1436ad57e2be4d9763b695eef131b28ba648df46
markd
  Thu Jun 25 11:44:18 2020 -0700
added all.joiner schema for new gencode structure

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index e955e52..2665775 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -1399,35 +1399,30 @@
 identifier wgEncodeGencodePdbV19
 "Link together Gencode Pdb table with Attributes table"
     hg19,hg38.wgEncodeGencodePdbV19.transcriptId dupeOk
     hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.02
 
 identifier wgEncodeGencodePubMedV19
 "Link together Gencode Pubmed table with Attributes table"
     hg19,hg38.wgEncodeGencodePubMedV19.transcriptId dupeOk
     hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId  minCheck=0.635488
 
 identifier wgEncodeGencodeRefSeqV19
 "Link together Gencode RefSeq table with Attributes table"
     hg19,hg38.wgEncodeGencodeRefSeqV19.transcriptId dupeOk
     hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.05
 
-identifier wgEncodeGencodeRefSeqToRefGeneV19
-"Link together Gencode RefSeq table with refGene track"
-    hg19.wgEncodeGencodeRefSeqV19.rnaAcc dupeOk chopAfter=.
-    hg19.refGene.name minCheck=0.59
-
 identifier wgEncodeGencodeTagV19
 "Link together Gencode Tag table with Attributes table"
     hg19,hg38.wgEncodeGencodeTagV19.transcriptId dupeOk
     hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.373378
     hg19.wgEncodeGencodeRefSeqV19.transcriptId minCheck=0.9
 
 identifier wgEncodeGencodeTranscriptSourceV19
 "Link together Gencode Transcript Source table with Attributes table"
     hg19,hg38.wgEncodeGencodeTranscriptSourceV19.transcriptId
     hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId
 
 identifier wgEncodeGencodeTranscriptSupportV19
 "Link together Gencode Transcript Support table with Attributes table"
     hg19,hg38.wgEncodeGencodeTranscriptSupportV19.transcriptId dupeOk
     hg19,hg38.wgEncodeGencodeAttrsV19.transcriptId minCheck=0.25
@@ -5405,30 +5400,106 @@
     mm10.wgEncodeGencodeAnnotationRemarkVM25.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM25
 "Link together Gencode UniProt Support table with Attributes table"
     mm10.wgEncodeGencodeEntrezGeneVM25.transcriptId dupeOk
     mm10.wgEncodeGencodeEntrezGeneVM25.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM25
 "Link together Gencode Exon Support table with Attributes table"
     mm10.wgEncodeGencodeExonSupportVM25.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.90
 
 # end Gencode VM25
 
+# begin Gencode V35 (2020 reorganization)
+
+identifier gencodeAnnotAttrsV35
+"Link together Gencode Annotation Table with Attributes table"
+    hg38.gencodeAttrsV35.transcriptId
+    hg38.gencodeAnnotV35.name
+
+# gencode association tables (joined through gencodeAttrsV35)
+identifier gencodeGeneSourceV35
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.gencodeGeneSourceV35.geneId
+    hg38.gencodeAttrsV35.geneId
+
+identifier gencodeGeneSymbolV35
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.gencodeGeneSymbolV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.20
+
+identifier gencodePdbV35
+"Link together Gencode Pdb table with Attributes table"
+    hg38.gencodePdbV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.015
+
+identifier gencodePubMedV35
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.gencodePubMedV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId  minCheck=0.63
+
+identifier gencodeRefSeqV35
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.gencodeRefSeqV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.05
+
+identifier gencodeTagV35
+"Link together Gencode Tag table with Attributes table"
+    hg38.gencodeTagV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.36
+    hg38.gencodeRefSeqV35.transcriptId minCheck=0.9
+
+identifier gencodeTranscriptSourceV35
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.gencodeTranscriptSourceV35.transcriptId
+    hg38.gencodeAttrsV35.transcriptId
+
+identifier gencodeTranscriptSupportV35
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.gencodeTranscriptSupportV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.20
+
+identifier gencodeTranscriptionSupportLevelV35
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.gencodeTranscriptionSupportLevelV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.30
+
+identifier gencodeUniProtV35
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.gencodeUniProtV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.35
+
+identifier gencodeAnnotationRemarkV35
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.gencodeAnnotationRemarkV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.10
+
+identifier gencodeEntrezGeneV35
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.gencodeEntrezGeneV35.transcriptId dupeOk
+    hg38.gencodeEntrezGeneV35.transcriptId minCheck=0.35
+
+identifier gencodeExonSupportV35
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.gencodeExonSupportV35.transcriptId dupeOk
+    hg38.gencodeAttrsV35.transcriptId minCheck=0.80
+
+# end Gencode V35 (2020 reorganization)
+
 
 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