0f6f8c5cdfc1c5385c814102a4fa59afb08d2849
markd
  Wed Jul 31 23:45:27 2024 -0700
import of GENCODE v47, v47lift37, and vM36 pre-releases

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index 2c0133a..88f830a 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -20,78 +20,75 @@
 host=$(shell hostname)
 ppid=$(shell echo $$PPID)
 tmpExt = ${host}.${ppid}.tmp
 SHELL = bash -e
 export SHELLOPTS=pipefail
 
 ##
 # programs, etc
 ##
 mach = $(shell uname -m)
 
 ##
 # Release info and files from Sanger.
 # BEGIN EDIT THESE EACH RELEASE
 ##
-preRelease = no
-#preRelease = yes
+preRelease = yes
+#preRelease = no
 #db = hg38
-db = hg19
-#db = mm39
-ifeq (${db},mm10)
-    # mm10 lift back was never revewed and released
-    grcRefAssembly = GRCm38
-    verBase = M25
-    prevVer = M24
-    backmapTargetVer = M25
+#db = hg19
+db = mm39
+ifeq (${db},mm39)
+    ver = M36
+    prevVer = M35
+else ifeq (${db},hg38)
+    ver = 47
+    prevVer = 46
+else ifeq (${db},hg19)
+    verBase = 47
+    prevVerBase = 46
     ver = ${verBase}lift37
-    gencodeOrg = Gencode_mouse
-    ftpReleaseSubdir = release_${verBase}/GRCm38_mapping
-    annGffTypeName = chr_patch_hapl_scaff.annotation
-    isBackmap = yes
-else ifeq (${db},mm39)
+else
+    $(error unimplement genome database: ${db})
+endif
+# END EDIT THESE EACH RELEASE
+
+ifeq (${db},mm39)
     grcRefAssembly = GRCm39
-    ver = M35
-    prevVer = M34
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
-    ver = 46
-    prevVer = 44
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
 else ifeq (${db},hg19)
     grcRefAssembly = GRCh37
-    verBase = 46
-    prevVer = 45lift37
     ver = ${verBase}lift37
+    prevVer = ${prevVerBase}lift37
     backmapTargetVer = 19
     ftpReleaseSubdir = release_${verBase}/GRCh37_mapping
     gencodeOrg = Gencode_human
     annGffTypeName = annotation
     isBackmap = yes
     # caused by change in PAR gencode ids, backmap needs to be made smarted, until then,
     # just drop old transcipts that gets included
     dropIdsOpts = --drop=ENST00000302805.2
 else
     $(error unimplement genome database: ${db})
 endif
-# END EDIT THESE EACH RELEASE
-
 
 ifeq (${preRelease},yes)
     # pre-release
     baseUrl = rsync://ftp.ebi.ac.uk/pub/databases/havana/gencode_pre
 else
     # official release
     baseUrl = rsync://ftp.ebi.ac.uk/pub/databases/gencode
 endif
 
 rel = V${ver}
 releaseUrl = ${baseUrl}/${gencodeOrg}/${ftpReleaseSubdir}
 dataDir = data
 relDir = ${dataDir}/release_${ver}
 annotationGff = ${relDir}/gencode.v${ver}.${annGffTypeName}.gff3.gz
 polyAGff = ${relDir}/gencode.v${ver}.polyAs.gff3.gz