redmine #4018 1. Changed label in matrix from 1K562 -> K562 2. Updated Peaks to be default pack 3. Greyed check boxes were fixed once Peak view was set from default hide->peak 4. Turned off Peaks configuration box 5. Updated long and short labels for 4 track that were autogenerated by pipeline 6. Updated Release Notes section to have date and states that new experiments were added 7. In Methods section of track Description changed 300-500bp -> 300-500 bp 8. Added comma after phrase Also included for each cell type 9. Split the following sentence into 2 sentences: Peaks and signals displayed in this track are the results of pooled replicate sequence and alignment files for each replicate are available for download. This should be two sentences. 10. Updated the description in cv and track to state NTera-2 instead of Ntera2. Also in track description added name for what we call cell line. 11. Updated Reference link for Using ChIP-Seq Technology to Generate High-Resolution Profiles of... 13 In References updated _BLANK to have quotes around it 14. Removed spaces for the following reference: 2011; 6(2): e17121.
  • lines changed 4, context: html, text, full: html, text
    Fixes from code review added
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 308, context: html, text, full: html, text
    Moving alpha cv to beta
• src/hg/makeDb/trackDb/drosophila/dm1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Genome Biology
• src/hg/makeDb/trackDb/drosophila/dm2/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to Genome Biology
• src/hg/makeDb/trackDb/est.html
  • lines changed 1, context: html, text, full: html, text
    The URL for one of the journal articles was redirected to another URL. Replaced the existing URL with the new one.
  • lines changed 6, context: html, text, full: html, text
    Change the formatting of two links
• src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
  • lines changed 54, context: html, text, full: html, text
    Changed some wording to address Jim's code review feedback, Redmine issue #5002, and other issues that Brooke suggested when I told her I was working on this page
  • lines changed 32, context: html, text, full: html, text
    (1) Rebuilt the swissprot and proteins databases with new versions of the build scripts, (2) Rebuilt the Rfam alignments and updated the build process in hg19, (3) Modified the UCSC Genes build script to add the Rfam and tRNA transcripts to the txWalk transcripts (along with the antibodies) rather than using them as input to txWalk, (4) updated the new track details page based on feedback from Brooke
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 181, context: html, text, full: html, text
    added in expIds and dccAccessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV3.ra
  • lines changed 1, context: html, text, full: html, text
    Removing errant expVars line
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV7.ra
  • lines changed 15, context: html, text, full: html, text
    Adding freeze date to Gencode
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 156, context: html, text, full: html, text
    experimentified
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 1, context: html, text, full: html, text
    added objStatus to renamed item and explanation
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 7, context: html, text, full: html, text
    Added fake subId for CRG Alignability data for Kate's reporting.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 35, context: html, text, full: html, text
    added in expIds and dccAccessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 1, context: html, text, full: html, text
    added treatment to expVars
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Updated file name for obj wgEncodeRegTfbsCells from wgEncodeRegTfbsCells.tab.gz -> wgEncodeRegTfbsClusteredCells.tab.gz. Fixes Redmine #5513.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 7, context: html, text, full: html, text
    adding some missing origAssembly
  • lines changed 49, context: html, text, full: html, text
    Adding the geoAccessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 25, context: html, text, full: html, text
    added in expIds and dccAccessions
  • lines changed 724, context: html, text, full: html, text
    Added back 27 files that were renamed from k562b -> k562 between release 1 and 2. Following new release policy.
  • lines changed 17, context: html, text, full: html, text
    Added md5sum for PANC-1 files that didn't have that information and lacked the .bam.bai in the fileName list. Redmine #4018. Note 46.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
  • lines changed 78, context: html, text, full: html, text
    Updated metadata to used region as an experiment defining variable. Restoring CV terms that were previously deperated in Redmine #222. There will be 11 experiments. Redmine #222.
