1d776cf087b4b10409819b8119d39ad7fe8a894e
hiram
  Thu Sep 10 12:13:52 2020 -0700
adding rules for calJac4 refs #24074

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 1f4d384..f598ba6 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -12,31 +12,31 @@
 set apiMel apiMel1,apiMel2
 set aplCal aplCal1
 set aptMan aptMan1
 set aquChr aquChr2
 set astMex astMex1
 set balAcu balAcu1
 set bisBis bisBis1
 set bosTau bosTau2,bosTau3,bosTau4,bosTau5,bosTau6,bosTau7,bosTau8,bosTau9
 set braFlo braFlo1,braFlo2
 set bruMal bruMal1
 set caeAng caeAng1
 set caeJap caeJap1,caeJap3,caeJap4
 set caePb caePb1,caePb2,caePb3
 set caeRem caeRem2,caeRem3,caeRem4
 set caeSp11 caeSp111
-set calJac calJac1,calJac3
+set calJac calJac1,calJac3,calJac4
 set calMil calMil1
 set canFam canFam1,canFam2,canFam3,canFam4,canFam5
 set casCan casCan1
 set cavApe cavApe1
 set cavPor cavPor3
 set cb cb1,cb3,cb4
 set ce ce2,ce4,ce6,ce9,ce10,ce11
 set cebCap cebCap1
 set cerAty cerAty1
 set cerSim cerSim1
 set chiLan chiLan1
 set choHof choHof1
 set chlSab chlSab2
 set chrPic chrPic1,chrPic2
 set ci ci1,ci2,ci3
@@ -201,31 +201,31 @@
 set proteinDb proteins070202,proteins060115,proteins050415,proteins051015,proteins050415,proteins050315,proteins050201,proteins041115,proteins040515,proteins040315,proteins0111,proteins0305,proteins031112,proteins040115,proteins0405,proteins070403,proteins072003,proteins092903,proteins1129
 
 # Define zoo databases (currently not checked)
 set zooDb zooBaboon3,zooCat3,zooChicken3,zooChimp3,zooCow3,zooDog3,zooFugu3,zooHuman3,zooMouse3,zooPig3,zooRat3,zooTetra3,zooZebrafish3
 
 # Define ucscRetro databases
 set ucscRetroDb hg19,hg38,mm9,mm10
 
 # Set up list of databases we ignore and those we check.  Program
 # will complain about other databases.
 
 databasesChecked $gbd,$otherDb,hgFixed
 databasesIgnored mysql,lost+found,$proteinDb,$zooDb,sc1,hgcentraltest,hgcentralbeta,test,sp090821,sp080707,sp070202,sp060115,sp051015,sp050415,sp040915,sp040515,sp040315,sp040115,qapushq,mysql-save,hgcentralangie,go070111,go060330,customTracks,customTrash,10Kgenomes,BRfoo,abc,andy,bioCyc070327,bioCyc090623,bioCyc100514,bosTau3Old,ccds,ccds20080404,ccdsNew,ccds_before,ctd,ctd021508,ctdOld,dark,elegansWS176,encpipeline_aamp,encpipeline_beta,encpipeline_galt,encpipeline_kate,encpipeline_prod,encpipeline_test,entrez,euaGli13,eutHer13,fakeDataE0,fanKgTemp,fanKgTemp2,fanTest,fanTest2,gencode,germlineVar_hg18,go040501,go041115,go050521,go050726,go060211,go061219,go080130,goJill,hg15test,hg18kg11,hg18snp130,hg18test,hg19Haps,hg19Patch10,hg19Patch13,hg19Patch9,hg19Patch5,hg19Patch2,hg19Patch2i,hg38Patch2,hg38Patch3,hg38Patch5,hg38Patch6,hg38Patch7,hg38Patch9,hg38Patch11,hg19snp131,hg19snp132,hg19snp134,hg19snp135,hg19snp137,hg19snp138,hg19snp141,hg38snp141,hg19snp142,hg38snp142,hg19snp144,hg38snp144,hg19snp146,hg38snp146,hg19snp147,hg38snp147,hg19snp149,hg38snp149,hg19snp150,hg38snp150,hg19snp151,hg38snp151,mm10snp138,canFam3snp139,bosTau7snp138,bosTau8snp148,susScr3snp138,galGal4snp138,hgcentralgsid,hgcentralrhead,hgcentraltest2,hgcentraltestangie,hiv1,hivgne8,homIni13,homIni14,homIni20,homNea0,homPan20,influenza,information_schema,ismb2004,jkFoo,jorgetest,kgHg17FTemp,kgHg18ATemp,kgMm8ATemp,kgRn3DTemp,markd,markdCcds,markdMGC,membership,metaData_vsmalladi,metadata_krish,mikep,mm9Temp,mm10snp137,mmtv,nonAfr13,oldChoHof1,panTro2snp127,pathway,petMar0,pongo,proteins080707,proteins090821,qa,rah,reactome,rn4UCGenes,rn4snp130,snpCompare,snpFixed,sp100331,sp101005,t18,testMePrivl,tmpBioCychg18,tmpFoo12,tmpUcscGeneshg19,treeFam,uf,ug,vega33,vega40,visiGeneOld,visiGeneXml
 
