8debce5b56bcc570ddff4226bf9b04c30e4f6f29
markd
  Wed Feb 5 12:48:04 2025 -0800
import of GENCODE Versions VM37, V48, V48lift37

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 1384f0a68ff..1a388040333 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -4033,30 +4033,124 @@
     hg38.wgEncodeGencodeAnnotationRemarkV47.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV47
 "Link together Gencode UniProt Support table with Attributes table"
     hg38.wgEncodeGencodeEntrezGeneV47.transcriptId dupeOk
     hg38.wgEncodeGencodeEntrezGeneV47.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportV47
 "Link together Gencode Exon Support table with Attributes table"
     hg38.wgEncodeGencodeExonSupportV47.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV47.transcriptId minCheck=0.50
 
 # end Gencode V47
 
+# begin Gencode V48
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV48
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV48
+identifier wgEncodeGencodeBasicAttrsV48
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV48.transcriptId
+    hg38.wgEncodeGencodeBasicV48.name
+
+identifier wgEncodeGencodeCompAttrsV48
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV48.transcriptId
+    hg38.wgEncodeGencodeCompV48.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV48
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV48.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV48.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV48)
+identifier wgEncodeGencodeGeneSourceV48
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV48.geneId
+    hg38.wgEncodeGencodeAttrsV48.geneId
+
+identifier wgEncodeGencodeGeneSymbolV48
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV48
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.007
+
+identifier wgEncodeGencodePubMedV48
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId  minCheck=0.40
+
+identifier wgEncodeGencodeRefSeqV48
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV48
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV48.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV48
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV48
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV48.transcriptId
+    hg38.wgEncodeGencodeAttrsV48.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV48
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.01
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV48
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV48
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeAnnotationRemarkV48
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV48
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV48.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportV48
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV48.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV48.transcriptId minCheck=0.50
+
+# end Gencode V48
+
 # 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
@@ -6101,30 +6195,119 @@
     hg19.wgEncodeGencodeUniProtV47lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.28
 
 identifier wgEncodeGencodeAnnotationRemarkV47lift37
 "Link together Gencode Annotation Remark table with Attributes table"
     hg19.wgEncodeGencodeAnnotationRemarkV47lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV47lift37.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV47lift37
 "Link together Gencode UniProt Support table with Attributes table"
     hg19.wgEncodeGencodeEntrezGeneV47lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeEntrezGeneV47lift37.transcriptId minCheck=0.35
 
 # end Gencode V47lift37
 
+# begin Gencode V48lift37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV48lift37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV48lift37
+identifier wgEncodeGencodeBasicAttrsV48lift37
+"Link together Gencode Basic Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId
+    hg19.wgEncodeGencodeBasicV48lift37.name
+
+identifier wgEncodeGencodeCompAttrsV48lift37
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId
+    hg19.wgEncodeGencodeCompV48lift37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV48lift37
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId
+    hg19.wgEncodeGencodePseudoGeneV48lift37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV48lift37)
+identifier wgEncodeGencodeGeneSourceV48lift37
+"Link together Gencode Gene Source table with Attributes table"
+    hg19.wgEncodeGencodeGeneSourceV48lift37.geneId
+    hg19.wgEncodeGencodeAttrsV48lift37.geneId
+
+identifier wgEncodeGencodeGeneSymbolV48lift37
+"Link together Gencode gene symbol table with Attributes table"
+    hg19.wgEncodeGencodeGeneSymbolV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV48lift37
+"Link together Gencode Pdb table with Attributes table"
+    hg19.wgEncodeGencodePdbV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.007
+
+identifier wgEncodeGencodePubMedV48lift37
+"Link together Gencode Pubmed table with Attributes table"
+    hg19.wgEncodeGencodePubMedV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId  minCheck=0.40
+
+identifier wgEncodeGencodeRefSeqV48lift37
+"Link together Gencode RefSeq table with Attributes table"
+    hg19.wgEncodeGencodeRefSeqV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV48lift37
+"Link together Gencode RefSeq table with refGene track"
+    hg19.wgEncodeGencodeRefSeqV48lift37.rnaAcc dupeOk chopAfter=.
+    hg19.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV48lift37
+"Link together Gencode Tag table with Attributes table"
+    hg19.wgEncodeGencodeTagV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV48lift37
+"Link together Gencode Transcript Source table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSourceV48lift37.transcriptId
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV48lift37
+"Link together Gencode Transcript Support table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSupportV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.01
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV48lift37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptionSupportLevelV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV48lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeUniProtV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeAnnotationRemarkV48lift37
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg19.wgEncodeGencodeAnnotationRemarkV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV48lift37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV48lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeEntrezGeneV48lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeEntrezGeneV48lift37.transcriptId minCheck=0.35
+
+# end Gencode V48lift37
+
 # 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
@@ -8649,31 +8832,124 @@
     mm39.wgEncodeGencodeAnnotationRemarkVM36.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM36
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM36.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM36.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM36
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM36.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM36.transcriptId minCheck=0.50
 
 # end Gencode VM36
 
-# end Gencode VM36
+# begin Gencode VM37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM37
+identifier wgEncodeGencodeBasicAttrsVM37
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId
+    mm39.wgEncodeGencodeBasicVM37.name
+
+identifier wgEncodeGencodeCompAttrsVM37
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId
+    mm39.wgEncodeGencodeCompVM37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM37
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM37)
+identifier wgEncodeGencodeGeneSourceVM37
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM37.geneId
+    mm39.wgEncodeGencodeAttrsVM37.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM37
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM37
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.007
+
+identifier wgEncodeGencodePubMedVM37
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId  minCheck=0.40
+
+identifier wgEncodeGencodeRefSeqVM37
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM37
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM37.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM37
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM37
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM37.transcriptId
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM37
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.01
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM37
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeAnnotationRemarkVM37
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm39.wgEncodeGencodeAnnotationRemarkVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM37
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeEntrezGeneVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeEntrezGeneVM37.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM37
+"Link together Gencode Exon Support table with Attributes table"
+    mm39.wgEncodeGencodeExonSupportVM37.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM37.transcriptId minCheck=0.50
+
+# end Gencode VM37
+
 
 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