All File Changes

v262_base to v263_preview (2012-01-24 to 2012-01-31) v263

• python/lib/ucscgenomics/geo.py
  • lines changed 57, context: html, text, full: html, text
    added geo library and metaDb ra file library
• python/lib/ucscgenomics/mdb.py
  • lines changed 194, context: html, text, full: html, text
    added geo library and metaDb ra file library
• python/lib/ucscgenomics/mkChangeNotes.py
  • lines changed 8, context: html, text, full: html, text
    added md5sum repush options for those rare situations where something changes md5sums between releases, but retains the same filename, also added the outputting of an attic files list
  • lines changed 3, context: html, text, full: html, text
    attic for single release mode
• python/lib/ucscgenomics/ra.py
  • lines changed 113, context: html, text, full: html, text
    added cvValidate back into the tree
  • lines changed 77, context: html, text, full: html, text
    fixed merge conflict with ra.py
• python/lib/ucscgenomics/track.py
  • lines changed 89, context: html, text, full: html, text
    added cvValidate back into the tree
• python/lib/ucscgenomics/ucscUtils.py
  • lines changed 27, context: html, text, full: html, text
    changed over to Needleman-Wunsch for alignment of lists
  • lines changed 27, context: html, text, full: html, text
    This somehow included cv.ra changes that I don't remember adding in. Revert "changed over to Needleman-Wunsch for alignment of lists" This reverts commit c6bd349fa19566d37c1ac02a42865a9031420acb.
  • lines changed 27, context: html, text, full: html, text
    moved to Needleman-Wunsch for alignment of lists, left in code to convert to Smith-Waterman if this proves to be a bad decision
• python/programs/cvValidate/cvValidate
  • lines changed 34, context: html, text, full: html, text
    added cvValidate back into the tree
• src/hg/encode/encodeAnnounce/announceBoilerplate.html
  • lines changed 3, context: html, text, full: html, text
    Change contact link. Redmine 6568
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 71, context: html, text, full: html, text
    many efficiency improvements
  • lines changed 8, context: html, text, full: html, text
    fixed a bug where a link that used to be a file in the history persisted between passes of the history
• src/hg/encode/encodeQaCheckHgdownloadFiles/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/encode/encodeQaInit/makefile
  • lines changed 1, context: html, text, full: html, text
    changed clean message
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 35, context: html, text, full: html, text
    now prints sorted makefile for metaDb, and more status messages so you know what's going on
  • lines changed 8, context: html, text, full: html, text
    fixed a bug where if it is release 1, and no betaMetaDb.ra exists, the program would crash.
• src/hg/encode/encodeQaPrepareRelease/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/encode/encodeQaSqlRelease/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/encode/qaEncodeTracks2/makefile
  • lines changed 27, context: html, text, full: html, text
    adding in makefile for qaEncodeTracks
• src/hg/encode/qaTableCheck/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/encode/qaUpdateMetadata/makefile
  • lines changed 1, context: html, text, full: html, text
    changed makefile clean messages to reflect the script itself
• src/hg/hgGene/rgdInfo.c
  • lines changed 4, context: html, text, full: html, text
    change rn4 table name of genes_rat to rgdGene2Raw
• src/hg/hgGene/synonym.c
  • lines changed 1, context: html, text, full: html, text
    change rn4 table name of genes_rat to rgdGene2Raw
• src/hg/hgTracks/container.c
  • lines changed 1, context: html, text, full: html, text
    always step up through the ancestors when looking for track handlers (#6499)
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    always step up through the ancestors when looking for track handlers (#6499)
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    always step up through the ancestors when looking for track handlers (#6499)
• src/hg/hgTracks/searchTracks.c
  • lines changed 43, context: html, text, full: html, text
    Load trackList only if we have to; this will speedup entry page (see #5675)
• src/hg/hgTracks/simpleTracks.c
  • lines changed 35, context: html, text, full: html, text
    always step up through the ancestors when looking for track handlers (#6499)
• src/hg/hgc/hgc.c
  • lines changed 11, context: html, text, full: html, text
    redmine #6725 redirect URLs to new CloneDB (from Clone Registry)
• src/hg/hgc/vcfClick.c
  • lines changed 1, context: html, text, full: html, text
    VCF genotype details: one more proportion needed to be converted to percent, to match the rest.