 # Define various non-self chains
-set chainDest AilMel1,AmbMex1,AncCey1,AnoCar1,AnoCar2,AnoGam1,ApiMel1,ApiMel2,ApiMel3,ApiMel4,AplCal1,AscSuu1,BosTau1,BosTau2,BosTau3,BosTau4,BosTau6,BosTau7,BosTau8,BosTau9,BraFlo1,BraFlo2,BruMal1,BruMal2,BurXyl1,CaeAng1,CaeAng2,CaeJap1,CaeJap3,CaeJap4,CaePb1,CaePb2,CaePb3,CaeRem2,CaeRem3,CaeRem4,CaeSp111,CaeSp51,CalJac1,CalJac3,CalMil1,CanFam1,CanFam2,CanFam3,CanFam4,CanFam5,CanFamPoodle1,CavPor3,Cb1,Cb3,Cb4,Ce2,Ce4,Ce6,Ce9,Ce10,Ce11,ChlSab1,ChlSab2,ChoHof1,ChrPic2,Ci1,Ci2,CioSav2,ColAng1,CriGri1,CriGriChoV1,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,DanRer7,DanRer10,DasNov2,DasNov3,DipOrd1,DirImm1,Dm1,Dm2,Dm3,Dm6,Dp1,Dp2,Dp3,Dp4,DroAlb1,DroAna1,DroAna2,DroAna3,DroBia2,DroBip2,DroEle2,DroEre1,DroEre2,DroEug2,DroFic2,DroGri1,DroGri2,DroKik2,DroMir2,DroMoj1,DroMoj2,DroMoj3,DroPer1,DroPse3,DroRho2,DroSec1,DroSim1,DroSuz1,DroTak2,DroVir1,DroVir2,DroVir3,DroWil1,DroWil2,DroYak1,DroYak2,DroYak3,EchTel1,EnhLutNer1,EquCab1,EquCab2,EquCab3,EriEur1,EriEur2,FalPer1,FelCat3,FelCat4,FelCat5,FelCat8,FelCat9,Fr1,Fr2,Fr3,GadMor1,GalGal2,GalGal3,GalGal4,GalGal5,GalGal6,GalVar1,GasAcu1,GeoFor1,GorGor1,GorGor2,GorGor3,GorGor4,GorGor5,GorGor6,HaeCon1,HaeCon2,HetBac1,HetGla1,HetGla2,Hg16,Hg17,Hg18,Hg19,Hg19Patch2,Hg19Patch5,Hg19Patch9,Hg19Patch10,Hg19Patch13,Hg38Patch2,Hg38Patch3,Hg38Patch5,Hg38Patch6,Hg38Patch7,Hg38Patch9,Hg38Patch11,Hg38,LatCha1,LepWed1,LoaLoa1,LoxAfr2,LoxAfr3,MacEug1,MacEug2,MacFas5,MarVir1,MayZeb1,MelGal1,MelGal5,MelHap1,MelInc1,MelInc2,MelUnd1,MesAur1,MicMur1,MicMur2,MicMur3,MicOch1,Mm5,Mm6,Mm7,Mm8,Mm9,Mm10,Mm10Patch1,Mm10Patch4,Mm39,MonDom1,MonDom2,MonDom4,MonDom5,MusDom2,MyoLuc1,MyoLuc2,NanPar1,NasLar1,NecAme1,NeoSch1,NomLeu1,NomLeu2,NomLeu3,OchPri2,OncVol1,OreNil1,OreNil2,OreNil3,OrnAna1,OrnAna2,OryCun1,OryCun2,OryLat1,OryLat2,OtoGar1,OtoGar3,OviAri1,OviAri3,OviAri4,PanPan1,PanRed1,PanTro1,PanTro2,PanTro3,PanTro4,PanTro5,PanTro6,PapAnu2,PapAnu3,PapHam1,PelSin1,PetMar1,PetMar2,PetMar3,PonAbe2,PonAbe3,PriExs1,PriPac1,PriPac2,PriPac3,ProCap1,ProCoq1,PteVam1,RheMac1,RheMac2,RheMac3,RheMac8,RheMac10,RhiRox1,Rn3,Rn4,Rn5,Rn6,RegenRn0,SaiBol1,SorAra1,SpeTri1,SpeTri2,StrRat1,StrRat2,StrPur1,StrPur2,SusScr1,SusScr2,SusScr3,SusScr11,TaeGut1,TaeGut2,TarSyr1,TarSyr2,TetNig1,TetNig2,TriCas2,TriMan1,TriSpi1,TriSui1,TupBel1,TurTle1,TurTru1,TurTru2,VicPac1,VicPac2,XenLae2,XenTro1,XenTro2,XenTro3,XenTro7,XenTro9