  • lines changed 77, context: html, text, full: html, text
    added expIds and dcc accessions
  • lines changed 2, context: html, text, full: html, text
    Fixes issues in Redmine #222 1. Added the dummy table, wgEncodeUw5C to composite level metaData and added table 'by hand' to notes file 2. There is no whole-chromosome analysis as of yet. So I will commented that section for now and highlight the two other projects. 3. Updated the setnece "(Neuroblastoma cell line differentiated with retinoic acid, aka SKNSH)." -> "Updated sentence to be (neuroblastoma cell line differentiated, SKNSH, with retinoic acid)." 4. Fixed indenting to be the same for description of each view. 5. Moved the following waring to matrix view "In order to understand the Matrix data, you must download the associated primer data file." 6. Added link to cell growth protocols 7. Reordered the following sentence:"The interaction files provided map all the reads in the output sequence without a mismatch threshold." 8. Changed 2 -> Two in the following sentence: "2 replicates were performed ..." 9. Added space after greater than symbol for 'extending > 2 Mb' 10. Added space after greater than symbol for 'displaying correlation coefficient > 0.9' 11. No need for release notes for the first release. Removed this section 12. Removed extra <p> and paired up <p> with </p>
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 23, context: html, text, full: html, text
    renamed CD20+ to have it's donor id also.
  • lines changed 23, context: html, text, full: html, text
    added donor id's to cells that didn't have donors
  • lines changed 109, context: html, text, full: html, text
    restored lost metadata as seqPlatform this time
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 14, context: html, text, full: html, text
    added donor id's to cells that didn't have donors
  • lines changed 129, context: html, text, full: html, text
    some last second uw dnase name chages to add donor id's
  • lines changed 462, context: html, text, full: html, text
    added md5sums, bais to tfbs and removed origAssembly from Dnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 50, context: html, text, full: html, text
    updated md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 186, context: html, text, full: html, text
    added md5sums, bais to tfbs and removed origAssembly from Dnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging UW 5C on beta redmine 222
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 293, context: html, text, full: html, text
    staging metdb changes on beta for CSHL Long RNA-seq, redmine 43
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    fixing file name, redmine #5513
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 7, context: html, text, full: html, text
    staging metadata changes, redmine 4834
  • lines changed 49, context: html, text, full: html, text
    releasing GEO accession numbers for SUNY RIP GeneST, redmine 4834
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhHistone.ra
  • lines changed 2171, context: html, text, full: html, text
    Staging Sydh Histone hg19 onto beta 4018
  • lines changed 17, context: html, text, full: html, text
    Moving the md5sum addtions to beta #4018
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUw5C.ra
  • lines changed 766, context: html, text, full: html, text
    Staging UW 5C on beta redmine 222
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 4504, context: html, text, full: html, text
    Staging this track on beta 4460
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    fixing file name, redmine #5513
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 629, context: html, text, full: html, text
    preparing metdata and trackDb for release of SUNY RIP GeneST (Release 2), redmine 4834
  • lines changed 49, context: html, text, full: html, text
    releasing GEO accession numbers for SUNY RIP GeneST, redmine 4834
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhHistone.ra
  • lines changed 2183, context: html, text, full: html, text
    Preparing track DB for release to the RR #4018
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    preparing metdata and trackDb for release of SUNY RIP GeneST (Release 2), redmine 4834
  • lines changed 2, context: html, text, full: html, text
    Adding the geoAccessions
  • lines changed 2, context: html, text, full: html, text
    Staging Sydh Histone hg19 onto beta 4018
  • lines changed 2, context: html, text, full: html, text
    releasing GEO accession numbers for SUNY RIP GeneST, redmine 4834
  • lines changed 3, context: html, text, full: html, text
    Preparing track DB for release to the RR #4018
  • lines changed 2, context: html, text, full: html, text
    Staging this track on beta 4460
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    Staging UW 5C on beta redmine 222
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html
  • lines changed 54, context: html, text, full: html, text
    Adding text from Georgi and Brian
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
  • lines changed 12, context: html, text, full: html, text
    Fixes issues related to Redmine #43: 1. a. changed 'generate' -> 'generated' b. updated words in the following sentence 'They contain information about human RNAs > 200 nucleotides in length obtained as short reads off the Illumina GAIIx platform.' -> 'They contain information about human RNAs > 200 nucleotides in length that were obtained as short reads from the Illumina GAIIx platform.' c. since data is plural updated the sentence: '...there is also data from various subcellular...' -> '...there are also data from various...' 2. Changed 2 instances of RNA-Seq -> RNA-seq 3. Removed 4 instances of first person and changed to third person passive 4. Removed pubmed id in link and used the procotol name to link to the paper.
