1fd6ea4cb6bef2161c5fa1d951a8594d70eadcc9
markd
  Tue Apr 9 15:10:40 2019 -0700
import of GENCODE V30, V30lift37 and VM21

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index accd4e2..6803090 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -2332,30 +2332,126 @@
     hg38.wgEncodeGencodeAnnotationRemarkV29.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV29
 "Link together Gencode UniProt Support table with Attributes table"
     hg38.wgEncodeGencodeEntrezGeneV29.transcriptId dupeOk
     hg38.wgEncodeGencodeEntrezGeneV29.transcriptId minCheck=0.358209
 
 identifier wgEncodeGencodeExonSupportV29
 "Link together Gencode Exon Support table with Attributes table"
     hg38.wgEncodeGencodeExonSupportV29.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV29.transcriptId minCheck=0.95
 
 # end Gencode V29
 
+# begin Gencode V30
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV30
+# wgEncodeGencode2wayConsPseudoV30
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV30
+identifier wgEncodeGencodeBasicAttrsV30
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV30.transcriptId
+    hg38.wgEncodeGencodeBasicV30.name
+
+identifier wgEncodeGencodeCompAttrsV30
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV30.transcriptId
+    hg38.wgEncodeGencodeCompV30.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV30
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV30.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV30.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV30)
+identifier wgEncodeGencodeGeneSourceV30
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV30.geneId
+    hg38.wgEncodeGencodeAttrsV30.geneId
+
+identifier wgEncodeGencodeGeneSymbolV30
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV30
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV30
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV30
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV30
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV30.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV30
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.373378
+    hg38.wgEncodeGencodeRefSeqV30.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceV30
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV30.transcriptId
+    hg38.wgEncodeGencodeAttrsV30.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV30
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV30
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV30
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.358209
+
+identifier wgEncodeGencodeAnnotationRemarkV30
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV30
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV30.transcriptId minCheck=0.358209
+
+identifier wgEncodeGencodeExonSupportV30
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV30.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV30.transcriptId minCheck=0.95
+
+# end Gencode V30
+
 # 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
@@ -2777,30 +2873,122 @@
     hg19.wgEncodeGencodeUniProtV29lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.358209
 
 identifier wgEncodeGencodeAnnotationRemarkV29lift37
 "Link together Gencode Annotation Remark table with Attributes table"
     hg19.wgEncodeGencodeAnnotationRemarkV29lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV29lift37.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV29lift37
 "Link together Gencode UniProt Support table with Attributes table"
     hg19.wgEncodeGencodeEntrezGeneV29lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeEntrezGeneV29lift37.transcriptId minCheck=0.358209
 
 # end Gencode V29lift37
 
+# begin Gencode V30lift37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV30lift37
+# wgEncodeGencode2wayConsPseudoV30lift37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV30lift37
+identifier wgEncodeGencodeBasicAttrsV30lift37
+"Link together Gencode Basic Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId
+    hg19.wgEncodeGencodeBasicV30lift37.name
+
+identifier wgEncodeGencodeCompAttrsV30lift37
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId
+    hg19.wgEncodeGencodeCompV30lift37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV30lift37
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId
+    hg19.wgEncodeGencodePseudoGeneV30lift37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV30lift37)
+identifier wgEncodeGencodeGeneSourceV30lift37
+"Link together Gencode Gene Source table with Attributes table"
+    hg19.wgEncodeGencodeGeneSourceV30lift37.geneId
+    hg19.wgEncodeGencodeAttrsV30lift37.geneId
+
+identifier wgEncodeGencodeGeneSymbolV30lift37
+"Link together Gencode gene symbol table with Attributes table"
+    hg19.wgEncodeGencodeGeneSymbolV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV30lift37
+"Link together Gencode Pdb table with Attributes table"
+    hg19.wgEncodeGencodePdbV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV30lift37
+"Link together Gencode Pubmed table with Attributes table"
+    hg19.wgEncodeGencodePubMedV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV30lift37
+"Link together Gencode RefSeq table with Attributes table"
+    hg19.wgEncodeGencodeRefSeqV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV30lift37
+"Link together Gencode RefSeq table with refGene track"
+    hg19.wgEncodeGencodeRefSeqV30lift37.rnaAcc dupeOk chopAfter=.
+    hg19.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV30lift37
+"Link together Gencode Tag table with Attributes table"
+    hg19.wgEncodeGencodeTagV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.373378
+    hg19.wgEncodeGencodeRefSeqV30lift37.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceV30lift37
+"Link together Gencode Transcript Source table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSourceV30lift37.transcriptId
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV30lift37
+"Link together Gencode Transcript Support table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSupportV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV30lift37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptionSupportLevelV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV30lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeUniProtV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.358209
+
+identifier wgEncodeGencodeAnnotationRemarkV30lift37
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg19.wgEncodeGencodeAnnotationRemarkV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV30lift37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV30lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeEntrezGeneV30lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeEntrezGeneV30lift37.transcriptId minCheck=0.358209
+
+# end Gencode V30lift37
+
+
 
