b4cb35b2a3919b84f30a88b41e4a78277528c710
markd
  Thu Mar 11 15:24:33 2021 -0800
import of GENCODE V37

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index 5854798..64785c6 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -23,65 +23,67 @@
 SHELL = bash -e
 export SHELLOPTS=pipefail
 
 ##
 # programs, etc
 ##
 mach = $(shell uname -m)
 
 ##
 # Release info and files from Sanger.
 # BEGIN EDIT THESE EACH RELEASE
 #
 # - ensemblPrevVersion is use to get chrom name mappings for pre-release,
 #   as this doesn't change between release.
 ##
-#preRelease = no
-preRelease = yes
-#db = hg38
+preRelease = no
+#preRelease = yes
+db = hg38
 #db = hg19
 #db = mm10
-db = mm39
+#db = mm39
 ifeq (${db},mm10)
     grcRefAssembly = GRCm38
-    ver = M25
+    verBase = M25
     prevVer = M24
+    ver = ${verBase}lift37
     gencodeOrg = Gencode_mouse
-    ftpReleaseSubdir = release_${ver}
+    ftpReleaseSubdir = release_${verBase}/GRCm38_mapping
     annGffTypeName = chr_patch_hapl_scaff.annotation
-    ensemblVer = 100_38
-    ensemblPrevVer = 99_38
+    ensemblVer = 101_37      # only used to get genome chromsome name mappings, don't change
+    ensemblPrevVer = ${ensemblVer}  # doesn't change
     ensemblCDnaDb = mus_musculus_cdna_${ensemblPrevVer}
+    isBackmap = yes
 else ifeq (${db},mm39)
     grcRefAssembly = GRCm39
     ver = M26
     prevVer = 
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
     ensemblVer = 102_38
     ensemblPrevVer =
     ensemblCDnaDb = mus_musculus_cdna_${ensemblPrevVer}
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
-    ver = 36
-    prevVer = 35
+    ver = 37
+    prevVer = 36
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
-    ensemblVer = 102_38
-    ensemblPrevVer = 101_38
+    ensemblVer = 103_38
+    ensemblPrevVer = 102_38
     ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
 else ifeq (${db},hg19)
     grcRefAssembly = GRCh37
     verBase = 36
     ver = ${verBase}lift37
     backmapTargetVer = 19
     ftpReleaseSubdir = release_${verBase}/GRCh37_mapping
     prevVer = 35lift37
     gencodeOrg = Gencode_human
     annGffTypeName = annotation
     ensemblVer = 74_37      # only used to get genome chromsome name mappings, don't change
     ensemblPrevVer = ${ensemblVer}  # doesn't change
     ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
     isBackmap = yes
 else