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    Fix minor formatting error
• src/hg/htdocs/Neandertal/index.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken link
• src/hg/htdocs/admin/git.html
  • lines changed 15, context: html, text, full: html, text
    Added link to source via gitweb. Added instructions to construct a permanent URL to source code.
• src/hg/htdocs/goldenPath/help/customTrackLoad.html
  • lines changed 3, context: html, text, full: html, text
    Substituted character in password substitution instructions to make less ambiguous with @ that needs to come between password and domain in URL
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 3, context: html, text, full: html, text
    Substituted character in password substitution instructions to make less ambiguous with @ that needs to come between password and domain in URL
  • lines changed 24, context: html, text, full: html, text
    Added type, maxItems and bigDataUrl lines to the Track Lines section
• src/hg/htdocs/goldenPath/help/multiView.html
  • lines changed 6, context: html, text, full: html, text
    Checking in documentation (subtrack configuration) so that Pauline can further edit, redmine# 4665
  • lines changed 6, context: html, text, full: html, text
    Minor edits for clarity about redmine 4665 changes.
  • lines changed 1, context: html, text, full: html, text
    added EM tags to be consistent with the rest of the page for the subtrack configuration documentation, redmine# 4665
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 16, context: html, text, full: html, text
    Fixed broken links
  • lines changed 102, context: html, text, full: html, text
    Archived some items. Changed some links to not open new window.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 59, context: html, text, full: html, text
    Added new pubs from David, updated several existing entries with new journal info.
  • lines changed 1, context: html, text, full: html, text
    oops, left out year in Alfoldi citation.
• src/hg/htdocs/images/phylo/felCat4_6way.gif
  • lines changed 0, context: html, text, full: html, text
    edmine bug #6679 Use common name instead of assembly in the felCat4_6way.gif used in the conservation track
• src/hg/htdocs/indexNews.html
  • lines changed 97, context: html, text, full: html, text
    Archived some items. Changed some links to not open new window.
• src/hg/inc/trackDb.h
  • lines changed 2, context: html, text, full: html, text
    configurable off should be supported at composite/view and subtrack level. Before this it was only at subtrack level.
  • lines changed 2, context: html, text, full: html, text
    Discovered there is still reason to distinguish 'configurable off' from 'configureByPopup off'. The first is a superset but the second pretains only to retrieving cfg dialog by ajax.
• src/hg/js/hgHubConnect.js
  • lines changed 4, context: html, text, full: html, text
    make return key compatible with url checking (#6505)
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    Right-click 'clickThrough' cfg was erroneously providing 2 options on subtracks. Click-through is already provided by composite cfg option.
  • lines changed 28, context: html, text, full: html, text
    Use code that shlerps js and css files, and embedded js out of ajax returned html for popup cfg. The same code has been altered to fix getting warnBox contents out of the ajax results and putting them into the current page's warnBox.
• src/hg/js/hui.js
  • lines changed 5, context: html, text, full: html, text
    Fixed 2 bugs with filterBy's as seen on Encode Gencode V10. First, subtrack filterby's were getting the wrong name in some circumstances. Second, putting filterBy's inside a view cfg means they may have been hidden during setup. But ddcl's require visible multi-selects to be sized properly.
• src/hg/js/utils.js
  • lines changed 3, context: html, text, full: html, text
    Shlurping up warn messages in ajax results needed extending to multiple messages.
  • lines changed 102, context: html, text, full: html, text
    Use code that shlerps js and css files, and embedded js out of ajax returned html for popup cfg. The same code has been altered to fix getting warnBox contents out of the ajax results and putting them into the current page's warnBox.
• src/hg/lib/hui.c
  • lines changed 8, context: html, text, full: html, text
    add code in wigCfgUi to handle case where tdb isn't at parent level; fixes missing control in hgTrackUi (#6707)
  • lines changed 7, context: html, text, full: html, text
    Fixed 2 bugs with filterBy's as seen on Encode Gencode V10. First, subtrack filterby's were getting the wrong name in some circumstances. Second, putting filterBy's inside a view cfg means they may have been hidden during setup. But ddcl's require visible multi-selects to be sized properly.
