70fde199fda0e697d5c0e5e01470ff433fa00dc1
markd
  Tue May 14 00:06:40 2024 -0700
Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts.  This deals incorrectly included PAR transcript.

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 9037e64..985712f 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -5829,30 +5829,119 @@
     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 V46lift37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV46lift37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV46lift37
+identifier wgEncodeGencodeBasicAttrsV46lift37
+"Link together Gencode Basic Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId
+    hg19.wgEncodeGencodeBasicV46lift37.name
+
+identifier wgEncodeGencodeCompAttrsV46lift37
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId
+    hg19.wgEncodeGencodeCompV46lift37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV46lift37
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId
+    hg19.wgEncodeGencodePseudoGeneV46lift37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV46lift37)
+identifier wgEncodeGencodeGeneSourceV46lift37
+"Link together Gencode Gene Source table with Attributes table"
+    hg19.wgEncodeGencodeGeneSourceV46lift37.geneId
+    hg19.wgEncodeGencodeAttrsV46lift37.geneId
+
+identifier wgEncodeGencodeGeneSymbolV46lift37
+"Link together Gencode gene symbol table with Attributes table"
+    hg19.wgEncodeGencodeGeneSymbolV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV46lift37
+"Link together Gencode Pdb table with Attributes table"
+    hg19.wgEncodeGencodePdbV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV46lift37
+"Link together Gencode Pubmed table with Attributes table"
+    hg19.wgEncodeGencodePubMedV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV46lift37
+"Link together Gencode RefSeq table with Attributes table"
+    hg19.wgEncodeGencodeRefSeqV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV46lift37
+"Link together Gencode RefSeq table with refGene track"
+    hg19.wgEncodeGencodeRefSeqV46lift37.rnaAcc dupeOk chopAfter=.
+    hg19.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV46lift37
+"Link together Gencode Tag table with Attributes table"
+    hg19.wgEncodeGencodeTagV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV46lift37
+"Link together Gencode Transcript Source table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSourceV46lift37.transcriptId
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV46lift37
+"Link together Gencode Transcript Support table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSupportV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.02
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV46lift37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptionSupportLevelV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV46lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeUniProtV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV46lift37
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg19.wgEncodeGencodeAnnotationRemarkV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV46lift37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV46lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeEntrezGeneV46lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeEntrezGeneV46lift37.transcriptId minCheck=0.35
+
+# end Gencode V46lift37
+
 # 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