db0877a0f789518c170e95923feee7ad95e15b55
markd
  Sun Mar 22 09:14:47 2020 -0700
import of GENCODE V34 and VM25 prereleases

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 6a4d77f..6c3ebe2 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -2707,30 +2707,127 @@
     hg38.wgEncodeGencodeAnnotationRemarkV33.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV33
 "Link together Gencode UniProt Support table with Attributes table"
     hg38.wgEncodeGencodeEntrezGeneV33.transcriptId dupeOk
     hg38.wgEncodeGencodeEntrezGeneV33.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportV33
 "Link together Gencode Exon Support table with Attributes table"
     hg38.wgEncodeGencodeExonSupportV33.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV33.transcriptId minCheck=0.90
 
 # end Gencode V33
 
+# begin Gencode V34
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV34
+# wgEncodeGencode2wayConsPseudoV34
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV34
+identifier wgEncodeGencodeBasicAttrsV34
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV34.transcriptId
+    hg38.wgEncodeGencodeBasicV34.name
+
+identifier wgEncodeGencodeCompAttrsV34
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV34.transcriptId
+    hg38.wgEncodeGencodeCompV34.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV34
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV34.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV34.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV34)
+identifier wgEncodeGencodeGeneSourceV34
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV34.geneId
+    hg38.wgEncodeGencodeAttrsV34.geneId
+
+identifier wgEncodeGencodeGeneSymbolV34
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV34
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV34
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV34
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV34
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV34.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV34
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.36
+    hg38.wgEncodeGencodeRefSeqV34.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceV34
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV34.transcriptId
+    hg38.wgEncodeGencodeAttrsV34.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV34
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV34
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV34
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV34
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV34
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV34.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportV34
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV34.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV34.transcriptId minCheck=0.90
+
+# end Gencode V34
+
+
 
 # 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"
@@ -4932,30 +5029,127 @@
     mm10.wgEncodeGencodeAnnotationRemarkVM24.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM24.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM24
 "Link together Gencode UniProt Support table with Attributes table"
     mm10.wgEncodeGencodeEntrezGeneVM24.transcriptId dupeOk
     mm10.wgEncodeGencodeEntrezGeneVM24.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM24
 "Link together Gencode Exon Support table with Attributes table"
     mm10.wgEncodeGencodeExonSupportVM24.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM24.transcriptId minCheck=0.90
 
 # end Gencode VM24
 
+# begin Gencode VM25
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM25
+# wgEncodeGencode2wayConsPseudoVM25
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM25
+identifier wgEncodeGencodeBasicAttrsVM25
+"Link together Gencode Basic Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId
+    mm10.wgEncodeGencodeBasicVM25.name
+
+identifier wgEncodeGencodeCompAttrsVM25
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId
+    mm10.wgEncodeGencodeCompVM25.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM25
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId
+    mm10.wgEncodeGencodePseudoGeneVM25.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM25)
+identifier wgEncodeGencodeGeneSourceVM25
+"Link together Gencode Gene Source table with Attributes table"
+    mm10.wgEncodeGencodeGeneSourceVM25.geneId
+    mm10.wgEncodeGencodeAttrsVM25.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM25
+"Link together Gencode gene symbol table with Attributes table"
+    mm10.wgEncodeGencodeGeneSymbolVM25.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM25
+"Link together Gencode Pdb table with Attributes table"
+    mm10.wgEncodeGencodePdbVM25.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM25
+"Link together Gencode Pubmed table with Attributes table"
+    mm10.wgEncodeGencodePubMedVM25.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM25
+"Link together Gencode RefSeq table with Attributes table"
+    mm10.wgEncodeGencodeRefSeqVM25.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM25
+"Link together Gencode RefSeq table with refGene track"
+    mm10.wgEncodeGencodeRefSeqVM25.rnaAcc dupeOk chopAfter=.
+    mm10.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM25
+"Link together Gencode Tag table with Attributes table"
+    mm10.wgEncodeGencodeTagVM25.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.36
+    mm10.wgEncodeGencodeRefSeqVM25.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceVM25
+"Link together Gencode Transcript Source table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptSourceVM25.transcriptId
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM25
+"Link together Gencode Transcript Support table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptSupportVM25.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM25
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptionSupportLevelVM25.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM25
+"Link together Gencode UniProt Support table with Attributes table"
+    mm10.wgEncodeGencodeUniProtVM25.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM25.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM25
+"Link together Gencode Annotation Remark table with Attributes table"
+    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
+
+
 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