b6aee4c6471cddebd638fec8dbb988c29a69bc22
markd
  Thu Apr 23 21:58:41 2026 -0700
import of GENCODE V50, MV39, and V50lift37; added a command to do import with a single command

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index fd9bc7d642c..e6a60c300e7 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -789,54 +789,50 @@
 identifier wgEncodeGencodeClassesRel2
 "Link together Gencode gene model (Known) and class for Jan 2009 Data Version"
     hg18.wgEncodeGencodeClassesRel2.name
     hg18.wgEncodeGencodeAutoRel2.name unique
     hg18.wgEncodeGencodeManualRel2.name unique
     hg18.wgEncodeGencodePolyaRel2.name unique
 
 identifier wgEncodeGencodeClassesV3
 "Link together Gencode gene model (Known) and class for July 2009 Data Version"
     hg18.wgEncodeGencodeClassesV3.name
     hg18.wgEncodeGencodeAutoV3.name unique
     hg18.wgEncodeGencodeManualV3.name unique
     hg18.wgEncodeGencodePolyaV3.name unique
 
 ##
-# GENCODE macro-driven definitions (recent releases)
-# To add a new release: append the version token to the set lines below.
-# Older releases (pre-V44, pre-VM35) remain literal above because their
-# minCheck values were tuned per-release and would need individual stanzas.
-# The macro uses the loosest (V49/VM38) minCheck values, which is safe
-# because earlier releases in the set already passed tighter thresholds.
+# GENCODE macro-driven definitions
+# To add new release: append version token to set lines below.
+# Tune minCheck values to fit all releases in set.
 ##
 
-set gencodeHg38Vers V20,V21,V22,V23,V24,V25,V26,V27,V28,V29,V30,V31,V32,V33,V34,V35,V36,V37,V38,V39,V40,V41,V42,V43,V44,V45,V46,V47,V48,V49
-set gencodeHg38GeneSymbolVers V29,V30,V31,V32,V33,V34,V35,V36,V37,V38,V39,V40,V41,V42,V43,V44,V45,V46,V47,V48,V49
-set gencodeHg38EntrezGeneVers V22,V23,V24,V25,V26,V27,V28,V29,V30,V31,V32,V33,V34,V35,V36,V37,V38,V39,V40,V41,V42,V43,V44,V45,V46,V47,V48,V49
+set gencodeHg38Vers V20,V21,V22,V23,V24,V25,V26,V27,V28,V29,V30,V31,V32,V33,V34,V35,V36,V37,V38,V39,V40,V41,V42,V43,V44,V45,V46,V47,V48,V49,V50
+set gencodeHg38GeneSymbolVers V29,V30,V31,V32,V33,V34,V35,V36,V37,V38,V39,V40,V41,V42,V43,V44,V45,V46,V47,V48,V49,V50
+set gencodeHg38EntrezGeneVers V22,V23,V24,V25,V26,V27,V28,V29,V30,V31,V32,V33,V34,V35,V36,V37,V38,V39,V40,V41,V42,V43,V44,V45,V46,V47,V48,V49,V50
+set gencodeHg38RefSeqToRefGeneLowVers V23,V24,V25,V26,V27,V28,V29
+set gencodeHg38RefSeqToRefGeneVers V30,V31,V32,V33,V34,V35,V36,V37,V38,V39,V40,V41,V42,V43,V44,V45,V46,V47,V48,V49,V50
 
