Commits for hiram

v313_preview2 to v313_base (2015-03-02 to 2015-03-09) v313

• can not compare unsigned to less than zero found by Mac compiler Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn) refs #9741
  
  • src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c - lines changed 1, context: html, text, full: html, text
• collect all new chain/nets into one composite before proper sorting refs #14560
  
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/newChainNet.ra - lines changed 1018, context: html, text, full: html, text
• added search rule for hg38 patch2 haplotype names refs #14167
  
  • src/hg/makeDb/trackDb/human/hg38/hg38Patch2.ra - lines changed 7, context: html, text, full: html, text
• catching up with new assemblies nasLar rhiRox fukDam cavAep camBac camDro bosInd bisBis aquChr gavGan vipBer nanPar refs #14560
  
  • src/hg/utils/phyloTrees/placentals.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/primates.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/vertebrates.txt - lines changed 12, context: html, text, full: html, text
• output in format ready for trackDb override statements refs #14560
  
  • src/hg/utils/phyloTrees/findScores.pl - lines changed 7, context: html, text, full: html, text
• differenate info message about where sciName comes from refs #14560
  
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 3, context: html, text, full: html, text
• fixup some distances based on 17-way hg38 track and upgrade to rn6 and felCat8 refs #14560
  
  • src/hg/utils/phyloTrees/183way.nh - lines changed 7, context: html, text, full: html, text
• adding nasLar1 and xenTro1 refs #14560
  
  • src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab - lines changed 2, context: html, text, full: html, text
• updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
  
  • src/hg/utils/phyloTrees/191way.nh - lines changed 191, context: html, text, full: html, text
• updated to: ponAbe3 dipOrd2 pteVam2 proCap2 ornAna5 aquChr2 melGal5 croPor2 and added new: fukDam1 cavApe1 camBac1 camDro1 bosind1 bisBis1 vipBer1 nanpar1 refs #14560
  
  • src/hg/utils/phyloTrees/120way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/120way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/122way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/122way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/123way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/123way.scientificNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/126way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/129way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/130way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/131way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/166way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/171way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/172way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/174way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/181way.commonNames.nh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/181way.scientificNames.nh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/183way.commonNames.nh - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/183way.scientificNames.nh - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/191way.commonNames.nh - lines changed 191, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/191way.scientificNames.nh - lines changed 191, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 22, context: html, text, full: html, text
• update to 191-way refs #14560
  
  • src/hg/utils/phyloTrees/191way.dissect.txt - lines changed 2667, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/191wayChainNet.pl - lines changed 219, context: html, text, full: html, text
• adding Golden Eagle refs #14560
  
  • src/hg/htdocs/images/Aquila_chrysaetos.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• correct sciName for Golden Eagle refs #14560
  
  • src/hg/htdocs/images/Aquila_chrysaetos_canadensis.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• correct sciName for Golden Eagle refs #14560
  
  • src/hg/htdocs/images/Aquila_chrysaetos.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding Golden Eagle refs #14560
  
  • src/hg/makeDb/trackDb/birds/aquChr2/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/aquChr2/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/aquChr2/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/aquChr2/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding Golden Eagle refs #14560
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• add gold table search rule refs #14560
  
  • src/hg/makeDb/trackDb/birds/aquChr2/trackDb.ra - lines changed 5, context: html, text, full: html, text
• Added aquChr2; refs #14560
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 23, context: html, text, full: html, text
• Added aquChr Aquila chrysaetos canadensis refs #14560
  
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• photo courtesy Lauren Dobson Texas A and M University refs #14560
  
  • src/hg/htdocs/images/Bison_bison_bison.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding Bison bisBis1 refs #14560
  
  • src/hg/makeDb/trackDb/bison/bisBis1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bison/bisBis1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bison/bisBis1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bison/bisBis1/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• v313 final build refs #14887
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v313
  
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text