+set chainDest AilMel1,AmbMex1,AncCey1,AnoCar1,AnoCar2,AnoGam1,ApiMel1,ApiMel2,ApiMel3,ApiMel4,AplCal1,AscSuu1,BosTau1,BosTau2,BosTau3,BosTau4,BosTau6,BosTau7,BosTau8,BosTau9,BraFlo1,BraFlo2,BruMal1,BruMal2,BurXyl1,CaeAng1,CaeAng2,CaeJap1,CaeJap3,CaeJap4,CaePb1,CaePb2,CaePb3,CaeRem2,CaeRem3,CaeRem4,CaeSp111,CaeSp51,CalJac1,CalJac3,CalJac4,CalMil1,CanFam1,CanFam2,CanFam3,CanFam4,CanFam5,CanFamPoodle1,CavPor3,Cb1,Cb3,Cb4,Ce2,Ce4,Ce6,Ce9,Ce10,Ce11,ChlSab1,ChlSab2,ChoHof1,ChrPic2,Ci1,Ci2,CioSav2,ColAng1,CriGri1,CriGriChoV1,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,DanRer7,DanRer10,DasNov2,DasNov3,DipOrd1,DirImm1,Dm1,Dm2,Dm3,Dm6,Dp1,Dp2,Dp3,Dp4,DroAlb1,DroAna1,DroAna2,DroAna3,DroBia2,DroBip2,DroEle2,DroEre1,DroEre2,DroEug2,DroFic2,DroGri1,DroGri2,DroKik2,DroMir2,DroMoj1,DroMoj2,DroMoj3,DroPer1,DroPse3,DroRho2,DroSec1,DroSim1,DroSuz1,DroTak2,DroVir1,DroVir2,DroVir3,DroWil1,DroWil2,DroYak1,DroYak2,DroYak3,EchTel1,EnhLutNer1,EquCab1,EquCab2,EquCab3,EriEur1,EriEur2,FalPer1,FelCat3,FelCat4,FelCat5,FelCat8,FelCat9,Fr1,Fr2,Fr3,GadMor1,GalGal2,GalGal3,GalGal4,GalGal5,GalGal6,GalVar1,GasAcu1,GeoFor1,GorGor1,GorGor2,GorGor3,GorGor4,GorGor5,GorGor6,HaeCon1,HaeCon2,HetBac1,HetGla1,HetGla2,Hg16,Hg17,Hg18,Hg19,Hg19Patch2,Hg19Patch5,Hg19Patch9,Hg19Patch10,Hg19Patch13,Hg38Patch2,Hg38Patch3,Hg38Patch5,Hg38Patch6,Hg38Patch7,Hg38Patch9,Hg38Patch11,Hg38,LatCha1,LepWed1,LoaLoa1,LoxAfr2,LoxAfr3,MacEug1,MacEug2,MacFas5,MarVir1,MayZeb1,MelGal1,MelGal5,MelHap1,MelInc1,MelInc2,MelUnd1,MesAur1,MicMur1,MicMur2,MicMur3,MicOch1,Mm5,Mm6,Mm7,Mm8,Mm9,Mm10,Mm10Patch1,Mm10Patch4,Mm39,MonDom1,MonDom2,MonDom4,MonDom5,MusDom2,MyoLuc1,MyoLuc2,NanPar1,NasLar1,NecAme1,NeoSch1,NomLeu1,NomLeu2,NomLeu3,OchPri2,OncVol1,OreNil1,OreNil2,OreNil3,OrnAna1,OrnAna2,OryCun1,OryCun2,OryLat1,OryLat2,OtoGar1,OtoGar3,OviAri1,OviAri3,OviAri4,PanPan1,PanRed1,PanTro1,PanTro2,PanTro3,PanTro4,PanTro5,PanTro6,PapAnu2,PapAnu3,PapHam1,PelSin1,PetMar1,PetMar2,PetMar3,PonAbe2,PonAbe3,PriExs1,PriPac1,PriPac2,PriPac3,ProCap1,ProCoq1,PteVam1,RheMac1,RheMac2,RheMac3,RheMac8,RheMac10,RhiRox1,Rn3,Rn4,Rn5,Rn6,RegenRn0,SaiBol1,SorAra1,SpeTri1,SpeTri2,StrRat1,StrRat2,StrPur1,StrPur2,SusScr1,SusScr2,SusScr3,SusScr11,TaeGut1,TaeGut2,TarSyr1,TarSyr2,TetNig1,TetNig2,TriCas2,TriMan1,TriSpi1,TriSui1,TupBel1,TurTle1,TurTru1,TurTru2,VicPac1,VicPac2,XenLae2,XenTro1,XenTro2,XenTro3,XenTro7,XenTro9
 