 # 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"
@@ -3807,30 +3995,126 @@
     mm10.wgEncodeGencodeAnnotationRemarkVM18.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM18
 "Link together Gencode UniProt Support table with Attributes table"
     mm10.wgEncodeGencodeEntrezGeneVM18.transcriptId dupeOk
     mm10.wgEncodeGencodeEntrezGeneVM18.transcriptId minCheck=0.358209
 
 identifier wgEncodeGencodeExonSupportVM18
 "Link together Gencode Exon Support table with Attributes table"
     mm10.wgEncodeGencodeExonSupportVM18.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM18.transcriptId minCheck=0.95
 
 # end Gencode VM18
 
+# begin Gencode VM21
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM21
+# wgEncodeGencode2wayConsPseudoVM21
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM21
+identifier wgEncodeGencodeBasicAttrsVM21
+"Link together Gencode Basic Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId
+    mm10.wgEncodeGencodeBasicVM21.name
+
+identifier wgEncodeGencodeCompAttrsVM21
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId
+    mm10.wgEncodeGencodeCompVM21.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM21
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId
+    mm10.wgEncodeGencodePseudoGeneVM21.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM21)
+identifier wgEncodeGencodeGeneSourceVM21
+"Link together Gencode Gene Source table with Attributes table"
+    mm10.wgEncodeGencodeGeneSourceVM21.geneId
+    mm10.wgEncodeGencodeAttrsVM21.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM21
+"Link together Gencode gene symbol table with Attributes table"
+    mm10.wgEncodeGencodeGeneSymbolVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM21
+"Link together Gencode Pdb table with Attributes table"
+    mm10.wgEncodeGencodePdbVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM21
+"Link together Gencode Pubmed table with Attributes table"
+    mm10.wgEncodeGencodePubMedVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM21
+"Link together Gencode RefSeq table with Attributes table"
+    mm10.wgEncodeGencodeRefSeqVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM21
+"Link together Gencode RefSeq table with refGene track"
+    mm10.wgEncodeGencodeRefSeqVM21.rnaAcc dupeOk chopAfter=.
+    mm10.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM21
+"Link together Gencode Tag table with Attributes table"
+    mm10.wgEncodeGencodeTagVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.373378
+    mm10.wgEncodeGencodeRefSeqVM21.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceVM21
+"Link together Gencode Transcript Source table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptSourceVM21.transcriptId
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM21
+"Link together Gencode Transcript Support table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptSupportVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM21
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptionSupportLevelVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM21
+"Link together Gencode UniProt Support table with Attributes table"
+    mm10.wgEncodeGencodeUniProtVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.358209
+
+identifier wgEncodeGencodeAnnotationRemarkVM21
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm10.wgEncodeGencodeAnnotationRemarkVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM21
+"Link together Gencode UniProt Support table with Attributes table"
+    mm10.wgEncodeGencodeEntrezGeneVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeEntrezGeneVM21.transcriptId minCheck=0.358209
+
+identifier wgEncodeGencodeExonSupportVM21
+"Link together Gencode Exon Support table with Attributes table"
+    mm10.wgEncodeGencodeExonSupportVM21.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM21.transcriptId minCheck=0.95
+
+# end Gencode VM21
+
 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
 
 identifier ECgeneName dependency