  • lines changed 5, context: html, text, full: html, text
    Fixes for Redmine #43 1. Changed external links to internal links for data from same biological replicates. GIS RNA-PET is a link to genome-preview since this is not released yet, the rest are relative links. 2. Changed is -> are since data is plural in the following sentence:"Data is available from biological replicates of several cell lines"
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    Fixes for Redmine #43 1. Updated hypertext link for STAR information to be Gineras lab, instead of actual url. 2. Updated wording in the sentence about threshold to make it clear that the user should use the threshold. Changed "The IDR values for each element are included in the files for end-users to threshold on." -> "The IDR values for each element are included in the files for end-users to use as a threshold." 3. Fixed spelling of explanation 4. Fixed double the's "... the the ..." 5. Fixed spelling of signals 6. Fixed spelling of available.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 64, context: html, text, full: html, text
    Long labels and commenting out one track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.html
  • lines changed 3, context: html, text, full: html, text
    Starting the change for the Alignments label
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    Added description of the tag XA. Redmine #42.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
  • lines changed 137, context: html, text, full: html, text
    Removing the view and attempting to fix the labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html
  • lines changed 39, context: html, text, full: html, text
    releasing Release2 of SUNY RIP GeneST, redmine 4834
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
  • lines changed 1, context: html, text, full: html, text
    Adding the geoAccessions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 110, context: html, text, full: html, text
    releasing Release2 of SUNY RIP GeneST, redmine 4834
  • lines changed 1, context: html, text, full: html, text
    removing the html line, redmine 4834
  • lines changed 1, context: html, text, full: html, text
    releasing GEO accession numbers for SUNY RIP GeneST, redmine 4834
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
  • lines changed 51, context: html, text, full: html, text
    Preparing track DB for release to the RR #4018
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.html
  • lines changed 6, context: html, text, full: html, text
    Vanessa's html suggestions
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    These changes are related to QA fixes of this track. Redmine #4018 1. Changed label in matrix from 1K562 -> K562 2. Updated Peaks to be default pack 3. Greyed check boxes were fixed once Peak view was set from default hide->peak 4. Turned off Peaks configuration box 5. Updated long and short labels for 4 track that were autogenerated by pipeline 6. Updated Release Notes section to have date and states that new experiments were added 7. In Methods section of track Description changed 300-500bp -> 300-500 bp 8. Added comma after phrase Also included for each cell type 9. Split the following sentence into 2 sentences: Peaks and signals displayed in this track are the results of pooled replicate sequence and alignment files for each replicate are available for download. This should be two sentences. 10. Updated the description in cv and track to state NTera-2 instead of Ntera2. Also in track description added name for what we call cell line. 11. Updated Reference link for Using ChIP-Seq Technology to Generate High-Resolution Profiles of... 13 In References updated _BLANK to have quotes around it 14. Removed spaces for the following reference: 2011; 6(2): e17121.
  • lines changed 3, context: html, text, full: html, text
    Forgot 13. In References updated _BLANK to have quotes around it, in last commit.
  • lines changed 1, context: html, text, full: html, text
    Fixed overhanging period in link. Redmine #4018. Note #42.
  • lines changed 4, context: html, text, full: html, text
    Updated hyperlinks to not expose the url but to have human readable text. Redmine #4018.