  • lines changed 12, context: html, text, full: html, text
    configurable off should be supported at composite/view and subtrack level. Before this it was only at subtrack level.
  • lines changed 2, context: html, text, full: html, text
    Discovered there is still reason to distinguish 'configurable off' from 'configureByPopup off'. The first is a superset but the second pretains only to retrieving cfg dialog by ajax.
• src/hg/lib/kgXref.sql
  • lines changed 9, context: html, text, full: html, text
    Addressing code review feedback - thanks, Braney! Restored some lost indices, and expanded two description lines slightly
• src/hg/lib/knownCanonical.as
  • lines changed 2, context: html, text, full: html, text
    Addressing code review feedback - thanks, Braney! Restored some lost indices, and expanded two description lines slightly
  • lines changed 1, context: html, text, full: html, text
    Made the description of the protein field more generic, reflecting that the protein accession might or might not be the UniProt ID
  • lines changed 1, context: html, text, full: html, text
    Changing a description line - for the last time. I refuse to change it again\!
• src/hg/lib/knownCanonical.sql
  • lines changed 5, context: html, text, full: html, text
    Follow-up to changing knownCanonical.as as part of this week's code review: changing the products of knownCanonical.as
  • lines changed 1, context: html, text, full: html, text
    Made the description of the protein field more generic, reflecting that the protein accession might or might not be the UniProt ID
  • lines changed 1, context: html, text, full: html, text
    Changing a description line - for the last time. I refuse to change it again\!
• src/hg/lib/rgdGene2Raw.as
  • lines changed 42, context: html, text, full: html, text
    changing name of table genes_raw to rgdGene2Raw
• src/hg/lib/rgdGene2Raw.sql
  • lines changed 46, context: html, text, full: html, text
    changing name of table genes_raw to rgdGene2Raw
• src/hg/lib/trackDbCustom.c
  • lines changed 9, context: html, text, full: html, text
    configurable off should be supported at composite/view and subtrack level. Before this it was only at subtrack level.
  • lines changed 5, context: html, text, full: html, text
    Discovered there is still reason to distinguish 'configurable off' from 'configureByPopup off'. The first is a superset but the second pretains only to retrieving cfg dialog by ajax.
• src/hg/liftOver/liftOver.c
  • lines changed 4, context: html, text, full: html, text
    Modified the warning message
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 58, context: html, text, full: html, text
    Finished bosTau7 LASTZ with hg19 and mm9.
• src/hg/makeDb/doc/canFam2.txt
  • lines changed 55, context: html, text, full: html, text
    Finished LASTZ between bosTau7 vs canFam2, monDom5, and rn4.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release2.notes
  • lines changed 261, context: html, text, full: html, text
    updated the notes for haib tfbs
  • lines changed 163, context: html, text, full: html, text
    corrected notes
  • lines changed 12, context: html, text, full: html, text
    updated notes
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwRepliSeq.release1.notes
  • lines changed 47, context: html, text, full: html, text
    Renamed all SK-N-SH_RA files to SK-N-SH based on lab information. Updated meta-data, notes file, trackDb, files.txt and md5sum.txt. Redmine #4577.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuHistone.release1.notes
  • lines changed 465, context: html, text, full: html, text
    Added correct release notes for this release. Redmine #111.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuTfbs.release1.notes
  • lines changed 354, context: html, text, full: html, text
    Added correct release notes for this release. Redmine #110.
• src/hg/makeDb/doc/felCat4.txt
  • lines changed 2, context: html, text, full: html, text
    edmine bug #6679 Use common name instead of assembly in the felCat4_6way.gif used in the conservation track
• src/hg/makeDb/doc/hg19.txt
  • lines changed 55, context: html, text, full: html, text
    Finished bosTau7 LASTZ with hg19 and mm9.
  • lines changed 14, context: html, text, full: html, text
    load new cosmic data (v257) - #6730
  • lines changed 9, context: html, text, full: html, text
    add some notes
• src/hg/makeDb/doc/hgFixed.txt
  • lines changed 13, context: html, text, full: html, text
    Updated to 2011-12-31 version of REBASE (201)
• src/hg/makeDb/doc/mm9.txt
  • lines changed 55, context: html, text, full: html, text
    Finished bosTau7 LASTZ with hg19 and mm9.
