All File Changes

v276_preview2 to v276_base (2012-11-13 to 2012-11-20) v276

• python/lib/ucscGb/encode/cv.py
  • lines changed 14, context: html, text, full: html, text
    added support for new cv terms (cell and antibody) as well as some bugfixes for library
• python/lib/ucscGb/encode/encodeUtils.py
  • lines changed 49, context: html, text, full: html, text
    added support for new cv terms (cell and antibody) as well as some bugfixes for library
• python/lib/ucscGb/encode/mdb.py
  • lines changed 1, context: html, text, full: html, text
    added support for new cv terms (cell and antibody) as well as some bugfixes for library
• python/lib/ucscGb/encode/track.py
  • lines changed 23, context: html, text, full: html, text
    added support for new cv terms (cell and antibody) as well as some bugfixes for library
• python/lib/ucscGb/externalData/geo/soft.py
  • lines changed 671, context: html, text, full: html, text
    added support for new cv terms (cell and antibody) as well as some bugfixes for library
• python/lib/ucscGb/externalData/geo/submission.py
  • lines changed 2, context: html, text, full: html, text
    added support for new cv terms (cell and antibody) as well as some bugfixes for library
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 31, context: html, text, full: html, text
    fix bug in keeping track of error message introduced last cycle (#9609). Also fix bug in unlisted hubs where assembly was listed incorrectly.
• src/hg/hgTables/identifiers.c
  • lines changed 12, context: html, text, full: html, text
    temporary tables will now be created in a special database hgTemp
• src/hg/hgTracks/vcfTrack.c
  • lines changed 36, context: html, text, full: html, text
    VCF with mixed haploid status, for example on chrX where females are diploid andmales are haploid, was having gtHapIx assigned in two different ways, not good.
    Same formula for gtHapIx now applies to both diploid and haploid genotypes.
    We no longer have the invariant that the number of clustered haplotypes is the
    same as the max gtHapIx number, but it all works, trust me. :)
    
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/hgc/numtsClick.c
  • lines changed 11, context: html, text, full: html, text
    Code Review #9591: combined duplicated blocks of code in numtsClick.c
• src/hg/htdocs/ENCODE/dataStandards.html
  • lines changed 1, context: html, text, full: html, text
    No longer New
• src/hg/htdocs/ENCODE/dataSummary.html
  • lines changed 14, context: html, text, full: html, text
    Add warning about versioned data. Redmine #9563
• src/hg/htdocs/ENCODE/dataSummaryMouse.html
  • lines changed 15, context: html, text, full: html, text
    Add warning about versioned data. Redmine #9563
• src/hg/htdocs/ENCODE/index.html
  • lines changed 6, context: html, text, full: html, text
    Update Education & Outreach page and restore link on main page
• src/hg/htdocs/ENCODE/usageResources.html
  • lines changed 8, context: html, text, full: html, text
    Update Education & Outreach page and restore link on main page
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 15, context: html, text, full: html, text
    Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 37, context: html, text, full: html, text
    added announcement about OpenHelix encode tutorials
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 10, context: html, text, full: html, text
    adding the advance access location of the NAR paper for 2013. I will change the citation to the more usual style when the paper version gets printed. Yes, the rule is to only list the first 10 authors, but I think that we usually list all of the authors for our NAR papers!
  • lines changed 2, context: html, text, full: html, text
    a little more polish: italics, open in new tab/window.
  • lines changed 1, context: html, text, full: html, text
    a little more polish: looks like we have been announcing E-pubs.
• src/hg/htdocs/indexNews.html
  • lines changed 68, context: html, text, full: html, text
    added announcement about OpenHelix encode tutorials
• src/hg/lib/dgv.as
  • lines changed 2, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/lib/dgv.sql
  • lines changed 3, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    Tweak to 10-year-old code: in hGetCtBedRange, when we need a placeholderfor a column in the sql query, use "0" instead of the startField. It's a
    tiny bit more efficient and hopefully less eye-catching for Jorge. :)
    Speaking of efficiency, the CGIs could use a position-only (bed3) version.
    