  • lines changed 7, context: html, text, full: html, text
    Fixed hyperlinks to be on 'Chip and Library Protocol' and 'detailed protocol' instead of the institute. Redmine #4018.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
  • lines changed 15, context: html, text, full: html, text
    These changes are related to QA fixes of this track. Redmine #4018 1. Changed label in matrix from 1K562 -> K562 2. Updated Peaks to be default pack 3. Greyed check boxes were fixed once Peak view was set from default hide->peak 4. Turned off Peaks configuration box 5. Updated long and short labels for 4 track that were autogenerated by pipeline 6. Updated Release Notes section to have date and states that new experiments were added 7. In Methods section of track Description changed 300-500bp -> 300-500 bp 8. Added comma after phrase Also included for each cell type 9. Split the following sentence into 2 sentences: Peaks and signals displayed in this track are the results of pooled replicate sequence and alignment files for each replicate are available for download. This should be two sentences. 10. Updated the description in cv and track to state NTera-2 instead of Ntera2. Also in track description added name for what we call cell line. 11. Updated Reference link for Using ChIP-Seq Technology to Generate High-Resolution Profiles of... 13 In References updated _BLANK to have quotes around it 14. Removed spaces for the following reference: 2011; 6(2): e17121.
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    Added controlId and geoSampleAccession columns to hgFileUi. Redmine #4018.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 287, context: html, text, full: html, text
    Preparing track DB for release to the RR #4018
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
  • lines changed 46, context: html, text, full: html, text
    Fixes issues in Redmine #222 1. Added the dummy table, wgEncodeUw5C to composite level metaData and added table 'by hand' to notes file 2. There is no whole-chromosome analysis as of yet. So I will commented that section for now and highlight the two other projects. 3. Updated the setnece "(Neuroblastoma cell line differentiated with retinoic acid, aka SKNSH)." -> "Updated sentence to be (neuroblastoma cell line differentiated, SKNSH, with retinoic acid)." 4. Fixed indenting to be the same for description of each view. 5. Moved the following waring to matrix view "In order to understand the Matrix data, you must download the associated primer data file." 6. Added link to cell growth protocols 7. Reordered the following sentence:"The interaction files provided map all the reads in the output sequence without a mismatch threshold." 8. Changed 2 -> Two in the following sentence: "2 replicates were performed ..." 9. Added space after greater than symbol for 'extending > 2 Mb' 10. Added space after greater than symbol for 'displaying correlation coefficient > 0.9' 11. No need for release notes for the first release. Removed this section 12. Removed extra <p> and paired up <p> with </p>
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
  • lines changed 1, context: html, text, full: html, text
    changed filesort order
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html
  • lines changed 5, context: html, text, full: html, text
    Adding release 2 notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra
  • lines changed 1, context: html, text, full: html, text
    Adding release 2 notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 17, context: html, text, full: html, text
    renamed CD20+ to have it's donor id also.
  • lines changed 8, context: html, text, full: html, text
    added donor id's to cells that didn't have donors
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 9, context: html, text, full: html, text
    Fixes for track. Redmine #4460.1. Removed extra quotation mark 2. Update false discovery percent to be spelled out 3. Added space between > and 0.9. The greater than symbol is html compliant. 4. Changed Release Month to be October. 5. Removed numeric indication of number of experiments and state experiments were added. 6. Added miss closing paragraph tags 12)Moved the closing tag from after list in Release Notes to before list in release notes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 9, context: html, text, full: html, text
    added donor id's to cells that didn't have donors
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    some last second uw dnase name chages to add donor id's
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    Updated tag for WI38 hydroxytamoxifen to go from WI30 -> WI38. Removed Treatment column as this is redundant since this is collapsed in the Cell Label.
• src/hg/makeDb/trackDb/intronEst.html
  • lines changed 1, context: html, text, full: html, text
    The URL for one of the journal articles was redirected to another URL. Replaced the existing URL with the new one.
  • lines changed 6, context: html, text, full: html, text
    Change the formatting of two links
• src/hg/makeDb/trackDb/mgcFullMrna.html
  • lines changed 8, context: html, text, full: html, text
    Changed link so its target would open in a new tab. Changed the formatting of another link. Removed the second link to the MGC since it was already linked earlier in the page.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 72, context: html, text, full: html, text
    Added controlId as a number that corresponds to the labExpId of the given control experiment. Also update control for 2 Experiments that had stated None but were Control 32bp.