 # Define databases that support known genes
 set kgDb $hg,$mm,rn3
 # Older format (KG 2)
 set kgDb2 hg16,hg17,mm7,mm8,rn3,rn4
 # Newer format (KG 3 aka UCSC Genes)
 set kgDb3 hg18,hg19,hg38,mm9,mm10
 
 # Protein browser databases.
 set pbDb hg18,hg17,hg16,mm7,mm8,mm9,rn3
 set pbDb1 hg17,hg16,mm7,mm8,mm9,rn3
 set pbDb2 rn3
 set pbDb3 hg16,hg17,hg18
 
 # Define databases that support family browser (gene sorter)
@@ -6047,31 +6047,31 @@
     $hgSplit,hg19,!hg18.gl.frag $split chopAfter=_
     $hg,!hg16,!hg17,!hg18.gold.frag
     $hgSplit,!hg18.gold.frag $split
     hg18.gl.frag $split chopAfter=_ minCheck=0.95
     hg18.gold.frag $split minCheck=0.90
 
 identifier wgsContigAccession typeOf=seqExtFile
 "Genbank accession.version of whole-genome shotgun contig"
     $wgs.contigAcc.acc
 
 identifier wgsContigName
 "Sequencing project name for whole-genome shotgun contigs."
     $wgs.contigAcc.contig
     $wgs,!panTro1.gold.frag $split full
 
-set notProteinAccession !ailMel1,!allMis1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!ci3,!colAng1,!cotJap2,!criGriChoV1,criGri1,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!dm3,!dm6,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat8,!felCat9,!fr2,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!manPen1,!macFas5,!manLeu1,!micMur2,!micMur3,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAr4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!petMar2,!priPac3,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!susScr3,!taeGut2,!tarSyr2,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notProteinAccession !ailMel1,!allMis1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calJac4,!calMil1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!ci3,!colAng1,!cotJap2,!criGriChoV1,criGri1,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!dm3,!dm6,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat8,!felCat9,!fr2,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!manPen1,!macFas5,!manLeu1,!micMur2,!micMur3,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAr4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!petMar2,!priPac3,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!susScr3,!taeGut2,!tarSyr2,!vicPac2,!xenLae2,!xenTro7,!xenTro9
 
 identifier proteinAccession fuzzy
 "Genbank protein accession."
     $kgDb.kgProtAlias.alias
     $kgDb.kgSpAlias.alias minCheck=0.1
     $kgDb.kgXref.protAcc
     hgFixed.refLink.protAcc
 
