f86cc1e3f913432f81ad47733aae8e78ab9500c6
markd
  Mon May 27 12:06:58 2019 -0700
output total number of aligned bases in pslStats -overallStats

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index 04a93e0..159f4bc 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -24,69 +24,57 @@
 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.
 ##
 #db = hg38
-#db = hg19
-db = mm10
-#db = grcHhh38
+db = hg19
+#db = mm10
 #preRelease = no
 preRelease = yes
 ifeq (${db},mm10)
     grcRefAssembly = GRCm38
     ver = M22
     prevVer = M21
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
     ensemblVer = 97_38
     ensemblPrevVer = 96_38
     ensemblCDnaDb = mus_musculus_cdna_${ensemblPrevVer}
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
     ver = 31
     prevVer = 30
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
     ensemblVer = 97_38
     ensemblPrevVer = 96_38
     ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
-else ifeq (${db},grcHhh38)
-    # hg38 with patches
-    grcRefAssembly = GRCh38
-    ver = 28
-    prevVer = 27
-    gencodeOrg = Gencode_human
-    ftpReleaseSubdir = release_${ver}
-    annGffTypeName = chr_patch_hapl_scaff.annotation
-    ensemblVer = 94_38
-    ensemblPrevVer = 93_38
-    ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
 else ifeq (${db},hg19)
     grcRefAssembly = GRCh37
-    verBase = 30
+    verBase = 31
     ver = ${verBase}lift37
     ftpReleaseSubdir = release_${verBase}/GRCh37_mapping
     prevVer = 29lift37
     gencodeOrg = Gencode_human
     annGffTypeName = annotation
     ensemblVer = 74_37      # only used to get genome chromsome name mappings
     ensemblPrevVer = ${ensemblVer}  # doesn't change
     ensemblCDnaDb = homo_sapiens_cdna_${ensemblPrevVer}
     isBackmap = yes
 else
     $(error unimplement genome database: ${db})
 endif
 # END EDIT THESE EACH RELEASE