-set gencodeHg19LiftVers V24lift37,V26lift37,V27lift37,V28lift37,V29lift37,V30lift37,V31lift37,V32lift37,V33lift37,V34lift37,V35lift37,V36lift37,V37lift37,V38lift37,V39lift37,V40lift37,V41lift37,V42lift37,V43lift37,V44lift37,V45lift37,V46lift37,V47lift37,V48lift37,V49lift37
-set gencodeHg19LiftGeneSymbolVers V29lift37,V30lift37,V31lift37,V32lift37,V33lift37,V34lift37,V35lift37,V36lift37,V37lift37,V38lift37,V39lift37,V40lift37,V41lift37,V42lift37,V43lift37,V44lift37,V45lift37,V46lift37,V47lift37,V48lift37,V49lift37
-set gencodeHg19LiftEntrezGeneVers V24lift37,V28lift37,V29lift37,V30lift37,V31lift37,V32lift37,V33lift37,V34lift37,V35lift37,V36lift37,V37lift37,V38lift37,V39lift37,V40lift37,V41lift37,V42lift37,V43lift37,V44lift37,V45lift37,V46lift37,V47lift37,V48lift37,V49lift37
+set gencodeHg19LiftVers V24lift37,V26lift37,V27lift37,V28lift37,V29lift37,V30lift37,V31lift37,V32lift37,V33lift37,V34lift37,V35lift37,V36lift37,V37lift37,V38lift37,V39lift37,V40lift37,V41lift37,V42lift37,V43lift37,V44lift37,V45lift37,V46lift37,V47lift37,V48lift37,V49lift37,V50lift37
+set gencodeHg19LiftGeneSymbolVers V29lift37,V30lift37,V31lift37,V32lift37,V33lift37,V34lift37,V35lift37,V36lift37,V37lift37,V38lift37,V39lift37,V40lift37,V41lift37,V42lift37,V43lift37,V44lift37,V45lift37,V46lift37,V47lift37,V48lift37,V49lift37,V50lift37
+set gencodeHg19LiftEntrezGeneVers V24lift37,V28lift37,V29lift37,V30lift37,V31lift37,V32lift37,V33lift37,V34lift37,V35lift37,V36lift37,V37lift37,V38lift37,V39lift37,V40lift37,V41lift37,V42lift37,V43lift37,V44lift37,V45lift37,V46lift37,V47lift37,V48lift37,V49lift37,V50lift37
 set gencodeHg19LiftEntrezGeneLowVers V26lift37,V27lift37
-
-set gencodeMm39Vers VM26,VM27,VM28,VM29,VM30,VM31,VM32,VM33,VM34,VM35,VM36,VM37,VM38
-
-set gencodeHg38RefSeqToRefGeneLowVers V23,V24,V25,V26,V27,V28,V29
-set gencodeHg38RefSeqToRefGeneVers V30,V31,V32,V33,V34,V35,V36,V37,V38,V39,V40,V41,V42,V43,V44,V45,V46,V47,V48,V49
 set gencodeHg19LiftRefSeqToRefGeneLowVers V24lift37,V26lift37,V27lift37,V28lift37,V29lift37
-set gencodeHg19LiftRefSeqToRefGeneVers V30lift37,V31lift37,V32lift37,V33lift37,V34lift37,V35lift37,V36lift37,V37lift37,V38lift37,V39lift37,V40lift37,V41lift37,V42lift37,V43lift37,V44lift37,V45lift37,V46lift37,V47lift37,V48lift37,V49lift37
-set gencodeMm39RefSeqToRefGeneVers VM26,VM27,VM28,VM29,VM30,VM31,VM32,VM33,VM34,VM35,VM36,VM37,VM38
+set gencodeHg19LiftRefSeqToRefGeneVers V30lift37,V31lift37,V32lift37,V33lift37,V34lift37,V35lift37,V36lift37,V37lift37,V38lift37,V39lift37,V40lift37,V41lift37,V42lift37,V43lift37,V44lift37,V45lift37,V46lift37,V47lift37,V48lift37,V49lift37,V50lift37
+
+set gencodeMm39Vers VM26,VM27,VM28,VM29,VM30,VM31,VM32,VM33,VM34,VM35,VM36,VM37,VM38,VM39
+set gencodeMm39RefSeqToRefGeneVers VM26,VM27,VM28,VM29,VM30,VM31,VM32,VM33,VM34,VM35,VM36,VM37,VM38,VM39
 
 ##
 # hg38
 ##
 
 identifier wgEncodeGencodeBasicAttrs[${gencodeHg38Vers}]
 "Link together Gencode Basic Table with Attributes table"
     hg38.wgEncodeGencodeAttrs[].transcriptId
     hg38.wgEncodeGencodeBasic[].name
 
 identifier wgEncodeGencodeCompAttrs[${gencodeHg38Vers}]
 "Link together Gencode Comprehensive Table with Attributes table"
     hg38.wgEncodeGencodeAttrs[].transcriptId
     hg38.wgEncodeGencodeComp[].name