 identifier estOrMrnaAccession
 "Genbank EST or mRNA accession."
     hgFixed.gbSeq.acc
     hgFixed.gbCdnaInfo.acc unique
     hgFixed.imageClone.acc
     $gbd,!ce2,!hg16,!hg17,!hg18,!mm7.altGraphX.mrnaRefs comma
     ce2.altGraphX.mrnaRefs comma minCheck=0.96
@@ -6635,52 +6635,52 @@
 "An image cDNA clone ID"
     hgFixed.imageClone.imageId
 
 identifier humanFosmidId
 "Human Fosmid (~50kb genomic sequence) clone"
     $hg.fosEndPairs.name dupeOk
 
 identifier humanFosmidEndId
 "Identifier of read from one end of human formid."
     $hg.all_fosends.qName dupeOk
     $hg.fosEndPairs.lfNames comma
 
 ## TYPED TO HERE %%%
 # Mapping Stuff, STS, etc.
 
-set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calJac4,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier dbStsId external=dbSts fuzzy
 "NCBI dbSTS (Sequenced Tagged Site, aka mapping sequence) ID"
     $hg.all_sts_primer.qName chopBefore=dbSTS_
     $gbd,$notDbStsId.all_sts_seq.qName
     $gbd,$notDbStsId.stsInfo2.dbSTSid
 
 identifier ucscStsId
 "UCSC STS (Sequenced Tagged Site, aka mapping sequence) ID"
     $gbd.stsInfo2.identNo
     $gbd.stsAlias.identNo
     $gbd.stsMap.identNo
 
 identifier ucscMouseStsId
 "UCSC Mouse STS (Sequenced Tagged Site, aka mapping sequence) ID"
     $mm.stsInfoMouseNew.identNo
     $mm.stsAlias.identNo
     $mm.all_sts_primer.qName chopAfter=_ minCheck=0.99
     $mm.stsMapMouseNew.identNo
 
-set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calJac4,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier stsName fuzzy
 "STS (Sequenced Tagged Site, aka mapping sequence) Name"
     $hg.fishClones.stsNames comma
     $gbd,$notStsName.stsInfo2.otherNames comma
     $mm,!mm39.stsInfoMouseNew.alias separator=;
 
 identifier stsTrueName typeOf=stsName
 "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
     $gbd,!hg16.stsInfo2.name
     $gbd.stsAlias.trueName
     $gbd.stsMap.name
 
 identifier stsTrueNameHg16 typeOf=stsName
 "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name for hg16"
@@ -6766,31 +6766,31 @@
     $hg.jaxOrtholog.mouseSymbol
     hgFixed.refLink.name
     visiGene.gene.name
 
 # Model Organism Database Identifiers
 
 identifier jaxMgiId
 "Jackson Labs Mouse Gene Identifier"
     $hg.jaxOrtholog.mgiId
 
 identifier wormBaseIsoformCluster
 "Overlapping (after splicing) WormBase transcripts"
     $ce.sangerCanonical.clusterId
     $ce.sangerIsoforms.clusterId full
 
-set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calJac4,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier wormBaseId external=WormBase dependency
 "WormBase (C. elegans) ORF ID"
     $ce.sangerGene.name
     $gbd,$notWormBaseId.ceBlastTab.target minCheck=0.90
     $ce.kimExpDistance.query minCheck=0.68
     $ce.kimExpDistance.target minCheck=0.66
     $ce.orfToGene.name
     $ce.sangerBlastTab.query
     $ce.sangerBlastTab.target
     $ce.sangerCanonical.transcript
     $ce.sangerIsoforms.transcript
     $ce.sangerLinks.orfName minCheck=0.96
     $ce.sangerPep.name minCheck=0.96
     $ce.sangerToKim.name
@@ -6810,31 +6810,31 @@
 
 identifier wormBaseRnaGene external=WormBase dependency
 "WormBase (C. elegans) RNA genes"
     $ce.sangerRnaGene.name
 
 identifier flyBaseRefId
 "FlyBase (Drosophila) Reference (Literature)"
     $dm.fbRef.id
     $dm.fbPhenotype.fbRef
 
 identifier flyBaseAlleleId
 "FlyBase (Drosophila) Allele ID"
     $dm.fbAllele.id
     $dm.fbPhenotype.fbAllele exclude=0
 