  • lines changed 127, context: html, text, full: html, text
    Updated treatment to be descriptive of what the was actually done to the cells. Moved cell state into cell version. THIS IS A TRIAL. Redmine #3733, note #40.
  • lines changed 575, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 21, context: html, text, full: html, text
    Updated Obj names to have control in them for objs that failed to have control.
  • lines changed 6, context: html, text, full: html, text
    Added expVars and composite metadata.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 121, context: html, text, full: html, text
    Added controlId as a number that corresponds to the labExpId of the given control experiment. Also update control for 2 Experiments that had stated None but were Control 32bp.
  • lines changed 241, context: html, text, full: html, text
    Updated treatment to be descriptive of what the was actually done to the cells. Moved cell state into cell version. THIS IS A TRIAL. Redmine #3733, note #40.
  • lines changed 819, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 68, context: html, text, full: html, text
    Added expVars and composite metadata and renamed obj that was missed in initial rename.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars and composite metadata.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra
  • lines changed 3, context: html, text, full: html, text
    Updated 'Shade of lowest-scoring items' to be 55%. Also updated Signal View range 0:1 and removed individual configuration of Signal Sub-tracks.
  • lines changed 4, context: html, text, full: html, text
    Removed Protocol has a dimension, as this is not a major variable changing in the track.
  • lines changed 9, context: html, text, full: html, text
    Added controlId as a number that corresponds to the labExpId of the given control experiment. Also update control for 2 Experiments that had stated None but were Control 32bp.
  • lines changed 10, context: html, text, full: html, text
    Updated dimensions to be treatment x factor because cell line was the same. Also updated defaults for the 2 tracks.
  • lines changed 1, context: html, text, full: html, text
    Updated treatment to be descriptive of what the was actually done to the cells. Moved cell state into cell version. THIS IS A TRIAL. Redmine #3733, note #40.
  • lines changed 88, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 8, context: html, text, full: html, text
    Updated Obj names to have control in them for objs that failed to have control.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Updated 'Shade of lowest-scoring items' to be 55%. Also updated Signal View range 0:1 and removed individual configuration of Signal Sub-tracks.
  • lines changed 4, context: html, text, full: html, text
    Removed Protocol has a dimension, as this is not a major variable changing in the track.
  • lines changed 8, context: html, text, full: html, text
    Updated dimensions to be treatment x factor because cell line was the same. Also updated defaults for the 2 tracks.
  • lines changed 1, context: html, text, full: html, text
    Updated treatment to be descriptive of what the was actually done to the cells. Moved cell state into cell version. THIS IS A TRIAL. Redmine #3733, note #40.
  • lines changed 170, context: html, text, full: html, text
    Updated Treatments to be descriptive of the exact treatment used and not the differentiation state and treatment. Redmine #3733.
  • lines changed 2, context: html, text, full: html, text
    Added expVars and composite metadata and renamed obj that was missed in initial rename.
• src/hg/makeDb/trackDb/mrna.html
  • lines changed 1, context: html, text, full: html, text
    The URL for one of the journal articles was redirected to another URL. Replaced the existing URL with the new one.
  • lines changed 6, context: html, text, full: html, text
    Change the formatting of two links
• src/hg/makeDb/trackDb/phastConsElements.html
  • lines changed 9, context: html, text, full: html, text
    Made PHAST a link to assist users who want more info. Fixed some html formatting.
• src/hg/makeDb/trackDb/refGene.html
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    Change two links so their target would open in a new tab when clicked. Changed the formatting of one link.
• src/hg/makeDb/trackDb/sacCer/sacCer3/gold.html
  • lines changed 2, context: html, text, full: html, text
    Axed a needles colon and put the link across more words since it seemed to make more sense that way.
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
  • lines changed 7, context: html, text, full: html, text
    Minor grammar corrections and added correct styling to table
• src/hg/makeDb/trackDb/trackDb.ra
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    temporarily check in a nextNcbiIncidentDb track to verify new auto track procedure
• src/hg/makeDb/trackDb/xenTro/intronEst.html
  • lines changed 4, context: html, text, full: html, text
    Changed the format of a link. One of the journal links was being redirected to a new URL. Changed to link to point straight to the new URL.
