be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 08f1133..f90361b 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -2896,31 +2896,125 @@
     hg38.wgEncodeGencodeAnnotationRemarkV35.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV35.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV35
 "Link together Gencode UniProt Support table with Attributes table"
     hg38.wgEncodeGencodeEntrezGeneV35.transcriptId dupeOk
     hg38.wgEncodeGencodeEntrezGeneV35.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportV35
 "Link together Gencode Exon Support table with Attributes table"
     hg38.wgEncodeGencodeExonSupportV35.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV35.transcriptId minCheck=0.90
 
 # end Gencode V35
 
+# begin Gencode V36
 
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV36
+# wgEncodeGencode2wayConsPseudoV36
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV36
+identifier wgEncodeGencodeBasicAttrsV36
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV36.transcriptId
+    hg38.wgEncodeGencodeBasicV36.name
+
+identifier wgEncodeGencodeCompAttrsV36
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV36.transcriptId
+    hg38.wgEncodeGencodeCompV36.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV36
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV36.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV36.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV36)
+identifier wgEncodeGencodeGeneSourceV36
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV36.geneId
+    hg38.wgEncodeGencodeAttrsV36.geneId
+
+identifier wgEncodeGencodeGeneSymbolV36
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV36
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV36
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV36
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV36
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV36.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV36
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.36
+    hg38.wgEncodeGencodeRefSeqV36.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceV36
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV36.transcriptId
+    hg38.wgEncodeGencodeAttrsV36.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV36
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.08
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV36
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV36
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV36
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV36
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV36.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportV36
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV36.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV36.transcriptId minCheck=0.80
+
+# end Gencode V36
 
 # 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"
@@ -3890,30 +3984,121 @@
     hg19.wgEncodeGencodeUniProtV35lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeAnnotationRemarkV35lift37
 "Link together Gencode Annotation Remark table with Attributes table"
     hg19.wgEncodeGencodeAnnotationRemarkV35lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV35lift37
 "Link together Gencode UniProt Support table with Attributes table"
     hg19.wgEncodeGencodeEntrezGeneV35lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeEntrezGeneV35lift37.transcriptId minCheck=0.35
 
 # end Gencode V35lift37
 
+# begin Gencode V36lift37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV36lift37
+# wgEncodeGencode2wayConsPseudoV36lift37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV36lift37
+identifier wgEncodeGencodeBasicAttrsV36lift37
+"Link together Gencode Basic Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId
+    hg19.wgEncodeGencodeBasicV36lift37.name
+
+identifier wgEncodeGencodeCompAttrsV36lift37
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId
+    hg19.wgEncodeGencodeCompV36lift37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV36lift37
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId
+    hg19.wgEncodeGencodePseudoGeneV36lift37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV36lift37)
+identifier wgEncodeGencodeGeneSourceV36lift37
+"Link together Gencode Gene Source table with Attributes table"
+    hg19.wgEncodeGencodeGeneSourceV36lift37.geneId
+    hg19.wgEncodeGencodeAttrsV36lift37.geneId
+
+identifier wgEncodeGencodeGeneSymbolV36lift37
+"Link together Gencode gene symbol table with Attributes table"
+    hg19.wgEncodeGencodeGeneSymbolV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV36lift37
+"Link together Gencode Pdb table with Attributes table"
+    hg19.wgEncodeGencodePdbV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV36lift37
+"Link together Gencode Pubmed table with Attributes table"
+    hg19.wgEncodeGencodePubMedV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV36lift37
+"Link together Gencode RefSeq table with Attributes table"
+    hg19.wgEncodeGencodeRefSeqV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV36lift37
+"Link together Gencode RefSeq table with refGene track"
+    hg19.wgEncodeGencodeRefSeqV36lift37.rnaAcc dupeOk chopAfter=.
+    hg19.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV36lift37
+"Link together Gencode Tag table with Attributes table"
+    hg19.wgEncodeGencodeTagV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId minCheck=0.36
+    hg19.wgEncodeGencodeRefSeqV36lift37.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceV36lift37
+"Link together Gencode Transcript Source table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSourceV36lift37.transcriptId
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV36lift37
+"Link together Gencode Transcript Support table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSupportV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId minCheck=0.08
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV36lift37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptionSupportLevelV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV36lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeUniProtV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV36lift37
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg19.wgEncodeGencodeAnnotationRemarkV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV36lift37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV36lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeEntrezGeneV36lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeEntrezGeneV36lift37.transcriptId minCheck=0.35
+
+# end Gencode V36lift37
+
 
 
 # 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