b8b9d9c2a21c34a52d876df57e215c53722e53e6
markd
  Wed Jul 10 20:02:51 2019 -0700
fixed problem loading gencode 2way consensus pseudogenes from GFF3

diff --git src/hg/makeDb/outside/gencode/gencodeLoad.mk src/hg/makeDb/outside/gencode/gencodeLoad.mk
index c7875bc..b7ee42a 100644
--- src/hg/makeDb/outside/gencode/gencodeLoad.mk
+++ src/hg/makeDb/outside/gencode/gencodeLoad.mk
@@ -24,32 +24,32 @@
 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 = 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
@@ -268,31 +268,31 @@
 
 # grab subset name from file pattern (this is what tr command below does)
 ${tableDir}/${tablePre}%${rel}.gp: ${gencodeGp} ${gencodeTsv}
 	@mkdir -p $(dir $@)
 	${gencodeMakeTracks}  $$(echo $* | tr A-Z a-z) ${gencodeGp} ${gencodeTsv} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${tableTagTab}: ${tableAttrsTab}
 ${tableAttrsTab}: ${gencodeGp} ${gencodeTsv}
 	@mkdir -p $(dir $@)
 	${gencodeMakeAttrs} ${gencodeGp} ${gencodeTsv} $@.${tmpExt} ${tableTagTab}
 	mv -f $@.${tmpExt} $@
 
 ${table2WayConsPseudoGp}: ${pseudo2WayGff}
 	@mkdir -p $(dir $@)
-	zcat $< | tawk '$$3=="transcript"{$$3 = "exon"} {print $$0}' | gff3ToGenePred stdin $@.${tmpExt}
+	gff3ToGenePred -allowMinimalGenes $< $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${tablePolyAGp}: ${polyAGff} ${ensemblToUcscChain}
 	@mkdir -p $(dir $@)
 	${gencodePolyaGxfToGenePred} $< ${ensemblToUcscChain} $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${tableUniProtTab}: ${tableSwissProtMeta} ${tableTrEMBLMeta} ${gencodeTsv}
 	@mkdir -p $(dir $@)
 	((${metaFilterCmdGz} ${tableSwissProtMeta} | tawk '{print $$0,"SwissProt"}') && (${metaFilterCmdGz}  ${tableTrEMBLMeta} | tawk '{print $$0,"TrEMBL"}')) | sort -k 1,1 > $@.${tmpExt}
 	mv -f $@.${tmpExt} $@
 
 ${ensemblToUcscChain}:
 	@mkdir -p $(dir $@)
 	${ensToUcscChromMap} ${ensemblCDnaDb} ${grcRefAssembly} ${db} /dev/stdout | pslSwap stdin stdout | pslToChain stdin $@.${tmpExt}