• src/hg/makeDb/trackDb/xenTro/mgcFullMrna.html
  • lines changed 9, context: html, text, full: html, text
    Changed link so its target would open in a new tab. Changed the formatting of another link. Removed the second link to the MGC since it was already linked earlier in the page. Corrected the BLAT citation.
• src/hg/makeDb/trackDb/xenoMrna.html
  • lines changed 1, context: html, text, full: html, text
    The URL for one of the journal articles was redirected to another URL. Replaced the existing URL with the new one.
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    Change the formatting of two links
• src/hg/makeDb/trackDb/xenoRefGene.html
  • lines changed 2, context: html, text, full: html, text
    Changed two hyperlinks so their target URL opens in a new tab
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    Change the formatting of a link
• src/hg/makeDb/trackDb/zebrafish/affyZonWildType.html
  • lines changed 7, context: html, text, full: html, text
    The journal article link was being redirected. Changed the link to go directly to the new URL. Corrected citation format.
• src/hg/makeDb/trackDb/zebrafish/danRer1/bacEndPairs.html
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    Replaced link to NIOB with link to Hubrecht Institute
• src/hg/makeDb/trackDb/zebrafish/danRer1/bacEndSingles.html
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    Replaced link to NIOB with link to Hubrecht Institute
• src/hg/makeDb/trackDb/zebrafish/danRer2/bacEndPairs.html
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    Replaced link to NIOB with link to Hubrecht Institute
• src/hg/makeDb/trackDb/zebrafish/danRer2/bacEndSingles.html
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    Replaced link to NIOB with link to Hubrecht Institute
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndPairs.html
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    Changed broken link to NIOB to point to Hubrecht Institute
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndSingles.html
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    Changed broken link to NIOB to point to Hubrecht Institute
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndPairs.html
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    Replaced link to NIOB with link to Hubrecht Institute
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndSingles.html
  • lines changed 2, context: html, text, full: html, text
    Replaced link to NIOB with link to Hubrecht Institute
• src/hg/makeDb/trackDb/zebrafish/danRer5/affyConsensusAndTargetZonWildType.html
  • lines changed 2, context: html, text, full: html, text
    The journal article link was being redirected. Changed the link to go directly to the new URL. Corrected citation format.
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
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    reordered orgs based on the phylo tree
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
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    reordered orgs based on the phylo tree
• src/hg/utils/automation/HgDb.pm
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    added functionality to set the hg.conf file via environment variable like how QA'ers do it.
• src/hg/utils/automation/doAutoTrack.pl
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/cleanup.sh
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/commonHeader.inc
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/download.sh
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/incidentDb.ra
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/load.sh
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/loadInProgressTable.sh
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/process.sh
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/push.sh
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    initial version of the auto track procedures
• src/hg/utils/automation/incidentDb/verify.sh
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    initial version of the auto track procedures
• src/hg/wikiMods/README.1.16.3
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    wiki patches for version 1.16.3
• src/hg/wikiMods/extensions.SpecialUserloginUCSC.php
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    wiki patches for version 1.16.3
• src/hg/wikiMods/extensions.SpecialUserlogoutUCSC.php
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    wiki patches for version 1.16.3
• src/hg/wikiMods/includes.specials.SpecialUserloginUCSC.php
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    wiki patches for version 1.16.3
• src/hg/wikiMods/includes.specials.SpecialUserlogoutUCSC.php
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    wiki patches for version 1.16.3
• src/hg/wikiMods/includes.templates.UserloginUCSC.php
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    wiki patches for version 1.16.3
• src/lib/vcf.c
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    Fixed an incorrect regex substr index for VCF FILTER or ALT header defs.
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    Loosened regex and handle new non-numeric values of ##FORMAT's "Number"introduced in VCF 4.1.
• src/utils/qa/weeklybld/buildEnv.csh
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    v258 final build

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