Commits for hiram

v297_preview to v297_preview2 (2014-03-03 to 2014-03-10) v297

• corrected hg19 to rn4 rn5 lastz procedure refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 5, context: html, text, full: html, text
• correct table load altSeqLiftOverPsl for Hg19 Diff track refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 3, context: html, text, full: html, text
• add altSeqLiftOver check rule refs #11681
  • src/hg/makeDb/schema/all.joiner - lines changed 6, context: html, text, full: html, text
• document hg38ContigDiff table procedure refs #11681
  • src/hg/makeDb/doc/hg19.txt - lines changed 9, context: html, text, full: html, text
• adding hg38ContigDiff identifier for hg19 and hg38 refs #11681
  • src/hg/makeDb/schema/all.joiner - lines changed 5, context: html, text, full: html, text
• moving chainNetLegacy.ra up refs #11681
  • src/hg/makeDb/trackDb/human/chainNetLegacy.ra - lines changed 546, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetLegacy.ra - lines changed 546, context: html, text, full: html, text
• moving chainNetLegacy.ra up one to share with hg19 and hg38 refs #11681
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
• improve error message about chr names refs #12821
  • src/hg/lib/customFactory.c - lines changed 1, context: html, text, full: html, text
• fixup a couple of the URLs refs #12796
  • src/hg/utils/automation/EnsGeneAutomate.pm - lines changed 4, context: html, text, full: html, text
• add altLocations to the ignore list for hg18 refs #11681
  • src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text
• updated ideogram from NCBI refs #11681
  • src/hg/makeDb/doc/hg38.txt - lines changed 39, context: html, text, full: html, text
• very quick genome browser build procedure refs #252
  • src/hg/makeDb/doc/quickAssembly.txt - lines changed 200, context: html, text, full: html, text
• add rules for seqNcbiAltSequence and extNcbiAltSequence tables in hg38 refs #11681
  • src/hg/makeDb/schema/all.joiner - lines changed 6, context: html, text, full: html, text
• better linkage of altSeqLiftOverPsl seqNcbiAltSequence extNcbiAltSequence tables refs #11681
  • src/hg/makeDb/schema/all.joiner - lines changed 13, context: html, text, full: html, text
• add the dbDb/clade/genomeClade table additions refs #252
  • src/hg/makeDb/doc/quickAssembly.txt - lines changed 54, context: html, text, full: html, text
• moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
  • src/hg/makeDb/trackDb/human/chainNetFr2.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetFr3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetGalGal3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetGalGal4.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetVertebrate.ra - lines changed 340, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetFr2.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetFr3.ra - lines changed 15, context: html, text, full: html, text
  • 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
  • src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra - lines changed 340, context: html, text, full: html, text
• moving composite chainNetVertebrate up one level to use in hg38 also refs #11681
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
• default on for knownGene and refGene refs #11681
  • src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra - lines changed 4, context: html, text, full: html, text
• moving chainNetPrimate.ra up one so it can be used in hg38 too refs #11681
  • src/hg/makeDb/trackDb/human/chainNetOtoGar1.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetOtoGar3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 204, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRBestOtoGar1.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRBestOtoGar3.ra - lines changed 15, context: html, text, full: html, text
  • 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/chainNetPrimate.ra - lines changed 204, 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 1, context: html, text, full: html, text
• correct use of include html for chainNetPrimate refs #11681
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19primateChainNet.html - lines changed 202, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/primateChainNet.html - lines changed 202, context: html, text, full: html, text
• now using same chain net composites as hg19 refs #11681
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 3, context: html, text, full: html, text
• chainNetPrimate has moved up one level refs #11681
  • src/hg/makeDb/trackDb/human/hg38/chainNetPrimate.ra - lines changed 215, context: html, text, full: html, text
• moving chainNetPlacental up one level refs #11681
  • src/hg/makeDb/trackDb/human/chainNetEchTel1.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetEchTel2.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetOviAri1.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetOviAri3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 388, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRn4.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetRn5.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetSusScr2.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetSusScr3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetTurTru1.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetTurTru2.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetVicPac1.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetVicPac2.ra - lines changed 15, context: html, text, full: html, text
  • 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/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 388, 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
  • src/hg/makeDb/trackDb/human/hg19/chainNetSusScr2.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetSusScr3.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetTurTru1.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/chainNetTurTru2.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
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
• correct usage of description html pages for vertebrate and placental chain nets refs #11681
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetVertebrate.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19mammalChainNet.html - lines changed 160, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html - lines changed 206, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/placentalChainNet.html - lines changed 160, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/vertebrateChainNet.html - lines changed 206, context: html, text, full: html, text
• adding felCat5 to the placental composite refs #11681
  • src/hg/makeDb/trackDb/human/chainNetFelCat4.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetFelCat5.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetLegacy.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetPlacental.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
• adding lamprey genes from Carson Holt/Jeramiah Smith refs #9153
  • src/hg/makeDb/trackDb/lamprey/petMar2/lampreyGene.html - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lamprey/petMar2/trackDb.ra - lines changed 11, context: html, text, full: html, text
• add geneNameAsName2 option to the gtfToGenePred refs #12796
  • src/hg/utils/automation/doEnsGeneUpdate.pl - lines changed 1, context: html, text, full: html, text
• were not correctly identifying on name2 in ensGene table refs #12796
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text
• v297 preview2 refs #12656
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text