src/hg/makeDb/schema/all.joiner 1.805

Index: src/hg/makeDb/schema/all.joiner
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/schema/all.joiner,v
retrieving revision 1.804
retrieving revision 1.805
diff -b -B -U 4 -r1.804 -r1.805
--- src/hg/makeDb/schema/all.joiner	20 May 2010 22:04:15 -0000	1.804
+++ src/hg/makeDb/schema/all.joiner	25 May 2010 16:32:08 -0000	1.805
@@ -96,9 +96,9 @@
 databasesChecked $gbd,$otherDb
 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
 
 # Define various non-self chains
-set chainDest Hg16,Hg17,Hg18,Hg19,Mm5,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,TetNig1,TetNig2,XenTro1,XenTro2,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar1,Ce2,Ce4,Ce6,OrnAna1,CaePb1,CaePb2,CaeRem2,CaeRem3,CaeJap1,Cb3,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CalJac3,CavPor3,PetMar1,BraFlo1,TaeGut1,GorGor1,AplCal1,PapHam1,TarSyr1,OtoGar1,MicMur1,LoxAfr2,LoxAfr3,SusScr1,SusScr2,AilMel1,FelCatV17e,CanFamPoodle1,ChoHof1,DasNov2,DipOrd1,EchTel1,EriEur1,MacEug1,MyoLuc1,OchPri2,OryCun1,OryCun2,ProCap1,PteVam1,SorAra1,SpeTri1,TupBel1,TurTru1,VicPac1
+set chainDest Hg16,Hg17,Hg18,Hg19,Mm5,Mm6,Mm7,Mm8,Mm9,Rn3,Rn4,Cb1,Dm1,Dm2,Dm3,Dp1,Dp2,Dp3,PanTro1,PanTro2,GalGal2,GalGal3,Fr1,Fr2,DanRer1,DanRer2,DanRer3,DanRer4,DanRer5,DanRer6,CanFam1,CanFam2,DroYak1,DroYak2,DroAna1,DroAna2,DroMoj1,DroMoj2,DroVir1,DroVir2,DroEre1,DroSec1,DroSim1,DroGri1,DroPer1,DroWil1,AnoGam1,ApiMel1,ApiMel2,ApiMel3,TetNig1,TetNig2,XenTro1,XenTro2,MonDom1,MonDom2,MonDom4,MonDom5,RheMac1,RheMac2,BosTau1,BosTau2,BosTau3,BosTau4,FelCat3,GasAcu1,OryLat1,OryLat2,EquCab1,EquCab2,AnoCar1,Ce2,Ce4,Ce6,OrnAna1,CaePb1,CaePb2,CaeRem2,CaeRem3,CaeJap1,Cb3,PriPac1,StrPur1,StrPur2,Ci1,Ci2,PonAbe2,CalJac1,CalJac3,CavPor3,PetMar1,BraFlo1,TaeGut1,GorGor1,AplCal1,PapHam1,TarSyr1,OtoGar1,MicMur1,LoxAfr2,LoxAfr3,SusScr1,SusScr2,AilMel1,FelCatV17e,CanFamPoodle1,ChoHof1,DasNov2,DipOrd1,EchTel1,EriEur1,MacEug1,MyoLuc1,OchPri2,OryCun1,OryCun2,ProCap1,PteVam1,SorAra1,SpeTri1,TupBel1,TurTru1,VicPac1
 
 # Define databases that support known genes
 set kgDb $hg,$mm,$rn
 # Older format (KG 2)
@@ -1780,8 +1780,14 @@
 "FlyBase Xref as of 2004 for dp3"
     dp3.flyBase2004Xref.name
     dp3.flyBaseGene.name
 
+identifier flyregId external=FlyReg
+"FlyReg motif name"
+    $dm.flyregMotif.name
+    $dm.flyreg.name minCheck=0.8
+    $dm.flyreg2.name minCheck=0.8
+
 identifier sgdIsoformCluster
 "Overlapping (after splicing) SGD (Yeast) transcripts"
     $sacCer.sgdCanonical.clusterId
     $sacCer.sgdIsoforms.clusterId full
@@ -2164,8 +2170,10 @@
 
 identifier bgiGeneId external=BGI
 "BGI Gene ID"
     $galGal.bgiGene.name
+    $galGal.bgiGeneInfo.name minCheck=0.1
+    $galGal.bgiGenePep.name minCheck=0.95
     $galGal.bgiGeneSnp.geneName minCheck=0.1
 
 # Other Identifiers
 
@@ -2970,10 +2978,10 @@
     axtInfo
     bam%
     blatFr1
     chromInfo
-    cpgIsland
-    cpgIslandExt
+    contamination
+    cpgIsland%
     ctgPos
     ctgPos2
     cytoBand
     cytoBandIdeo
@@ -3117,16 +3125,19 @@
 tablesIgnored $ci
     snapGene
 
 tablesIgnored $dm
+    %_myp2a
     anophelesEcores
+    bdtnp%Fdr%
+    fbGenscan
     fbGo
     fbRole
     fbUniProt
-    flyreg
-    flyreg2
+    mzD%
 
 tablesIgnored $galGal
+    bgiCov
     ecoresTetraodon
     supercontig
     caCondor454
 
@@ -3135,8 +3146,9 @@
     wz_ests
 
 tablesIgnored $canFam
     genomicSuperDups
+    mzH%
 
 tablesIgnored $anoGam
     anoEstNcl
 
@@ -3270,8 +3282,9 @@
     snp126ExceptionDesc
     switchDbTss
     syntenyMouse
     syntenyRat
+    tajd%
     targetScanS
     vistaEnhancers
     wgRna
     zoom1_affyTranscriptome