05a3d177bf35df451f750276c274efc25b8acc70
markd
  Fri May 13 14:28:34 2022 -0700
import of gencode VM30 pre-release

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 91f7bce..d09cc00 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -6802,30 +6802,125 @@
     mm39.wgEncodeGencodeAnnotationRemarkVM29.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM29
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM29.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM29.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM29
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM29.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.80
 
 # end Gencode VM29
 
+# begin Gencode VM30
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM30
+# wgEncodeGencode2wayConsPseudoVM30
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM30
+identifier wgEncodeGencodeBasicAttrsVM30
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId
+    mm39.wgEncodeGencodeBasicVM30.name
+
+identifier wgEncodeGencodeCompAttrsVM30
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId
+    mm39.wgEncodeGencodeCompVM30.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM30
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM30.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM30)
+identifier wgEncodeGencodeGeneSourceVM30
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM30.geneId
+    mm39.wgEncodeGencodeAttrsVM30.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM30
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM30
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM30
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM30
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM30
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM30.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM30
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM30
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM30.transcriptId
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM30
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.04
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM30
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM30
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM30
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm39.wgEncodeGencodeAnnotationRemarkVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM30
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeEntrezGeneVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeEntrezGeneVM30.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM30
+"Link together Gencode Exon Support table with Attributes table"
+    mm39.wgEncodeGencodeExonSupportVM30.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.80
+
+# end Gencode VM30
+
 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