• src/hg/makeDb/doc/monDom5.txt
  • lines changed 57, context: html, text, full: html, text
    Finished LASTZ between bosTau7 vs canFam2, monDom5, and rn4.
• src/hg/makeDb/doc/proteins/111004.txt
  • lines changed 40, context: html, text, full: html, text
    Notes on Reactome v39 updating in the proteome database.
• src/hg/makeDb/doc/rn4.txt
  • lines changed 61, context: html, text, full: html, text
    Finished LASTZ between bosTau7 vs canFam2, monDom5, and rn4.
  • lines changed 20, context: html, text, full: html, text
    continuing with rgdGene2 end game
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 16, context: html, text, full: html, text
    1: when I tried to load the blast tabs at the end of the script, I discovered that some of the files I needed had been deleted earlier on. So, I moved that cleanup step to the very end, after the loading of the blast tabs. 2: in building the keggPathway table, replaced a SELECT statement with a SELECT DISTINCT, to avoid (more) tables of millions of duplicated lines
  • lines changed 2, context: html, text, full: html, text
    addressing note 12 in Redmine 5674: set up the code so that in future executions, whenever a new known Gene blat server is set up, the server is identified by version number along with the keyword hg19Kg
  • lines changed 2, context: html, text, full: html, text
    addressing note 12 in Redmine 5674: set up the code so that in future executions, whenever a new known Gene blat server is set up, the server is identified by version number along with the keyword hg19Kg
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 3, context: html, text, full: html, text
    adding some upstreamMaf definitions for felCat4, felCat3, monDom4
• src/hg/makeDb/schema/all.joiner
  • lines changed 98, context: html, text, full: html, text
    Adding GencodeV10 to all.joiner to describe how tables are linked
• src/hg/makeDb/trackDb/README
  • lines changed 37, context: html, text, full: html, text
    Updated information about 'configurable' and 'configureByPopup' redmine 6742.
• src/hg/makeDb/trackDb/cat/felCat4/ctgPos2.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/cat/felCat4/gap.html
  • lines changed 3, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/cat/felCat4/gold.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/cow/bosTau6/ctgPos2.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/cow/bosTau6/gap.html
  • lines changed 3, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/cow/bosTau7/ctgPos2.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Fixing capitolization
  • lines changed 1, context: html, text, full: html, text
    Added more human redable label for Osteobl.
  • lines changed 252, context: html, text, full: html, text
    scraped new cell types from wiki
  • lines changed 108, context: html, text, full: html, text
    fixed order and certain protocol references
  • lines changed 3, context: html, text, full: html, text
    Fixed link to Rajinder Kaul faculty page, error found in checkLinks.
  • lines changed 336, context: html, text, full: html, text
    correct comment locations - Willy
  • lines changed 3, context: html, text, full: html, text
    Willy's copy was liek an hour old, putting in other changes back
  • lines changed 16, context: html, text, full: html, text
    Changed tissues to be lower case. Redmine #6744
  • lines changed 4, context: html, text, full: html, text
    Added protocol for orderId for Spleen for Stam lab.
  • lines changed 193, context: html, text, full: html, text
    Added new registration and protocols for 16 mouse tissues/cells.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 34, context: html, text, full: html, text
    Moved over all approved changes from beta/cv.ra. Redmine #6683. Removed duplicated lines caused by use of raMerge. Redmine #5977.
  • lines changed 324, context: html, text, full: html, text
    changed over to Needleman-Wunsch for alignment of lists
  • lines changed 324, context: html, text, full: html, text
    This somehow included cv.ra changes that I don't remember adding in. Revert "changed over to Needleman-Wunsch for alignment of lists" This reverts commit c6bd349fa19566d37c1ac02a42865a9031420acb.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 11, context: html, text, full: html, text
    Added patch release of revoking subId 943 due to incorrect rawdata files submitted. Redmine #6731
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Added patch release of revoking subId 943 due to incorrect rawdata files submitted. Redmine #6731
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.patch.ra
  • lines changed 2392, context: html, text, full: html, text
    Added patch release of revoking subId 943 due to incorrect rawdata files submitted. Redmine #6731
• src/hg/makeDb/trackDb/human/hg19/cosmic.html
  • lines changed 3, context: html, text, full: html, text
    add version number (v57) and make pack description accurate
  • lines changed 1, context: html, text, full: html, text
    put dataVersion in trackDb instead of in the html
  • lines changed 2, context: html, text, full: html, text
    word-smithing
• src/hg/makeDb/trackDb/human/hg19/ctgPos.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link
• src/hg/makeDb/trackDb/human/hg19/knownGeneNew.html
  • lines changed 23, context: html, text, full: html, text
    Added some links and made several small punctuation and grammar changes.
