cf2ea277055c7881254552745ce3e38e0d23f9a5
markd
  Mon Mar 4 20:36:11 2024 -0800
import of GENCODE V46 prerelease

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index adcb55c..48dbc2d 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -3844,30 +3844,124 @@
     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 V46
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV46
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV46
+identifier wgEncodeGencodeBasicAttrsV46
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV46.transcriptId
+    hg38.wgEncodeGencodeBasicV46.name
+
+identifier wgEncodeGencodeCompAttrsV46
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV46.transcriptId
+    hg38.wgEncodeGencodeCompV46.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV46
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV46.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV46.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV46)
+identifier wgEncodeGencodeGeneSourceV46
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV46.geneId
+    hg38.wgEncodeGencodeAttrsV46.geneId
+
+identifier wgEncodeGencodeGeneSymbolV46
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV46
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV46
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV46
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV46
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV46.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV46
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV46
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV46.transcriptId
+    hg38.wgEncodeGencodeAttrsV46.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV46
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.02
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV46
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV46
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV46
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV46
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV46.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportV46
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV46.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV46.transcriptId minCheck=0.50
+
+# end Gencode V46
+
 # 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