c6753d13e623ebd80e64ebff2296f7d596695442
markd
  Wed Jul 10 19:46:37 2019 -0700
added test case for transcipt-only annotations

diff --git src/hg/utils/gff3ToGenePred/tests/makefile src/hg/utils/gff3ToGenePred/tests/makefile
index 09788a6..30b9b15 100644
--- src/hg/utils/gff3ToGenePred/tests/makefile
+++ src/hg/utils/gff3ToGenePred/tests/makefile
@@ -1,29 +1,30 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 gff3ToGenePred = ${DESTBINDIR}/gff3ToGenePred
 
 # sh commands to deal with gff3ToGenePred shouldhave failed and didn't 
 cmdShouldFail = echo "Error: command should have failed" >&2; false
 
 all::
 
 test:: geneMRnaTest noGeneMRnaTest geneMRnaHonorTest discontinuousTest multCdsOutOfExonTest \
 	noIdTest errCases1Test bogusQuotesTest noExonsTest geneTranscriptTest transcriptCdsParentTest \
 	minimalGenesTest geneDefaultStatusUnknownTest useNameTest nameAttrIdTest nameAttrNameTest \
-	frameShiftTest mm10GencodeTest ncbiSegmentsTest ncbiProblemsTest makeBadTest
+	frameShiftTest mm10GencodeTest ncbiSegmentsTest ncbiProblemsTest makeBadTest \
+	transcriptOnlyTest
 
 geneMRnaTest: mkout
 	${gff3ToGenePred} input/geneMRna.gff3 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 
 noGeneMRnaTest: mkout
 	${gff3ToGenePred} input/noGeneMRna.gff3 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 
 geneMRnaHonorTest: mkout
 	${gff3ToGenePred} -honorStartStopCodons input/geneMRna.gff3 output/$@.gp
 	diff expected/$@.gp output/$@.gp
 
 geneDefaultStatusUnknownTest: mkout
 	${gff3ToGenePred} -defaultCdsStatusToUnknown input/geneMRna.gff3 output/$@.gp
@@ -108,20 +109,26 @@
 # various NCBI problem cases
 ncbiProblemsTest: mkout
 	${gff3ToGenePred} -warnAndContinue -geneNameAttr=gene -refseqHacks -attrsOut=output/$@.attrs input/ncbiProblems.gff3 output/$@.gp > output/$@.out 2>&1
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.attrs output/$@.attrs
 	diff expected/$@.out output/$@.out
 
 # -warnAndContinue on maker file with missing gene/mrna records.  This test this option on
 # GFF3 parse tests, not just genePred conversion
 makeBadTest:  mkout
 	${gff3ToGenePred} -warnAndContinue -attrsOut=output/$@.attrs input/makerBad.gff3 output/$@.gp > output/$@.out 2>&1
 	diff expected/$@.gp output/$@.gp
 	diff expected/$@.attrs output/$@.attrs
 	diff expected/$@.out output/$@.out
 
+# pseudogene annotations as transcripts-only.  Yet another non-standard variation
+transcriptOnlyTest: mkout
+	${gff3ToGenePred} -allowMinimalGenes input/transcriptOnly.gff3 output/$@.gp
+	diff expected/$@.gp output/$@.gp
+
+
 mkout:
 	@mkdir -p output
 
 clean::
 	rm -rf output