308bed30e11953a0dc802743c98181ce7f409dd9
markd
  Tue Oct 10 20:23:18 2023 -0700
import of pre-release of GENCODE V45, VM34, and V45lift37

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 2a74ba6..adcb55c 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -3750,30 +3750,124 @@
     hg38.wgEncodeGencodeAnnotationRemarkV44.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV44
 "Link together Gencode UniProt Support table with Attributes table"
     hg38.wgEncodeGencodeEntrezGeneV44.transcriptId dupeOk
     hg38.wgEncodeGencodeEntrezGeneV44.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportV44
 "Link together Gencode Exon Support table with Attributes table"
     hg38.wgEncodeGencodeExonSupportV44.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.50
 
 # end Gencode V44
 
+# begin Gencode V45
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV45
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV45
+identifier wgEncodeGencodeBasicAttrsV45
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV45.transcriptId
+    hg38.wgEncodeGencodeBasicV45.name
+
+identifier wgEncodeGencodeCompAttrsV45
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV45.transcriptId
+    hg38.wgEncodeGencodeCompV45.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV45
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV45.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV45.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV45)
+identifier wgEncodeGencodeGeneSourceV45
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV45.geneId
+    hg38.wgEncodeGencodeAttrsV45.geneId
+
+identifier wgEncodeGencodeGeneSymbolV45
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV45
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV45
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV45
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV45
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV45.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV45
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV45
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV45.transcriptId
+    hg38.wgEncodeGencodeAttrsV45.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV45
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.02
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV45
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV45
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV45
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV45
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV45.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportV45
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV45.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV45.transcriptId minCheck=0.50
+
+# end Gencode V45
+
 # begin Gencode V24lift37
 
 # gencode genepreds with no associations
 # wgEncodeGencodePolyaV24lift37
 # wgEncodeGencode2wayConsPseudoV24lift37
 
 # gencode genepreds with joining through wgEncodeGencodeAttrsV24lift37
 identifier wgEncodeGencodeBasicAttrsV24lift37
 "Link together Gencode Basic Table with Attributes table"
     hg19.wgEncodeGencodeAttrsV24lift37.transcriptId
     hg19.wgEncodeGencodeBasicV24lift37.name
 
 identifier wgEncodeGencodeCompAttrsV24lift37
 "Link together Gencode Comprehensive Table with Attributes table"
     hg19.wgEncodeGencodeAttrsV24lift37.transcriptId
@@ -5551,30 +5645,119 @@
     hg19.wgEncodeGencodeUniProtV44lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV44lift37.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeAnnotationRemarkV44lift37
 "Link together Gencode Annotation Remark table with Attributes table"
     hg19.wgEncodeGencodeAnnotationRemarkV44lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV44lift37.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV44lift37
 "Link together Gencode UniProt Support table with Attributes table"
     hg19.wgEncodeGencodeEntrezGeneV44lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeEntrezGeneV44lift37.transcriptId minCheck=0.35
 
 # end Gencode V44lift37
 
+# begin Gencode V45lift37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV45lift37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV45lift37
+identifier wgEncodeGencodeBasicAttrsV45lift37
+"Link together Gencode Basic Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId
+    hg19.wgEncodeGencodeBasicV45lift37.name
+
+identifier wgEncodeGencodeCompAttrsV45lift37
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId
+    hg19.wgEncodeGencodeCompV45lift37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV45lift37
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId
+    hg19.wgEncodeGencodePseudoGeneV45lift37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV45lift37)
+identifier wgEncodeGencodeGeneSourceV45lift37
+"Link together Gencode Gene Source table with Attributes table"
+    hg19.wgEncodeGencodeGeneSourceV45lift37.geneId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.geneId
+
+identifier wgEncodeGencodeGeneSymbolV45lift37
+"Link together Gencode gene symbol table with Attributes table"
+    hg19.wgEncodeGencodeGeneSymbolV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV45lift37
+"Link together Gencode Pdb table with Attributes table"
+    hg19.wgEncodeGencodePdbV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV45lift37
+"Link together Gencode Pubmed table with Attributes table"
+    hg19.wgEncodeGencodePubMedV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV45lift37
+"Link together Gencode RefSeq table with Attributes table"
+    hg19.wgEncodeGencodeRefSeqV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV45lift37
+"Link together Gencode RefSeq table with refGene track"
+    hg19.wgEncodeGencodeRefSeqV45lift37.rnaAcc dupeOk chopAfter=.
+    hg19.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV45lift37
+"Link together Gencode Tag table with Attributes table"
+    hg19.wgEncodeGencodeTagV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV45lift37
+"Link together Gencode Transcript Source table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSourceV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV45lift37
+"Link together Gencode Transcript Support table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSupportV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId minCheck=0.02
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV45lift37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptionSupportLevelV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV45lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeUniProtV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV45lift37
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg19.wgEncodeGencodeAnnotationRemarkV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV45lift37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV45lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeEntrezGeneV45lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeEntrezGeneV45lift37.transcriptId minCheck=0.35
+
+# end Gencode V45lift37
+
 # begin Gencode VM2
 
 # gencode genepreds with no associations
 # wgEncodeGencodePolyaVM2
 # wgEncodeGencode2wayConsPseudoVM2
 
 # gencode genepreds with joining through wgEncodeGencodeAttrsVM2
 identifier wgEncodeGencodeBasicAttrsVM2
 "Link together Gencode Basic Table with Attributes table"
     mm10.wgEncodeGencodeAttrsVM2.transcriptId
     mm10.wgEncodeGencodeBasicVM2.name
 
 identifier wgEncodeGencodeCompAttrsVM2
 "Link together Gencode Comprehensive Table with Attributes table"
     mm10.wgEncodeGencodeAttrsVM2.transcriptId
@@ -7818,30 +8001,124 @@
     mm39.wgEncodeGencodeAnnotationRemarkVM33.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM33
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM33.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM33.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM33
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM33.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.50
 
 # end Gencode VM33
 
+# begin Gencode VM34
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM34
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM34
+identifier wgEncodeGencodeBasicAttrsVM34
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId
+    mm39.wgEncodeGencodeBasicVM34.name
+
+identifier wgEncodeGencodeCompAttrsVM34
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId
+    mm39.wgEncodeGencodeCompVM34.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM34
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM34.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM34)
+identifier wgEncodeGencodeGeneSourceVM34
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM34.geneId
+    mm39.wgEncodeGencodeAttrsVM34.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM34
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM34
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM34
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM34
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM34
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM34.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM34
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM34
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM34.transcriptId
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM34
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.02
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM34
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM34
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM34
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm39.wgEncodeGencodeAnnotationRemarkVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM34
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeEntrezGeneVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeEntrezGeneVM34.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM34
+"Link together Gencode Exon Support table with Attributes table"
+    mm39.wgEncodeGencodeExonSupportVM34.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.50
+
+# end Gencode VM34
+
 identifier wgEncodeGencodeClassesV3Hg19
 "Link together Gencode gene model (Known) and class for July 2009 Data Version"
     hg19.wgEncodeGencodeClassesV3.name
     hg19.wgEncodeGencodeAutoV3.name unique
     hg19.wgEncodeGencodeManualV3.name unique
     hg19.wgEncodeGencodePolyaV3.name unique
 
 identifier acemblyName dependency
 "Link together Acembly gene model structure and peptide."
     $hg,$mm.acembly.name
     $hg,!hg17,$mm.acemblyPep.name unique minCheck=0.90
     hg17.acemblyPep.name unique minCheck=0.63
     $hg,$mm.acemblyClass.name full unique
 
 identifier ECgeneName dependency