1fe89284953dd069f7155892bdcb8306adea13ef
markd
  Thu Nov 3 21:31:54 2022 -0700
import of v42lift37

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index 8d1456d..b0b77d8 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -23,89 +23,92 @@
 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
 #db = hg38
-#db = hg19
-db = mm39
+db = hg19
+#db = mm39
 #db = mm10
 ifeq (${db},mm10)
     grcRefAssembly = GRCm38
     verBase = M25
     prevVer = M24
     backmapTargetVer = M25
     ver = ${verBase}lift37
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${verBase}/GRCm38_mapping
     annGffTypeName = chr_patch_hapl_scaff.annotation
     isBackmap = yes
 else ifeq (${db},mm39)
     grcRefAssembly = GRCm39
     ver = M31
     prevVer = M30
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
     ver = 42
     prevVer = 41
     gencodeOrg = Gencode_human
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
 else ifeq (${db},hg19)
     grcRefAssembly = GRCh37
-    verBase = 41
+    verBase = 42
+    prevVer = 41lift37
     ver = ${verBase}lift37
-    prevVer = 38lift37
     backmapTargetVer = 19
     ftpReleaseSubdir = release_${verBase}/GRCh37_mapping
     gencodeOrg = Gencode_human
     annGffTypeName = annotation
     isBackmap = yes
 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
 pseudo2WayGff = ${relDir}/gencode.v${ver}.2wayconspseudos.gff3.gz
 polyAGff = ${relDir}/gencode.v${ver}.polyAs.gff3.gz
+ifneq (${isBackmap},yes)
    transcriptRanks = ${relDir}/gencode.v${ver}.transcript_rankings.txt.gz
+   transcriptRanksOpt = --transcriptRanks=${transcriptRanks}
+endif
 
 gencodeBinDir = ${HOME}/kent/src/hg/makeDb/outside/gencode/bin
 gencodeMakeTracks = ${gencodeBinDir}/gencodeMakeTracks
 gencodeMakeAttrs = ${gencodeBinDir}/gencodeMakeAttrs
 gencodeExonSupportToTable = ${gencodeBinDir}/gencodeExonSupportToTable
 gencodeGxfToGenePred = ${gencodeBinDir}/gencodeGxfToGenePred
 gencodePolyaGxfToGenePred = ${gencodeBinDir}/gencodePolyaGxfToGenePred
 gencodeGxfToAttrs = ${gencodeBinDir}/gencodeGxfToAttrs
 buildGencodeToUcscLift = ${HOME}/kent/src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
 gencodeBackMapMetadataIds = ${gencodeBinDir}/gencodeBackMapMetadataIds
 encodeAutoSqlDir = ${HOME}/kent/src/hg/lib/encode
 
 ##
 # intermediate data not loaded into tracks
 ##
@@ -354,42 +357,42 @@
 	@mkdir -p $(dir $@)
 	zcat $< | tawk '$$1!~/^ENSTR/' | sort -k 1,1 | ${metaFilterCmd} /dev/stdin > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ##
 # intermediate data for ensembl/havana, not loaded into databases
 ##
 ${gencodeGp}: ${annotationGff} ${gencodeToUcscChain}
 	@mkdir -p $(dir $@)
 	${gencodeGxfToGenePred} ${db} ${annotationGff} ${gencodeToUcscChain} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 	touch $@
 ${gencodeTsv}: ${annotationGff}
 	@mkdir -p $(dir $@)
-	${gencodeGxfToAttrs} --transcriptRanks=${transcriptRanks} ${annotationGff} $@.${tmpExt}
+	${gencodeGxfToAttrs} ${transcriptRanksOpt} ${annotationGff} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${targetGencodeTsv}:
 	@mkdir -p $(dir $@)
 	hgsql ${db}  -e 'select * from wgEncodeGencodeAttrsV${backmapTargetVer}' > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 
 # check attributes so code can be updated to handle new biotypes
 checkAttrs: ${annotationGff}
-	${gencodeGxfToAttrs} --transcriptRanks=${transcriptRanks} ${annotationGff} /dev/null
+	${gencodeGxfToAttrs} ${transcriptRanksOpt} ${annotationGff} /dev/null
 
 ##
 # load tables
 #  browser commands use static tmp file name, so use lock file to serialize
 ##
 loadLock = flock load.lock
 
 loadTables: ${genePredExtTables:%=${loadedDir}/%.genePredExt.loaded} \
 	    ${genePredTables:%=${loadedDir}/%.genePred.loaded} \
 	    ${tabTables:%=${loadedDir}/%.tab.loaded}
 
 ${loadedDir}/%.genePredExt.loaded: ${tableDir}/%.gp
 	@mkdir -p $(dir $@)
 	${loadLock} hgLoadGenePred -genePredExt ${db} $* $<
 	touch $@