-set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn4,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calJac4,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn4,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier flyBaseGeneId external=FlyBase
 "FlyBase (Drosophila) Gene ID"
     $dm.fbGene.geneId
     $dm.bdgpExprLink.flyBaseId minCheck=0.95
     dm1.bdgpGeneInfo.flyBaseId minCheck=0.95
     dm1.bdgpNonCodingInfo.flyBaseId minCheck=0.20
     dm1.bdgpSwissProt.flyBaseId minCheck=0.95
     $dm.fbAllele.geneId
     $dm.fbPhenotype.geneId
     $dm.fbSynonym.geneId
     $dm.fbTranscript.geneId minCheck=0.95
     dm1.flyBaseSwissProt.flyBaseId minCheck=0.95
     $dm,!dm1.flyBase2004Xref.fbgn minCheck=0.90
     $dm,!dm1.pscreen.geneIds comma minCheck=0.95
@@ -6928,31 +6928,31 @@
     $dm.flyreg2.name minCheck=0.8
 
 identifier sgdIsoformCluster
 "Overlapping (after splicing) SGD (Yeast) transcripts"
     $sacCer.sgdCanonical.clusterId
     $sacCer.sgdIsoforms.clusterId full
 
 identifier sgdProtHomologId
 "sacCer protHomolog protein ID"
     $sacCer.protHomolog.proteinID dupeOk
     $sacCer.samSubdir.proteinId
 
 identifier sgdId external=SGD
 "Sacchromyces Genome Database ID - Coding or other"
 
-set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calJac4,!calMil1,!canFam4,!canFam5,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!mm39,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier sgdCodingId typeOf=sgdId dependency
 "Sacchromyces Genome Database ID"
     $sacCer.sgdGene.name
     $gbd,$notSgdCodingId.scBlastTab.target minCheck=0.90
     $sacCer.sgdBlastTab.query
     $sacCer.sgdBlastTab.target
     $sacCer.ceBlastTab.query
     $sacCer.dmBlastTab.query
     $sacCer,!sacCer1.drBlastTab.query
     $sacCer.hgBlastTab.query minCheck=0.999
     $sacCer.mmBlastTab.query
     $sacCer.rnBlastTab.query
     sacCer2.knownBlastTab.query
     $sacCer.choExpDistance.target minCheck=0.60
@@ -7070,31 +7070,31 @@
 "Ensemble Gene ID"
     $gbd.ensemblXref3.gene dupeOk
 
 identifier ensemblProteinId external=Ensembl
 "Ensemble Translated Protein ID"
     $gbd.ensTranscript.translation_name dupeOk
     $gbd.ensGtp.protein chopAfter=.
     $gbd.sfAssign.seqID minCheck=0.01
 
 identifier ensemblProteinId3 external=Ensembl
 "Ensemble Translated Protein ID"
     $gbd.ensemblXref3.protein dupeOk
     $gbd.sfAssign.seqID minCheck=0.01
 
 
-set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!canFam4,!canFam5,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!gorGor6,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!mm39,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenCho1,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!calJac4,!canFam4,!canFam5,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!gorGor6,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!mm39,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenCho1,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier ensemblTranscriptId external=Ensembl dependency
 "Ensembl Transcript ID"
     $ensGeneDb,$notEnsemblTranscriptId.ensGene.name dupeOk
     $gbd,$notEnsemblTranscriptId.ensGeneXref.transcript_name minCheck=0.95
     $ensGeneDb,$notEnsemblTranscriptId.ensGtp.transcript minCheck=0.94
     $ensGeneDb,$notEnsemblTranscriptId.ensPep.name minCheck=0.93
     $gbd,$notEnsemblTranscriptId.ensTranscript.transcript_name minCheck=0.20
     $gbd,$notEnsemblTranscriptId.ensInfo.name minCheck=0.9
     $ensGeneDb,$notEnsemblTranscriptId.ensemblToGeneName.name minCheck=0.94
     $ensGeneDb,$notEnsemblTranscriptId.ensemblSource.name minCheck=0.96
     !hg38,$kgDb,!mm39.knownToEnsembl.value chopAfter=.
     $kgDb,!mm39.rgdGene2ToEnsembl.value chopAfter=.
     $danRer.ensZfishBlastTab.query
     $danRer.ensZfishBlastTab.target