778cb733e935272196ce9dc65f51bdc38ebccebb
markd
  Tue Sep 3 10:51:42 2019 -0700
import of prerelease of GENCODE V32, VM23, and V32lift37

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 003c36e..04c1dab 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -2518,30 +2518,126 @@
     hg38.wgEncodeGencodeAnnotationRemarkV31.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV31
 "Link together Gencode UniProt Support table with Attributes table"
     hg38.wgEncodeGencodeEntrezGeneV31.transcriptId dupeOk
     hg38.wgEncodeGencodeEntrezGeneV31.transcriptId minCheck=0.358209
 
 identifier wgEncodeGencodeExonSupportV31
 "Link together Gencode Exon Support table with Attributes table"
     hg38.wgEncodeGencodeExonSupportV31.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV31.transcriptId minCheck=0.90
 
 # end Gencode V31
 
+# begin Gencode V32
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV32
+# wgEncodeGencode2wayConsPseudoV32
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV32
+identifier wgEncodeGencodeBasicAttrsV32
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV32.transcriptId
+    hg38.wgEncodeGencodeBasicV32.name
+
+identifier wgEncodeGencodeCompAttrsV32
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV32.transcriptId
+    hg38.wgEncodeGencodeCompV32.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV32
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV32.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV32.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV32)
+identifier wgEncodeGencodeGeneSourceV32
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV32.geneId
+    hg38.wgEncodeGencodeAttrsV32.geneId
+
+identifier wgEncodeGencodeGeneSymbolV32
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV32
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV32
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV32
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV32
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV32.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV32
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.36
+    hg38.wgEncodeGencodeRefSeqV32.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceV32
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV32.transcriptId
+    hg38.wgEncodeGencodeAttrsV32.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV32
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV32
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV32
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV32
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV32
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV32.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportV32
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV32.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV32.transcriptId minCheck=0.90
+
+# end Gencode V32
+
 # 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
@@ -3146,30 +3242,121 @@
     hg19.wgEncodeGencodeUniProtV31lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeAnnotationRemarkV31lift37
 "Link together Gencode Annotation Remark table with Attributes table"
     hg19.wgEncodeGencodeAnnotationRemarkV31lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeAttrsV31lift37.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV31lift37
 "Link together Gencode UniProt Support table with Attributes table"
     hg19.wgEncodeGencodeEntrezGeneV31lift37.transcriptId dupeOk
     hg19.wgEncodeGencodeEntrezGeneV31lift37.transcriptId minCheck=0.35
 
 # end Gencode V31lift37
 
+# begin Gencode V32lift37
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV32lift37
+# wgEncodeGencode2wayConsPseudoV32lift37
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV32lift37
+identifier wgEncodeGencodeBasicAttrsV32lift37
+"Link together Gencode Basic Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId
+    hg19.wgEncodeGencodeBasicV32lift37.name
+
+identifier wgEncodeGencodeCompAttrsV32lift37
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId
+    hg19.wgEncodeGencodeCompV32lift37.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV32lift37
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId
+    hg19.wgEncodeGencodePseudoGeneV32lift37.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV32lift37)
+identifier wgEncodeGencodeGeneSourceV32lift37
+"Link together Gencode Gene Source table with Attributes table"
+    hg19.wgEncodeGencodeGeneSourceV32lift37.geneId
+    hg19.wgEncodeGencodeAttrsV32lift37.geneId
+
+identifier wgEncodeGencodeGeneSymbolV32lift37
+"Link together Gencode gene symbol table with Attributes table"
+    hg19.wgEncodeGencodeGeneSymbolV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV32lift37
+"Link together Gencode Pdb table with Attributes table"
+    hg19.wgEncodeGencodePdbV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV32lift37
+"Link together Gencode Pubmed table with Attributes table"
+    hg19.wgEncodeGencodePubMedV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV32lift37
+"Link together Gencode RefSeq table with Attributes table"
+    hg19.wgEncodeGencodeRefSeqV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV32lift37
+"Link together Gencode RefSeq table with refGene track"
+    hg19.wgEncodeGencodeRefSeqV32lift37.rnaAcc dupeOk chopAfter=.
+    hg19.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV32lift37
+"Link together Gencode Tag table with Attributes table"
+    hg19.wgEncodeGencodeTagV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.36
+    hg19.wgEncodeGencodeRefSeqV32lift37.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceV32lift37
+"Link together Gencode Transcript Source table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSourceV32lift37.transcriptId
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV32lift37
+"Link together Gencode Transcript Support table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptSupportV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV32lift37
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg19.wgEncodeGencodeTranscriptionSupportLevelV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV32lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeUniProtV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV32lift37
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg19.wgEncodeGencodeAnnotationRemarkV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeAttrsV32lift37.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV32lift37
+"Link together Gencode UniProt Support table with Attributes table"
+    hg19.wgEncodeGencodeEntrezGeneV32lift37.transcriptId dupeOk
+    hg19.wgEncodeGencodeEntrezGeneV32lift37.transcriptId minCheck=0.35
+
+# end Gencode V32lift37
+
 
