Commits for hiram

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

• done with lastz for tupChi1 and octDeg1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 11, context: html, text, full: html, text
• finishing off lastz runs for choHof1 oryAfe1 chrAsi1 dasNov3 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 14, context: html, text, full: html, text
• swapping eriEur2 starting lastz on sarHar1 macEug2 triMan1 conCri1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 240, context: html, text, full: html, text
• adding oviAri3 to the rule set refs #9409
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text
• finished with lastz for eriEur2 and continuing oryAfe1 and chrAsi1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 23, context: html, text, full: html, text
• lastz swaps for oryAfe1 chrAsi1 dasNov3 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 13, context: html, text, full: html, text
• finishing up lastz for chrAsi1 eleEdw1 dasNov3 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 17, context: html, text, full: html, text
• finishing lastz for oryAfe1 eleEdw1 conCri1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 16, context: html, text, full: html, text
• adding myoBra1 and gavGan1 refs #10272
  • src/hg/utils/phyloTrees/110way.commonNames.nh - lines changed 110, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/110way.nh - lines changed 110, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/110way.scientificNames.nh - lines changed 110, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/commonNames.sh - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/scientificNames.sh - lines changed 3, 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/chainNetOtoGar1.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetOtoGar3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetRBestOtoGar1.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetRBestOtoGar3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 34, context: html, text, full: html, text
• move vertebrate chainNet into separate file and adding Budgerigar refs #10272
  • src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra - lines changed 306, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 290, context: html, text, full: html, text
• better short title for aged-out/legacy chain net refs #10272
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra - lines changed 1, context: html, text, full: html, text
• moving bosTau6 and petMar1 into previousVersionsChainNet for mouse containers refs #10272
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra - lines changed 14, context: html, text, full: html, text
  • 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/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra - lines changed 1, context: html, text, full: html, text
• adding galGal4 and legacy out galGal3 refs #10272
  • src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text
• adding galGal4 refs #10272
  • src/hg/makeDb/trackDb/human/hg19/chainNetGalGal3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetGalGal4.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/chainNetPlacental.ra - lines changed 443, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetRn4.ra - lines changed 15, context: html, text, full: html, text
  • 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/trackDb.ra - lines changed 470, 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/chainNetLegacy.ra - lines changed 20, 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/human/hg19/chainNetLegacy.ra - lines changed 38, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetPrimate.ra - lines changed 204, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 214, context: html, text, full: html, text
• adding gorGor1 nomLeu1 rheMac2 to legacy chainNet refs #10272
  • src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetPrimate.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• add calJac1 felCat3 canFam2 oryCun1 mm9 to legacy chain net, add canFam3 to placental group refs #10272
  • src/hg/makeDb/trackDb/human/hg19/chainCanFam2.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 86, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/netCanFam2.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.chainNet.ra - lines changed 10, context: html, text, full: html, text
• upgrading from echTel1 to echTel2 chain net refs #9693
  • src/hg/makeDb/trackDb/human/hg19/chainNetEchTel1.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetEchTel2.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.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/chainNetLegacy.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetOviAri1.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetOviAri3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra - lines changed 15, context: html, text, full: html, text
• upgrade vicPac1 to vicPac2 chainNet refs #10833
  • src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetVicPac1.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetVicPac2.ra - lines changed 15, context: html, text, full: html, text
• finishing off lastz for sarHar1 triMan1 conCri1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 29, context: html, text, full: html, text
• starting lastz for lepWed1 felCat5 musFur1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 180, context: html, text, full: html, text
• swapping macEug2 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 4, context: html, text, full: html, text
• wrapping up lastz for macEug2 lepWed1 musFur1 and starting camFer1 and odoRosDiv1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 146, context: html, text, full: html, text
• finishing up lepWed1 musFur1 and felCat5 lastz runs refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 11, context: html, text, full: html, text
• finishing off lastz for felCat5 camFer1 odoRosDiv1 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 17, context: html, text, full: html, text
• done with camFer1 and odoRosDiv1 lastz chain net refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 14, context: html, text, full: html, text
• done with lastz felCat5 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 10, context: html, text, full: html, text
• lastz runs started on panPan1 latCha1 jacJac1 panHod1 capHir1 hetGla2 refs #10272
  • src/hg/makeDb/doc/hg19.txt - lines changed 375, context: html, text, full: html, text
• reducing the 110way to a benchMark100 refs #10272
  • src/hg/utils/phyloTrees/benchMark100.commonNames.nh - lines changed 100, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/benchMark100.nh - lines changed 100, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/benchMark100.scientificNames.nh - lines changed 100, context: html, text, full: html, text
  • src/hg/utils/phyloTrees/makefile - lines changed 8, context: html, text, full: html, text