b1a9de0fd2ebab6d3caf4197eecc2e75eb74162d
markd
  Mon May 24 13:53:35 2021 -0700
Added better handling of GTFs without correct frames on CDS. This also simplified the handling of GTF stop codons

diff --git src/hg/utils/gtfToGenePred/tests/makefile src/hg/utils/gtfToGenePred/tests/makefile
index 61ac115..7f49a48 100644
--- src/hg/utils/gtfToGenePred/tests/makefile
+++ src/hg/utils/gtfToGenePred/tests/makefile
@@ -1,87 +1,96 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 gtfToGenePred = ${DESTBINDIR}/gtfToGenePred
 genePredCheck = ${DESTBINDIR}/genePredCheck
 
 all:
 
 test: basic srcPre dups impliedStop ensembl geneNameAsName2 splitStop \
-	ignoreGroupWithoutExons ensemblSplicedStop ensemblWithVersions ensemblWithVersionsGeneName2
+	ignoreGroupWithoutExons ensemblSplicedStop ensemblWithVersions ensemblWithVersionsGeneName2 \
+	noFrame
 
 # basic conversion
 basic: mkdirs
 	${gtfToGenePred} -infoOut=output/$@.info input/basic.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.info output/$@.info
 
 # source prefix filtering
 srcPre: mkdirs
 	${gtfToGenePred} -infoOut=output/$@.info -sourcePrefix=mgc2 -sourcePrefix=mgc3 input/basic.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.info output/$@.info
 
 # error reporting
 dups: mkdirs
 	if ${gtfToGenePred} -allErrors input/dups.gtf output/$@.gp >output/$@.out 2>&1 ; then false ; else true ; fi
 	diff expected/$@.out output/$@.out
 	diff expected/$@.gp output/$@.gp
 
 impliedStop: mkdirs
 	${gtfToGenePred} -impliedStopAfterCds -infoOut=output/$@.info input/flybase.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.info output/$@.info
 
 # protein id, make sure -inclVersion does nothing for this file
 ensembl: mkdirs
 	${gtfToGenePred} -genePredExt -infoOut=output/$@.info -includeVersion input/ensembl.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.info output/$@.info
 
 # -geneNameAsName2, make sure -inclVersion does nothing for this file
 geneNameAsName2: mkdirs
 	${gtfToGenePred} -genePredExt -geneNameAsName2 -includeVersion input/ensembl.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 
 # split stop coding, produced bogus frame
 splitStop: mkdirs
 	${gtfToGenePred} -genePredExt input/splitStop.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 
 ignoreGroupWithoutExons: mkdirs
 	${gtfToGenePred} -genePredExt -ignoreGroupsWithoutExons -infoOut=output/$@.info input/geneFeature.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.info output/$@.info
 
 # this caused assert in assigning exon frame
 ensemblSplicedStop: mkdirs
 	${gtfToGenePred} -genePredExt input/ensemblSplicedStop.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 
 # including version numbers
 ensemblWithVersions: mkdirs
 	${gtfToGenePred} -genePredExt -includeVersion -infoOut=output/$@.info input/ensemblWithVersions.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.info output/$@.info
 
 # including version numbers with -geneNameAsName2
 ensemblWithVersionsGeneName2: mkdirs
 	${gtfToGenePred} -genePredExt -geneNameAsName2 -includeVersion -infoOut=output/$@.info input/ensemblWithVersions.gtf output/$@.gp
 	${genePredCheck} -verbose=0 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.info output/$@.info
 
+# 
+noFrame: mkdirs
+	${gtfToGenePred} -genePredExt -geneNameAsName2 -includeVersion -infoOut=output/$@.info input/noFrame.gtf output/$@.gp
+	${genePredCheck} -verbose=0 output/$@.gp
+	diff expected/$@.gp output/$@.gp
+	diff expected/$@.info output/$@.info
+
+
 mkdirs:
 	mkdir -p output
 
 clean:
 	rm -rf output