91e6c1e0eed9c2be10a8fbfea8126e3bc3093a81
markd
  Sat Jul 8 10:33:43 2023 -0700
fix invalid GFF3 test file

diff --git src/hg/utils/gff3ToPsl/tests/makefile src/hg/utils/gff3ToPsl/tests/makefile
index e68ac60..f09d8c2 100644
--- src/hg/utils/gff3ToPsl/tests/makefile
+++ src/hg/utils/gff3ToPsl/tests/makefile
@@ -3,31 +3,32 @@
 
 gff3ToPsl = ${DESTBINDIR}/gff3ToPsl
 pslRecalcMatch = ${DESTBINDIR}/pslRecalcMatch
 pslCheck = ${DESTBINDIR}/pslCheck
 pslStats = ${DESTBINDIR}/pslStats
 pslPretty = ${DESTBINDIR}/pslPretty
 
 # sh commands to deal with gff3ToPsl shouldhave failed and didn't 
 cmdShouldFail = echo "Error: command should have failed" >&2; false
 
 all::
 
 test:: patch1test grch38ToGrch37Test
 
 patch1test: mkout
-	${gff3ToPsl} input/chrom.sizes input/chrom.sizes input/haploMaps.gff stdout | sort -k 14 >  output/$@.psl
+	${gff3ToPsl} input/chrom.sizes input/chrom.sizes input/haploMaps.gff output/$@.unsorted.psl
+	sort -k 14 output/$@.unsorted.psl >  output/$@.psl
 	${pslCheck} -verbose=0 output/$@.psl
 	diff expected/$@.psl output/$@.psl
 #	some more extensive testing commented out
 #	${pslRecalcMatch} output/$@.psl /cluster/data/hg38/hg38.2bit /cluster/data/hg38/hg38.2bit output/$@.2.psl
 #	${pslCheck} -verbose=0 output/$@.2.psl
 #	${pslStats} output/$@.2.psl output/$@.2.stats
 #	diff expected/$@.2.stats output/$@.2.stats
 
 grch38ToGrch37Test:
 	${gff3ToPsl} input/GRCh37.p13.sizes input/GRCh38.p2.sizes input/GRCh38.p2-GRCh37.p13.gff stdout | sort -k14 -k16n -k17n > output/$@.psl
 	${pslCheck} -verbose=0 output/$@.psl
 	diff expected/$@.psl output/$@.psl
 
 mkout:
 	@mkdir -p output