  • lines changed 133, context: html, text, full: html, text
    Whitespace changes only.
  • lines changed 30, context: html, text, full: html, text
    Fixed a couple of typos, fixed quotes, and replaced UniProt copyright info with a citation in the References section, per discussion in Redmine #5685.
  • lines changed 1, context: html, text, full: html, text
    Changed Table Browser link to a relative one based on discussion in Redmine #6769.
  • lines changed 1, context: html, text, full: html, text
    A few last-minute documentation things for UCSC Genes
  • lines changed 2, context: html, text, full: html, text
    Fixing a grammatical error
  • lines changed 3, context: html, text, full: html, text
    Added a link to the tRNA Genes track in the first sentence and removed hgsid and hard-link to genome from the link to the tRNA Genes track in the Methods section.
• src/hg/makeDb/trackDb/human/hg19/knownGeneOld5.html
  • lines changed 2, context: html, text, full: html, text
    Corrected the count of transcripts that did not change and of the prior number of knownCanonical genes.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 17, context: html, text, full: html, text
    Fixed the naming of wgEncodeBroadHistoneDnd41Control objects to have control=std in the name following naming conenvtions. Also updated antibody to be Input. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV10.ra
  • lines changed 28, context: html, text, full: html, text
    Changed the dataVersion to Mar 2012
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 695, context: html, text, full: html, text
    adding in lots of replacement files
  • lines changed 29, context: html, text, full: html, text
    added in md5sums
  • lines changed 29, context: html, text, full: html, text
    revoking the old U87 experiments
  • lines changed 2141, context: html, text, full: html, text
    renaming Control to Reverse crosslinks
  • lines changed 2, context: html, text, full: html, text
    updated md5sum
  • lines changed 63, context: html, text, full: html, text
    expIds and one correction
  • lines changed 7, context: html, text, full: html, text
    update dates on things I missed
  • lines changed 1066, context: html, text, full: html, text
    updating gzipped files wth md5sums of the internal contents
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 119, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 166, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 81, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 18, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 263, context: html, text, full: html, text
    Removed files for experiment 707, bad rawdata. Data was never released so all occurance could be removed. Redmine #4486.
  • lines changed 880, context: html, text, full: html, text
    changed md5sums of gzips to internal contents
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 106, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 574, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 688, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
  • lines changed 121, context: html, text, full: html, text
    Renamed all SK-N-SH_RA files to SK-N-SH based on lab information. Updated meta-data, notes file, trackDb, files.txt and md5sum.txt. Redmine #4577.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 421, context: html, text, full: html, text
    uppdated md5sums for new files and internal contents of gzips
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    removing duplicate of wgEncodeGencodeV10.ra
  • lines changed 2, context: html, text, full: html, text
    sorting the makefile for cleanliness' sake
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV10.ra
  • lines changed 28, context: html, text, full: html, text
    cricket updated freeze date based, redmine #6230, 6581
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
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    sorting the makefile for cleanliness' sake
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    get the right lizard!
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    A few last-minute documentation things for UCSC Genes
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
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    Update tags to be release2 instead of just new.ra. Redmine #4145
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 4205, context: html, text, full: html, text
    Update tags to be release2 instead of just new.ra. Redmine #4145
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html
  • lines changed 166, context: html, text, full: html, text
    Update tags to be release2 instead of just new.ra. Redmine #4145
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.ra
  • lines changed 4205, context: html, text, full: html, text
    Update tags to be release2 instead of just new.ra. Redmine #4145
  • lines changed 597, context: html, text, full: html, text
    Made first pass at changing labels to be standard and fit under size restrictions. Redmine #4145.
