File Changes for hiram

v286_base to v287_preview (2013-07-09 to 2013-07-16) v287

• src/hg/makeDb/doc/hg19.txt
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    done with lastz for tupChi1 and octDeg1 refs #10272
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    finishing off lastz runs for choHof1 oryAfe1 chrAsi1 dasNov3 refs #10272
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    swapping eriEur2 starting lastz on sarHar1 macEug2 triMan1 conCri1 refs #10272
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    finished with lastz for eriEur2 and continuing oryAfe1 and chrAsi1 refs #10272
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    lastz swaps for oryAfe1 chrAsi1 dasNov3 refs #10272
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    finishing up lastz for chrAsi1 eleEdw1 dasNov3 refs #10272
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    finishing lastz for oryAfe1 eleEdw1 conCri1 refs #10272
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    finishing off lastz for sarHar1 triMan1 conCri1 refs #10272
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    starting lastz for lepWed1 felCat5 musFur1 refs #10272
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    swapping macEug2 refs #10272
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    wrapping up lastz for macEug2 lepWed1 musFur1 and starting camFer1 and odoRosDiv1 refs #10272
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    finishing up lepWed1 musFur1 and felCat5 lastz runs refs #10272
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    finishing off lastz for felCat5 camFer1 odoRosDiv1 refs #10272
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    done with camFer1 and odoRosDiv1 lastz chain net refs #10272
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    done with lastz felCat5 refs #10272
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    lastz runs started on panPan1 latCha1 jacJac1 panHod1 capHir1 hetGla2 refs #10272
• src/hg/makeDb/schema/all.joiner
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    adding oviAri3 to the rule set refs #9409
• src/hg/makeDb/trackDb/human/hg19/chainCanFam2.ra
  • lines changed 7, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetEchTel1.ra
  • lines changed 15, context: html, text, full: html, text
    upgrading from echTel1 to echTel2 chain net refs #9693
• src/hg/makeDb/trackDb/human/hg19/chainNetEchTel2.ra
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    upgrading from echTel1 to echTel2 chain net refs #9693
• src/hg/makeDb/trackDb/human/hg19/chainNetGalGal3.ra
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    adding galGal4 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetGalGal4.ra
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    adding galGal4 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra
  • lines changed 51, context: html, text, full: html, text
    adding galGal4 and legacy out galGal3 refs #10272
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    moving placental chain net to its own file and adding chainNetRn5 refs #10272
  • lines changed 38, context: html, text, full: html, text
    moving primate chainNet to its own file and adding panTro2 and panTro3 to legacy chain net refs #10272
  • lines changed 54, context: html, text, full: html, text
    adding gorGor1 nomLeu1 rheMac2 to legacy chainNet refs #10272
  • lines changed 86, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
  • lines changed 16, context: html, text, full: html, text
    upgrading from echTel1 to echTel2 chain net refs #9693
  • lines changed 16, context: html, text, full: html, text
    upgrading from oviAri1 to oviAri3 chain net refs #9409
  • lines changed 16, context: html, text, full: html, text
    upgrade vicPac1 to vicPac2 chainNet refs #10833
• src/hg/makeDb/trackDb/human/hg19/chainNetOtoGar1.ra
  • lines changed 16, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetOtoGar3.ra
  • lines changed 15, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetOviAri1.ra
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    upgrading from oviAri1 to oviAri3 chain net refs #9409
• src/hg/makeDb/trackDb/human/hg19/chainNetOviAri3.ra
  • lines changed 15, context: html, text, full: html, text
    upgrading from oviAri1 to oviAri3 chain net refs #9409
• src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra
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    moving placental chain net to its own file and adding chainNetRn5 refs #10272
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    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
  • lines changed 15, context: html, text, full: html, text
    upgrading from echTel1 to echTel2 chain net refs #9693
  • lines changed 15, context: html, text, full: html, text
    upgrading from oviAri1 to oviAri3 chain net refs #9409
  • lines changed 15, context: html, text, full: html, text
    upgrade vicPac1 to vicPac2 chainNet refs #10833
• src/hg/makeDb/trackDb/human/hg19/chainNetPrimate.ra
  • lines changed 204, context: html, text, full: html, text
    moving primate chainNet to its own file and adding panTro2 and panTro3 to legacy chain net refs #10272
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    adding gorGor1 nomLeu1 rheMac2 to legacy chainNet refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetRBestOtoGar1.ra
  • lines changed 16, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetRBestOtoGar3.ra
  • lines changed 15, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetRn4.ra
  • lines changed 15, context: html, text, full: html, text
    moving placental chain net to its own file and adding chainNetRn5 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetRn5.ra
  • lines changed 15, context: html, text, full: html, text
    moving placental chain net to its own file and adding chainNetRn5 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra
  • lines changed 306, context: html, text, full: html, text
    move vertebrate chainNet into separate file and adding Budgerigar refs #10272
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    adding galGal4 and legacy out galGal3 refs #10272
• src/hg/makeDb/trackDb/human/hg19/chainNetVicPac1.ra
  • lines changed 15, context: html, text, full: html, text
    upgrade vicPac1 to vicPac2 chainNet refs #10833
• src/hg/makeDb/trackDb/human/hg19/chainNetVicPac2.ra
  • lines changed 15, context: html, text, full: html, text
    upgrade vicPac1 to vicPac2 chainNet refs #10833
• src/hg/makeDb/trackDb/human/hg19/netCanFam2.ra
  • lines changed 7, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
• src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra
  • lines changed 10, context: html, text, full: html, text
    add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 34, context: html, text, full: html, text
    adding allMis1 and otoGar3 chain and net plus otoGar1 and otoGar3 reciprocal chain and net display on hgwdev refs #8750 #10272
  • lines changed 290, context: html, text, full: html, text
    move vertebrate chainNet into separate file and adding Budgerigar refs #10272
  • lines changed 2, context: html, text, full: html, text
    adding galGal4 and legacy out galGal3 refs #10272
  • lines changed 470, context: html, text, full: html, text
    moving placental chain net to its own file and adding chainNetRn5 refs #10272
  • lines changed 214, context: html, text, full: html, text
    moving primate chainNet to its own file and adding panTro2 and panTro3 to legacy chain net refs #10272
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
  • lines changed 1, context: html, text, full: html, text
    better short title for aged-out/legacy chain net refs #10272
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    moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
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    moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 14, context: html, text, full: html, text
    moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
• src/hg/utils/phyloTrees/110way.commonNames.nh
  • lines changed 110, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
• src/hg/utils/phyloTrees/110way.nh
  • lines changed 110, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
• src/hg/utils/phyloTrees/110way.scientificNames.nh
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    adding myoBra1 and gavGan1 refs #10272
• src/hg/utils/phyloTrees/benchMark100.commonNames.nh
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    reducing the 110way to a benchMark100 refs #10272
• src/hg/utils/phyloTrees/benchMark100.nh
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    reducing the 110way to a benchMark100 refs #10272
• src/hg/utils/phyloTrees/benchMark100.scientificNames.nh
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    reducing the 110way to a benchMark100 refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
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    adding myoBra1 and gavGan1 refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 8, context: html, text, full: html, text
    adding myoBra1 and gavGan1 refs #10272
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    reducing the 110way to a benchMark100 refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
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    adding myoBra1 and gavGan1 refs #10272