b610fbd43a68ff6fc49fcce3c638274831ca60ba
markd
  Tue Jul 12 13:04:52 2022 -0700
added All GENCODE V41lift37

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 4cfe7cf..31973ca 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -4912,30 +4912,120 @@
     hg19.wgEncodeGencodeUniProtV40lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV40lift37.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeAnnotationRemarkV40lift37
 "Link together Gencode Annotation Remark table with Attributes table"
     hg19.wgEncodeGencodeAnnotationRemarkV40lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV40lift37.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV40lift37
 "Link together Gencode UniProt Support table with Attributes table"
     hg19.wgEncodeGencodeEntrezGeneV40lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeEntrezGeneV40lift37.transcriptId minCheck=0.35
 
 # end Gencode V40lift37
 
+# begin Gencode V41lift37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV41lift37
+# wgEncodeGencode2wayConsPseudoV41lift37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV41lift37
+identifier wgEncodeGencodeBasicAttrsV41lift37
+"Link together Gencode Basic Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId
+    hg19.wgEncodeGencodeBasicV41lift37.name
+
+identifier wgEncodeGencodeCompAttrsV41lift37
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId
+    hg19.wgEncodeGencodeCompV41lift37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV41lift37
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId
+    hg19.wgEncodeGencodePseudoGeneV41lift37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV41lift37)
+identifier wgEncodeGencodeGeneSourceV41lift37
+"Link together Gencode Gene Source table with Attributes table"
+    hg19.wgEncodeGencodeGeneSourceV41lift37.geneId
+    hg19.wgEncodeGencodeAttrsV41lift37.geneId
+
+identifier wgEncodeGencodeGeneSymbolV41lift37
+"Link together Gencode gene symbol table with Attributes table"
+    hg19.wgEncodeGencodeGeneSymbolV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV41lift37
+"Link together Gencode Pdb table with Attributes table"
+    hg19.wgEncodeGencodePdbV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV41lift37
+"Link together Gencode Pubmed table with Attributes table"
+    hg19.wgEncodeGencodePubMedV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV41lift37
+"Link together Gencode RefSeq table with Attributes table"
+    hg19.wgEncodeGencodeRefSeqV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV41lift37
+"Link together Gencode RefSeq table with refGene track"
+    hg19.wgEncodeGencodeRefSeqV41lift37.rnaAcc dupeOk chopAfter=.
+    hg19.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV41lift37
+"Link together Gencode Tag table with Attributes table"
+    hg19.wgEncodeGencodeTagV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV41lift37
+"Link together Gencode Transcript Source table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSourceV41lift37.transcriptId
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV41lift37
+"Link together Gencode Transcript Support table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSupportV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId minCheck=0.04
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV41lift37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptionSupportLevelV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV41lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeUniProtV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV41lift37
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg19.wgEncodeGencodeAnnotationRemarkV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV41lift37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV41lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeEntrezGeneV41lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeEntrezGeneV41lift37.transcriptId minCheck=0.35
+
+# end Gencode V41lift37
+
 # 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