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    Fixed the naming of wgEncodeBroadHistoneDnd41Control objects to have control=std in the name following naming conenvtions. Also updated antibody to be Input. Redmine #4145.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
  • lines changed 10, context: html, text, full: html, text
    rewording the info on the basic set, redmine #6230
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    changing BioType to biotype and removing contradictory info from the comprehensive subtrack info about the exclusion of pseudogenes
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    updating filtering info to match the filter titles that we recently changed, Redmine #6230
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    fixing some wording issues in the TSL section; still some awkward wording I need to fix though, remdine #6230
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    moving info about Gencode Basic Set selection to the Methods section, redmine #6230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
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    Changing label names according to ticket 6230
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    This should be looked over with a fine-tooth comb. I added views, I use configurable off. I changed the views that we had, I changed filter labels. All is negotiated endlessly in ticket 6230.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.html
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    pre-qa fixes for haib tfbs
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    fixed link to not be going to a directory
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    made it more searchable
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    fixed missing period
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    added in release notes
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    fixed release notes
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    corrected capitalization of ChIP-seq
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    added in Flo's changes to the description page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 1, context: html, text, full: html, text
    pre-qa fixes for haib tfbs
  • lines changed 72, context: html, text, full: html, text
    revoking old U87 tracks
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    adding in remapped U87 tracks
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    fixed long labels
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    short labels for haib tfbs
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    renaming Control to Reverse crosslinks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
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    Removed files for experiment 707, bad rawdata. Data was never released so all occurance could be removed. Redmine #4486.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
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    Renamed all SK-N-SH_RA files to SK-N-SH based on lab information. Updated meta-data, notes file, trackDb, files.txt and md5sum.txt. Redmine #4577.
• src/hg/makeDb/trackDb/human/trackDb.ra
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    add dataVersion for cosmic track
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
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    Staging PSU TFBS (mm9) on beta, redmine# 110
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuTfbs.ra
  • lines changed 6542, context: html, text, full: html, text
    Staging PSU TFBS (mm9) on beta, redmine# 110
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Staging PSU TFBS (mm9) on beta, redmine# 110
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.ra
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    Fixed typo in color for which left out a digit. Was 204,121,16 changed to 204,121,167.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.new.ra
  • lines changed 6, context: html, text, full: html, text
    Fixed typo in color for which left out a digit. Was 204,121,16 changed to 204,121,167.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
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    Redmine #111 1. Changed Title from "Rationale for the Mouse ENCODE Project" -> "Reasons for the Mouse ENCODE Project" 2. Updated downloads page to link to the hgFileUi 3. Seperated contact name and email on seperate line 4. Added periods '.' after each title and made sure they were not hyperlinked.
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    Redmine #111 1. Removed first person useage in the "Rationale for the Mouse ENCODE Project" and renamed section from "Reasons for the Mouse ENCODE Project"
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    Fixes found by Pre-QA: Redmine #111 1. Changed Signal Display mode to mean+whiskers 2. Changed Description sentence to be third person voice. Updated working of "The contribution of DNA that with a function preserved in mammals versus t "Levels of three histone modifications are being determined" -> "Levels of three histone modifications were determined" 3. Fixed misspelled Alignments and change 'are being' -> 'were' 4. Deleted duplicate 'the' 5. Changed credits section to be passive voice.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
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    Updated Peak defaults to be Pack. Redmine #111.
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    Updated label for Immortal to be immortalized. Redmine #111.
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    Fixes found by Pre-QA: Redmine #111 1. Changed Signal Display mode to mean+whiskers 2. Changed Description sentence to be third person voice. Updated working of "The contribution of DNA that with a function preserved in mammals versus t "Levels of three histone modifications are being determined" -> "Levels of three histone modifications were determined" 3. Fixed misspelled Alignments and change 'are being' -> 'were' 4. Deleted duplicate 'the' 5. Changed credits section to be passive voice.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
  • lines changed 626, context: html, text, full: html, text
    Added release 2 for track for more data for MEL Cell line. Already included in input for MEL data. Redmine #6703.
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    Updated label for Immortal to be immortalized. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
  • lines changed 21, context: html, text, full: html, text
    Redmine #111 1. Changed Title from "Rationale for the Mouse ENCODE Project" -> "Reasons for the Mouse ENCODE Project" 2. Updated downloads page to link to the hgFileUi 3. Seperated contact name and email on seperate line 4. Added periods '.' after each title and made sure they were not hyperlinked.