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    fix bug in keeping track of error message introduced last cycle (#9609). Also fix bug in unlisted hubs where assembly was listed incorrectly.
• src/hg/lib/jksql.c
  • lines changed 10, context: html, text, full: html, text
    temporary tables will now be created in a special database hgTemp
• src/hg/liftUp/liftUp.c
  • lines changed 216, context: html, text, full: html, text
    adding the lift of .align files from Robert Hubley
• src/hg/makeDb/doc/bosTau6.txt
  • lines changed 26, context: html, text, full: html, text
    Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
• src/hg/makeDb/doc/hg17.txt
  • lines changed 90, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 92, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 77, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/makeDb/doc/nomLeu1.txt
  • lines changed 20, context: html, text, full: html, text
    construct liftOver to nomLeu2
• src/hg/makeDb/doc/susScr2.txt
  • lines changed 25, context: html, text, full: html, text
    Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 0, context: html, text, full: html, text
    make euronode-copy executable
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 9, context: html, text, full: html, text
    Added nomLeu2, papHam1, proCap1, pteVam1, sorAra1, susScr3, tarSyr1, tupBel and vicPac1
• src/hg/makeDb/genbank/src/ccds/createKeys.sql
  • lines changed 1, context: html, text, full: html, text
    the schema changes yet again
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 2, context: html, text, full: html, text
    the schema changes yet again
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
  • lines changed 10, context: html, text, full: html, text
    the schema changes yet again
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 2, context: html, text, full: html, text
    the schema changes yet again
• src/hg/makeDb/trackDb/alpaca/vicPac1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/armadillo/dasNov3/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/baboon/papAnu2/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/baboon/papHam1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/birds/geoFor1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
  • lines changed 2, context: html, text, full: html, text
    Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
• src/hg/makeDb/trackDb/birds/melUnd1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/cat/felCat5/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/chicken/galGal4/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/chimp/panTro4/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/chinchilla/chiLan1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Fixing url from Nr4a1 to NR4A1
  • lines changed 8, context: html, text, full: html, text
    Fixing JunD to JUND
  • lines changed 3, context: html, text, full: html, text
    Trying to further clarify the POL3 versus POL2
  • lines changed 1, context: html, text, full: html, text
    That human file for hardison was bogus, it was a pointer to the mouse file
  • lines changed 9, context: html, text, full: html, text
    Adding some periods and caplitalizing some E's before copying alpha cv.ra to beta cv.ra
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/dolphin/turTru2/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/gadMor/gadMor1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/gator/allMis1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/guineaPig/cavPor3/description.html
  • lines changed 2, context: html, text, full: html, text
    Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
• src/hg/makeDb/trackDb/hedgehog/eriEur1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 14, context: html, text, full: html, text
    Revoking files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 11, context: html, text, full: html, text
    Correcting the md5sums for these files
  • lines changed 2, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19Patch9/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Noticed that termRegex was misspelled, and regexes were in shell globformat instead of regex format. Also, semiShortCircuit is appropriate
    for very specific patterns that wouldn't appear in any other track.
    
  • lines changed 13, context: html, text, full: html, text
    Track #9401 (DGV update): loaded Nov. '12 data.
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/lamprey/petMar2/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/lancelet/braFlo2/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/latCha/latCha1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/manatee/triMan1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/megabat/pteVam1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
  • lines changed 1, context: html, text, full: html, text
    Added underscore to link to downloads page
  • lines changed 15, context: html, text, full: html, text
    update to correct information
• src/hg/makeDb/trackDb/moleRat/hetGla2/description.html
  • lines changed 118, context: html, text, full: html, text
    updating to new style home page
  • lines changed 3, context: html, text, full: html, text
    Replaced 'HTML' with 'HTTP'; corrected links
• src/hg/makeDb/trackDb/mouse/mm10Patch1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/mouse/mm10Strains1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 4, context: html, text, full: html, text
    reverted change to LicrTfbs since files are still there
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Noticed that termRegex was misspelled, and regexes were in shell globformat instead of regex format. Also, semiShortCircuit is appropriate
    for very specific patterns that wouldn't appear in any other track.
    
• src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/oreNil/oreNil2/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/other/centromers1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
• src/hg/makeDb/trackDb/pig/susScr3/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/pika/ochPri2/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/rat/rn5/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/rhesus/rheMac2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/rhesus/rheMac3/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/rhino/cerSim1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/rockHyrax/proCap1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/saiBol/saiBol1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/shrew/sorAra1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/sloth/choHof1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/squirrel/speTri2/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/tarsier/tarSyr1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/tenrec/echTel1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 67, context: html, text, full: html, text
    Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
• src/hg/makeDb/trackDb/treeShrew/tupBel1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/turtle/chrPic1/description.html
  • lines changed 1, context: html, text, full: html, text
    Edited link to downloads page - changed 'HTML' to 'HTTP'
• src/hg/makeDb/trackDb/xenTro/xenTro1/description.html
  • lines changed 2, context: html, text, full: html, text
    Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
• src/hg/makeDb/trackDb/xenTro/xenTro2/description.html
  • lines changed 2, context: html, text, full: html, text
    Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
• src/hg/makeDb/trackDb/xenTro/xenTro3/description.html
  • lines changed 10, context: html, text, full: html, text
    Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/description.html
  • lines changed 1, context: html, text, full: html, text
    Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
  • lines changed 1, context: html, text, full: html, text
    Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
• src/hg/utils/automation/configFiles/hetGla1.config.ra
  • lines changed 23, context: html, text, full: html, text
    update hetGla1 to be correct
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    Code Review #9591 Put back BLAT_APPLIST = blat gfClient gfServe which was accidentally removed.
• src/product/README.building.source
  • lines changed 3, context: html, text, full: html, text
    Feature #6336 (samtabix): The official git repository is now on genome-source.cse.ucsc.eduinstead of github.com.
    
• src/product/README.mysql.setup
  • lines changed 13, context: html, text, full: html, text
    temporary tables will now be created in a special database hgTemp
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v276 final build

• lines changed: 2068
• files changed: 120