All File Changes

v323_preview to v323_preview2 (2015-09-21 to 2015-09-28) v323

• src/browserbox/root/updateBrowser.sh
  • lines changed 5, context: html, text, full: html, text
    make gbib update script avoid errors if not running on virtualbox. no
    redmine. based on email by Carsten Kuenne via Bob.
    
• src/hg/cartReset/cartReset.c
  • lines changed 2, context: html, text, full: html, text
    Reducing cartReset delay from 2 seconds to 1 second, and its corresponding message. Fixes #8949.
    
• src/hg/gigAssembler/checkAgpAndFa/checkAgpAndFa.c
  • lines changed 2, context: html, text, full: html, text
    good to know chr name when error on start != prevEnd refs #16078
    
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 1, context: html, text, full: html, text
    Use track instead of table as annoStreamer name so we don't get a mismatch between mrna and all_mrna.
    
  • lines changed 1, context: html, text, full: html, text
    Oops, this should have been part of f66bc993 (Use track instead of table as annoStreamer name so we don't get a mismatch between mrna and all_mrna.)
    
• src/hg/hgTables/great.c
  • lines changed 2, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/hgTables/hgTables.h
  • lines changed 5, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/hgTracks/extTools.ra
  • lines changed 1, context: html, text, full: html, text
    custom track browser code is moving from his sandbox to the primer3 dev server.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 5, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/hgc/regMotif.c
  • lines changed 2, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 18, context: html, text, full: html, text
    adding announcement for keyboard shortcuts
    
• src/hg/htdocs/indexNews.html
  • lines changed 16, context: html, text, full: html, text
    adding announcement for keyboard shortcuts
    
• src/hg/htdocs/mirror.html
  • lines changed 4, context: html, text, full: html, text
    added explicit mention of Bielefeld on mirror page
    
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    fix a broken url per ann coe review. refs #16053
    
• src/hg/inc/jksql.h
  • lines changed 10, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/inc/jsHelper.h
  • lines changed 5, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/inc/web.h
  • lines changed 20, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/lib/annoGratorGpVar.c
  • lines changed 1, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/lib/annoStreamDb.c
  • lines changed 6, context: html, text, full: html, text
    It was a bug to take only smallest-bin items in subsequent chunk queries -- we lost some large-bin items that belonged to those subsequent chunk regions!
    
• src/hg/lib/customPp.c
  • lines changed 4, context: html, text, full: html, text
    adding comment after code review, refs #16057
    
  • lines changed 2, context: html, text, full: html, text
    rewording line after a code review concerned with code readability, refs #16057
    
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 70, context: html, text, full: html, text
    lastz run to danRer10 for user refs #15476
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 62, context: html, text, full: html, text
    lastz run to danRer10 for user refs #15476
    
• src/hg/makeDb/doc/rn6.txt
  • lines changed 61, context: html, text, full: html, text
    lastz run to danRer10 for user refs #15476
    
• src/hg/makeDb/trackDb/gc5Base.html
  • lines changed 13, context: html, text, full: html, text
    correcting missing html bits refs #16078
    
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 7, context: html, text, full: html, text
    add chromSizes argument to allow working independently of UCSC standard directory hierarchy refs #16078
    
  • lines changed 2, context: html, text, full: html, text
    add chromSizes argument to allow working independently of UCSC standard directory hierarchy refs #16078
    
• src/hg/utils/automation/genbank/agpToBbi.sh
  • lines changed 57, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/alternatesAgp.pl
  • lines changed 41, context: html, text, full: html, text
    catching up to todays versions refs #16078
    
• src/hg/utils/automation/genbank/assemblyDescription.pl
  • lines changed 83, context: html, text, full: html, text
    catching up to todays versions refs #16078
    
• src/hg/utils/automation/genbank/buildStats.pl
  • lines changed 84, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/checksOK.sh
  • lines changed 4, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/compositeAgp.pl
  • lines changed 53, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/compositeFasta.pl
  • lines changed 69, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/cpg.sh
  • lines changed 63, context: html, text, full: html, text
    catching up to todays versions refs #16078
    