  • lines changed 5, context: html, text, full: html, text
    Redmine #111 1. Removed first person useage in the "Rationale for the Mouse ENCODE Project" and renamed section from "Reasons for the Mouse ENCODE Project"
  • lines changed 8, context: html, text, full: html, text
    Fixes found by Pre-QA: Redmine #110 1. Changed Signal Display mode to mean+whiskers 2. Changed Description sentence to be third person voice. Updated working of "The contribution of DNA that with a function preserved in mammals versus that with a function in only one species will be discovered" 3. Fixed misspelled Alignments and change 'are being' -> 'were' 4. Deleted duplicate 'the' 5. Changed credits section to be passive voice.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    Updated Peak defaults to be Pack.Also changed default from G1E/GATA1 to G1E/GATA2 Redmine #110.
  • lines changed 2, context: html, text, full: html, text
    Fixes found by Pre-QA: Redmine #110 1. Changed Signal Display mode to mean+whiskers 2. Changed Description sentence to be third person voice. Updated working of "The contribution of DNA that with a function preserved in mammals versus that with a function in only one species will be discovered" 3. Fixed misspelled Alignments and change 'are being' -> 'were' 4. Deleted duplicate 'the' 5. Changed credits section to be passive voice.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 4, context: html, text, full: html, text
    Fixed typo in color for which left out a digit. Was 204,121,16 changed to 204,121,167.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
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    Fixed typo in color for which left out a digit. Was 204,121,16 changed to 204,121,167.
• src/hg/makeDb/trackDb/pig/susScr2/ctgPos2.html
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    Fixed broken link
• src/hg/makeDb/trackDb/pig/susScr2/gap.html
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    Fixed broken link
• src/hg/makeDb/trackDb/pig/susScr2/gold.html
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    Fixed broken link
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
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    Made some formatting corrections
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
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    Made some formatting corrections
• src/hg/makeDb/trackDb/sheep/oviAri1/ctgPos2.html
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    Fixed broken link
• src/hg/makeDb/trackDb/sheep/oviAri1/gap.html
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    Fixed broken link
• src/hg/makeDb/trackDb/sheep/oviAri1/gold.html
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    Fixed broken link
• src/hg/makeDb/trackDb/trackDb.ra
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    change NCBI Incident to GRC Incident
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    actually change the table name to get the grcIncidentDb to replace the ncbiIncidentDb
• src/hg/makeDb/trackDb/turkey/melGal1/ctgPos2.html
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    Fixed broken link
• src/hg/makeDb/trackDb/turkey/melGal1/gap.html
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    Fixed broken link
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
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    corrected spelling for Australian
• src/hg/oneShot/doRgdGene2UniProt/doRgdGene2UniProt.c
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    change rn4 table name of genes_rat to rgdGene2Raw
• src/hg/txGene/txGeneXref/txGeneXref.c
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    Changes to address git #2 note # 91 (see also # 6752). The descriptions were sometimes inconsistent with the gene symbol. This arose when the refLink description field was blank, and the code would end up pulling descriptions from GenBank records. And of course, every so often there's some paralog in GenBank that just aligns in the wrong place... So here's the new plan. For transcripts that overlap a RefSeq (i.e. refseq is not ""), get the gene symbol from refLink and the description from description. If the description is still blank when it comes time to look at the GenBank records, don\'t even bother with the GenBank records if the transcript is related to a RefSeq, just leave the descriptions blank (this shoudl be fairly rare).
• src/hg/utils/automation/loadCosmic.pl
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    create a loader for COSMIC data (mostly based on fan's entries in hg19.txt)
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    minor tweaks
• src/utils/qa/bigPush.csh
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    Added usage statement. Thanks, Vanessa.
• src/utils/qa/weeklybld/buildEnv.csh
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    v263 preview1
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
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    Fixed script to only send email when there are actual errors
• src/utils/qa/weeklybld/doNewBranch.csh
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    Added Kate to summary email and fixed range on example git log command
• src/utils/qa/weeklybld/doTrackCheckRobot.csh
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    Send message to browser-qa when TrackCheck is done

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• files changed: 228