06d7be056190c14b85e71bc12523f18ea6815b5e
markd
Mon Dec 7 00:50:29 2020 -0800
BLAT mmap index support merge with master
diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index c8fd089..08f1133 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -3825,31 +3825,31 @@
identifier wgEncodeGencodeCompAttrsV35lift37
"Link together Gencode Comprehensive Table with Attributes table"
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId
hg19.wgEncodeGencodeCompV35lift37.name
identifier wgEncodeGencodePseudoGeneAttrsV35lift37
"Link together Gencode PseudoGene Table with Attributes table"
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId
hg19.wgEncodeGencodePseudoGeneV35lift37.name
# gencode association tables (joined through wgEncodeGencodeAttrsV35lift37)
identifier wgEncodeGencodeGeneSourceV35lift37
"Link together Gencode Gene Source table with Attributes table"
hg19.wgEncodeGencodeGeneSourceV35lift37.geneId
- hg19.wgEncodeGencodeAttrsV35lift37.geneId
+ hg19.wgEncodeGencodeAttrsV35lift37.geneId minCheck=0.99
identifier wgEncodeGencodeGeneSymbolV35lift37
"Link together Gencode gene symbol table with Attributes table"
hg19.wgEncodeGencodeGeneSymbolV35lift37.transcriptId dupeOk
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.20
identifier wgEncodeGencodePdbV35lift37
"Link together Gencode Pdb table with Attributes table"
hg19.wgEncodeGencodePdbV35lift37.transcriptId dupeOk
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.015
identifier wgEncodeGencodePubMedV35lift37
"Link together Gencode Pubmed table with Attributes table"
hg19.wgEncodeGencodePubMedV35lift37.transcriptId dupeOk
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.63
@@ -3861,31 +3861,31 @@
identifier wgEncodeGencodeRefSeqToRefGeneV35lift37
"Link together Gencode RefSeq table with refGene track"
hg19.wgEncodeGencodeRefSeqV35lift37.rnaAcc dupeOk chopAfter=.
hg19.refGene.name minCheck=0.77
identifier wgEncodeGencodeTagV35lift37
"Link together Gencode Tag table with Attributes table"
hg19.wgEncodeGencodeTagV35lift37.transcriptId dupeOk
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.36
hg19.wgEncodeGencodeRefSeqV35lift37.transcriptId minCheck=0.9
identifier wgEncodeGencodeTranscriptSourceV35lift37
"Link together Gencode Transcript Source table with Attributes table"
hg19.wgEncodeGencodeTranscriptSourceV35lift37.transcriptId
- hg19.wgEncodeGencodeAttrsV35lift37.transcriptId
+ hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.99
identifier wgEncodeGencodeTranscriptSupportV35lift37
"Link together Gencode Transcript Support table with Attributes table"
hg19.wgEncodeGencodeTranscriptSupportV35lift37.transcriptId dupeOk
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.20
identifier wgEncodeGencodeTranscriptionSupportLevelV35lift37
"Link together Gencode Transcription Support Level table with Attributes table"
hg19.wgEncodeGencodeTranscriptionSupportLevelV35lift37.transcriptId dupeOk
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.30
identifier wgEncodeGencodeUniProtV35lift37
"Link together Gencode UniProt Support table with Attributes table"
hg19.wgEncodeGencodeUniProtV35lift37.transcriptId dupeOk
hg19.wgEncodeGencodeAttrsV35lift37.transcriptId minCheck=0.35
@@ -5401,53 +5401,132 @@
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
+# begin Gencode V35 (2020 reorganization quick change)
identifier gencodeAnnotV35
"Link together Gencode Annotation Table with Attributes table"
$gbd.gencodeAttrsV35.transcriptId
$gbd.gencodeGeneSymbolV35.transcriptId
$gbd.gencodePdbV35.transcriptId
$gbd.gencodePubMedV35.transcriptId
