File Changes for hiram

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

• src/hg/htdocs/images/Aquila_chrysaetos.jpg
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    adding Golden Eagle refs #14560
    
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    correct sciName for Golden Eagle refs #14560
    
• src/hg/htdocs/images/Aquila_chrysaetos_canadensis.jpg
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    correct sciName for Golden Eagle refs #14560
    
• src/hg/htdocs/images/Bison_bison_bison.jpg
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    photo courtesy Lauren Dobson Texas A and M University refs #14560
    
• src/hg/inc/versionInfo.h
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    New version number v313
    
• src/hg/makeDb/genbank/etc/genbank.conf
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    Added aquChr2; refs #14560
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
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    Added aquChr Aquila chrysaetos canadensis refs #14560
    
• src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c
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    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/trackDb/birds/aquChr2/description.html
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    adding Golden Eagle refs #14560
    
• src/hg/makeDb/trackDb/birds/aquChr2/gap.html
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    adding Golden Eagle refs #14560
    
• src/hg/makeDb/trackDb/birds/aquChr2/gold.html
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    adding Golden Eagle refs #14560
    
• src/hg/makeDb/trackDb/birds/aquChr2/trackDb.ra
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    adding Golden Eagle refs #14560
    
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    add gold table search rule refs #14560
    
• src/hg/makeDb/trackDb/bison/bisBis1/description.html
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    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/bison/bisBis1/gap.html
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    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/bison/bisBis1/gold.html
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    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/bison/bisBis1/trackDb.ra
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    adding Bison bisBis1 refs #14560
    
• src/hg/makeDb/trackDb/human/hg38/hg38Patch2.ra
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    added search rule for hg38 patch2 haplotype names refs #14167
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    collect all new chain/nets into one composite before proper sorting refs #14560
    
• src/hg/makeDb/trackDb/human/newChainNet.ra
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    collect all new chain/nets into one composite before proper sorting refs #14560
    
• src/hg/makeDb/trackDb/makefile
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    adding Golden Eagle refs #14560
    
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    adding Bison bisBis1 refs #14560
    
• src/hg/utils/phyloTrees/120way.commonNames.nh
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    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.scientificNames.nh
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    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/122way.commonNames.nh
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    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/122way.scientificNames.nh
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    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/123way.commonNames.nh
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    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/123way.scientificNames.nh
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    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/126way.commonNames.nh
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    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/129way.commonNames.nh
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    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/130way.commonNames.nh
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    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/131way.commonNames.nh
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    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/166way.commonNames.nh
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    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/171way.commonNames.nh
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    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/172way.commonNames.nh
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    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/174way.commonNames.nh
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    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/181way.commonNames.nh
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    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/181way.scientificNames.nh
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    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/183way.commonNames.nh
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    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/183way.nh
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    fixup some distances based on 17-way hg38 track and upgrade to rn6 and felCat8 refs #14560
    
• src/hg/utils/phyloTrees/183way.scientificNames.nh
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    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.commonNames.nh
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    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.dissect.txt
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    update to 191-way refs #14560
    
• src/hg/utils/phyloTrees/191way.nh
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    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.scientificNames.nh
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    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/191wayChainNet.pl
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    update to 191-way refs #14560
    
• src/hg/utils/phyloTrees/commonNames.sh
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    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/dbCommonScientificCladeOrderkey.tab
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    adding nasLar1 and xenTro1 refs #14560
    
• src/hg/utils/phyloTrees/findScores.pl
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    output in format ready for trackDb override statements refs #14560
    
• src/hg/utils/phyloTrees/makefile
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    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/placentals.txt
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    catching up with new assemblies nasLar rhiRox fukDam cavAep camBac camDro bosInd bisBis aquChr gavGan vipBer nanPar refs #14560
    
• src/hg/utils/phyloTrees/primates.txt
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    catching up with new assemblies nasLar rhiRox fukDam cavAep camBac camDro bosInd bisBis aquChr gavGan vipBer nanPar refs #14560
    
• src/hg/utils/phyloTrees/scientificNames.sh
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    differenate info message about where sciName comes from refs #14560
    
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    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/vertebrates.txt
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    catching up with new assemblies nasLar rhiRox fukDam cavAep camBac camDro bosInd bisBis aquChr gavGan vipBer nanPar refs #14560
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v313 final build refs #14887