 # 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"
@@ -4368,30 +4555,126 @@
     mm10.wgEncodeGencodeAnnotationRemarkVM22.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM22
 "Link together Gencode UniProt Support table with Attributes table"
     mm10.wgEncodeGencodeEntrezGeneVM22.transcriptId dupeOk
     mm10.wgEncodeGencodeEntrezGeneVM22.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM22
 "Link together Gencode Exon Support table with Attributes table"
     mm10.wgEncodeGencodeExonSupportVM22.transcriptId dupeOk
     mm10.wgEncodeGencodeAttrsVM22.transcriptId minCheck=0.90
 
 # end Gencode VM22
 
+# begin Gencode VM23
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM23
+# wgEncodeGencode2wayConsPseudoVM23
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM23
+identifier wgEncodeGencodeBasicAttrsVM23
+"Link together Gencode Basic Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId
+    mm10.wgEncodeGencodeBasicVM23.name
+
+identifier wgEncodeGencodeCompAttrsVM23
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId
+    mm10.wgEncodeGencodeCompVM23.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM23
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId
+    mm10.wgEncodeGencodePseudoGeneVM23.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM23)
+identifier wgEncodeGencodeGeneSourceVM23
+"Link together Gencode Gene Source table with Attributes table"
+    mm10.wgEncodeGencodeGeneSourceVM23.geneId
+    mm10.wgEncodeGencodeAttrsVM23.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM23
+"Link together Gencode gene symbol table with Attributes table"
+    mm10.wgEncodeGencodeGeneSymbolVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM23
+"Link together Gencode Pdb table with Attributes table"
+    mm10.wgEncodeGencodePdbVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM23
+"Link together Gencode Pubmed table with Attributes table"
+    mm10.wgEncodeGencodePubMedVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM23
+"Link together Gencode RefSeq table with Attributes table"
+    mm10.wgEncodeGencodeRefSeqVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM23
+"Link together Gencode RefSeq table with refGene track"
+    mm10.wgEncodeGencodeRefSeqVM23.rnaAcc dupeOk chopAfter=.
+    mm10.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM23
+"Link together Gencode Tag table with Attributes table"
+    mm10.wgEncodeGencodeTagVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.36
+    mm10.wgEncodeGencodeRefSeqVM23.transcriptId minCheck=0.9
+
+identifier wgEncodeGencodeTranscriptSourceVM23
+"Link together Gencode Transcript Source table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptSourceVM23.transcriptId
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM23
+"Link together Gencode Transcript Support table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptSupportVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM23
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm10.wgEncodeGencodeTranscriptionSupportLevelVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM23
+"Link together Gencode UniProt Support table with Attributes table"
+    mm10.wgEncodeGencodeUniProtVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM23
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm10.wgEncodeGencodeAnnotationRemarkVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM23
+"Link together Gencode UniProt Support table with Attributes table"
+    mm10.wgEncodeGencodeEntrezGeneVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeEntrezGeneVM23.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM23
+"Link together Gencode Exon Support table with Attributes table"
+    mm10.wgEncodeGencodeExonSupportVM23.transcriptId dupeOk
+    mm10.wgEncodeGencodeAttrsVM23.transcriptId minCheck=0.90
+
+# end Gencode VM23
+
 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