12a7062ec0510b37e2cb6e8c294b53d2b0af69e0
markd
  Tue Jan 21 18:24:46 2020 -0800
import of gencodeV33lift37

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index b3326cb..3a54078 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -23,35 +23,35 @@
 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.
 ##
-db = hg38
-#db = hg19
-db = mm10
-preRelease = no
-#preRelease = yes
+#db = hg38
+db = hg19
+#db = mm10
+#preRelease = no
+preRelease = yes
 ifeq (${db},mm10)
     grcRefAssembly = GRCm38
     ver = M24
     prevVer = M23
     gencodeOrg = Gencode_mouse
     ftpReleaseSubdir = release_${ver}
     annGffTypeName = chr_patch_hapl_scaff.annotation
     ensemblVer = 99_38
     ensemblPrevVer = 98_38
     ensemblCDnaDb = mus_musculus_cdna_${ensemblPrevVer}
 else ifeq (${db},hg38)
     grcRefAssembly = GRCh38
     ver = 33
     prevVer = 32
     gencodeOrg = Gencode_human
@@ -352,31 +352,31 @@
 ${tableAnnotationRemarkTab}: ${tableAnnotationRemarkMeta} ${metaFilterDepend}
 	@mkdir -p $(dir $@)
 	${metaFilterCmdGz} $<  | tawk '{print $$1,gensub("\\\\n|\\\\","","g",$$2)}' | sort -k 1,1 > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 # drop ENSTR entries that are a hack to support PAR sequences in GTF
 ${tableEntrezGeneTab}: ${tableEntrezGeneMeta} ${metaFilterDepend}
 	@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} ${ensemblToUcscChain}
 	@mkdir -p $(dir $@)
-	${gencodeGxfToGenePred} ${annotationGff} ${ensemblToUcscChain} $@.${tmpExt}
+	${gencodeGxfToGenePred} ${db} ${annotationGff} ${ensemblToUcscChain} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${tableTranscriptionSupportLevelData}: ${metaFilterDepend}
 	touch $@
 ${gencodeTsv}: ${annotationGff}
 	@mkdir -p $(dir $@)
 	${gencodeGxfToAttrs} --keepGoing ${annotationGff} $@.${tmpExt} --tslTabOut=${tableTranscriptionSupportLevelData}.${tmpExt}
 	mv -f ${tableTranscriptionSupportLevelData}.${tmpExt} ${tableTranscriptionSupportLevelData}
 	mv -f $@.${tmpExt} $@
 
 ${targetGencodeTsv}:
 	@mkdir -p $(dir $@)
 	hgsql ${db}  -e 'select * from wgEncodeGencodeAttrsV${backmapTargetVer}' > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@