• src/hg/utils/automation/genbank/cpgDescription.pl
  • lines changed 128, context: html, text, full: html, text
    catching up with todays versions refs #16078
    
• src/hg/utils/automation/genbank/cronUpdate.sh
  • lines changed 58, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/gapDescription.pl
  • lines changed 81, context: html, text, full: html, text
    catching up to todays versions refs #16078
    
• src/hg/utils/automation/genbank/gatewayPage.pl
  • lines changed 205, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/gc5Description.pl
  • lines changed 57, context: html, text, full: html, text
    catching up with todays versions refs #16078
    
• src/hg/utils/automation/genbank/hubIndexNcbi.sh
  • lines changed 83, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/idFromAsmRpt.pl
  • lines changed 100, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/idScan.sh
  • lines changed 16, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/ncbiBacteria.sh
  • lines changed 149, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/ncbiBacteriaHtml.sh
  • lines changed 101, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/ncbiHtml.sh
  • lines changed 96, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/ncbiToUcsc.sh
  • lines changed 397, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
  • lines changed 100, context: html, text, full: html, text
    catching up to todays versions refs #16078
    
  • lines changed 6, context: html, text, full: html, text
    catching up with todays versions refs #16078
    
• src/hg/utils/automation/genbank/noStructureAgp.pl
  • lines changed 53, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/noStructureFasta.pl
  • lines changed 49, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/rmsk.sh
  • lines changed 86, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
  • lines changed 9, context: html, text, full: html, text
    catching up to todays versions refs #16078
    
• src/hg/utils/automation/genbank/rmskDescription.pl
  • lines changed 151, context: html, text, full: html, text
    catching up with todays versions refs #16078
    
• src/hg/utils/automation/genbank/rsync.sh
  • lines changed 19, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/taxId.comName.tab
  • lines changed 10157, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/trackDb.sh
  • lines changed 196, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
  • lines changed 60, context: html, text, full: html, text
    catching up to todays versions refs #16078
    
• src/hg/utils/automation/genbank/unlocalizedAgp.pl
  • lines changed 59, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/unlocalizedFasta.pl
  • lines changed 65, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/unplacedAgp.pl
  • lines changed 35, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/hg/utils/automation/genbank/unplacedFasta.pl
  • lines changed 58, context: html, text, full: html, text
    capture scripts in use as of today 2015-09-24 refs #16078
    
• src/inc/common.h
  • lines changed 5, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/dyOut.h
  • lines changed 5, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/dystring.h
  • lines changed 5, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/hgap.h
  • lines changed 6, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/htmshell.h
  • lines changed 10, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/jsonWrite.h
  • lines changed 6, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/qa.h
  • lines changed 10, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/sqlNum.h
  • lines changed 5, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/tokenizer.h
  • lines changed 6, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/xap.h
  • lines changed 6, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/inc/xp.h
  • lines changed 5, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/lib/bbiWrite.c
  • lines changed 1, context: html, text, full: html, text
    change a constant in the bigBed code that wasn't quite right and
    resulted in an integer overflow bug.
    
• src/lib/psl.c
  • lines changed 31, context: html, text, full: html, text
    added checks for numBase and numInsert fields to pslCheck
    
  • lines changed 10, context: html, text, full: html, text
    simplified pslCheck code
    
• src/lib/sqlNum.c
  • lines changed 1, context: html, text, full: html, text
    added GNU-C attributes to function declarations in src/inc, src/hg/inc, and some CGIs so that the compiler can catch errors where the parameter list given by the user does not match their format string. These var-args functions are like printf.
    
• src/makefile
  • lines changed 3, context: html, text, full: html, text
    modifying cscope indexing a bit, refs #14062
    
• src/userApps/README
  • lines changed 1, context: html, text, full: html, text
    oops, fixed to correct new version URL
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v323 preview2 refs #16061
    

• lines changed: 13481
• files changed: 86