$gbd.gencodeRefSeqV35.transcriptId
$gbd.gencodeTagV35.transcriptId
$gbd.gencodeRefSeqV35.transcriptId minCheck=0.9
$gbd.gencodeTranscriptSourceV35.transcriptId minCheck=0.9
$gbd.gencodeTranscriptSupportV35.transcriptId
$gbd.gencodeTranscriptionSupportLevelV35.transcriptId
$gbd.gencodeUniProtV35.transcriptId
$gbd.gencodeAnnotationRemarkV35.transcriptId minCheck=0.9
$gbd.gencodeEntrezGeneV35.transcriptId
$gbd.gencodeExonSupportV35.transcriptId
$gbd.gencodeAnnotV35.name
identifier gencodeAnnotV35Gene
"Link together Gencode Annotation Table with Attributes table"
$gbd.gencodeGeneSourceV35.geneId
$gbd.gencodeAttrsV35.geneId
+# end Gencode V35 (2020 reorganization quick change)
+
+# begin Gencode V36 (2020 reorganization)
+
+identifier gencodeAnnotAttrsV36
+"Link together Gencode Annotation Table with Attributes table"
+ hg38.gencodeAttrsV36.transcriptId
+ hg38.gencodeAnnotV36.name
+
+# gencode association tables (joined through gencodeAttrsV36)
+identifier gencodeGeneSourceV36
+"Link together Gencode Gene Source table with Attributes table"
+ hg38.gencodeGeneSourceV36.geneId
+ hg38.gencodeAttrsV36.geneId
+
+identifier gencodeToGeneSymbolV36
+"Link together Gencode gene symbol table with Attributes table"
+ hg38.gencodeToGeneSymbolV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.20
+
+identifier gencodeToPdbV36
+"Link together Gencode Pdb table with Attributes table"
+ hg38.gencodeToPdbV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.015
+
+identifier gencodeToPubMedV36
+"Link together Gencode Pubmed table with Attributes table"
+ hg38.gencodeToPubMedV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.63
+
+identifier gencodeToRefSeqV36
+"Link together Gencode RefSeq table with Attributes table"
+ hg38.gencodeToRefSeqV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.05
+
+identifier gencodeTagV36
+"Link together Gencode Tag table with Attributes table"
+ hg38.gencodeTagV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.36
+ hg38.gencodeToRefSeqV36.transcriptId minCheck=0.9
+
+identifier gencodeTranscriptSourceV36
+"Link together Gencode Transcript Source table with Attributes table"
+ hg38.gencodeTranscriptSourceV36.transcriptId
+ hg38.gencodeAttrsV36.transcriptId
+
+identifier gencodeTranscriptSupportV36
+"Link together Gencode Transcript Support table with Attributes table"
+ hg38.gencodeTranscriptSupportV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.10
+
+identifier gencodeTranscriptionSupportLevelV36
+"Link together Gencode Transcription Support Level table with Attributes table"
+ hg38.gencodeTranscriptionSupportLevelV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.30
+
+identifier gencodeToUniProtV36
+"Link together Gencode UniProt Support table with Attributes table"
+ hg38.gencodeToUniProtV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.35
+
+identifier gencodeAnnotationRemarkV36
+"Link together Gencode Annotation Remark table with Attributes table"
+ hg38.gencodeAnnotationRemarkV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.10
+
+identifier gencodeToEntrezGeneV36
+"Link together Gencode Entrez table with Attributes table"
+ hg38.gencodeToEntrezGeneV36.transcriptId dupeOk
+ hg38.gencodeToEntrezGeneV36.transcriptId minCheck=0.35
+
+identifier gencodeExonSupportV36
+"Link together Gencode Exon Support table with Attributes table"
+ hg38.gencodeExonSupportV36.transcriptId dupeOk
+ hg38.gencodeAttrsV36.transcriptId minCheck=0.70
+
+# end Gencode V36 (2020 reorganization)
+
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