File Changes for hiram

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

• 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/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/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v323 preview2 refs #16061