e10c349f9e394f6dfa688a2c83111115428b9535
markd
  Wed Aug 28 23:49:05 2024 -0700
sort unpredictable output results

diff --git src/hg/hgGetAnn/tests/makefile src/hg/hgGetAnn/tests/makefile
index cbe359c..1d31491 100644
--- src/hg/hgGetAnn/tests/makefile
+++ src/hg/hgGetAnn/tests/makefile
@@ -1,85 +1,85 @@
 kentSrc = ../../..
 include ../../../inc/common.mk
 
 hgGetAnn = ${DESTBINDIR}/hgGetAnn
 
 # use hg15 to avoid incremental update
 DB=hg15
 
 all:
 
 test: chrRangeTests textTests
 
 ###
 # chrom range queries
 ###
 CHR_RANGE = chr5:112,253,464-112,324,832
 
 chrRangeTests: chrRangeGenePred chrRangePsl chrRangePslSplit chrRangePslKeepBin \
 	chrRangeGenePredColHeaders chrRangeGenePredTsvHeaders
 
 # range genePred
 chrRangeGenePred: mkdirs
 	${hgGetAnn} ${DB} refGene ${CHR_RANGE} stdout | sort > output/$@.gp
 	sort expected/$@.gp | diff - output/$@.gp
 
 # range psl single
 chrRangePsl: mkdirs
-	${hgGetAnn} ${DB} refSeqAli ${CHR_RANGE} output/$@.psl
-	diff expected/$@.psl output/$@.psl
+	${hgGetAnn} ${DB} refSeqAli ${CHR_RANGE} stdout | sort > output/$@.psl
+	sort expected/$@.psl | diff - output/$@.psl
 
 # range psl split
 chrRangePslSplit: mkdirs
-	${hgGetAnn} ${DB} intronEst chr4:56,225,976-56,230,912 output/$@.psl
-	diff expected/$@.psl output/$@.psl
+	${hgGetAnn} ${DB} intronEst chr4:56,225,976-56,230,912 stdout | sort > output/$@.psl
+	sort expected/$@.psl | diff - output/$@.psl
 
 # range psl keep bin, include spaces in query
 chrRangePslKeepBin: mkdirs
-	${hgGetAnn} -keepBin ${DB} blatFugu "chr5 112272300 112280228" output/$@.psl
-	diff expected/$@.psl output/$@.psl
+	${hgGetAnn} -keepBin ${DB} blatFugu "chr5 112272300 112280228" stdout | sort > output/$@.psl
+	sort expected/$@.psl | diff - output/$@.psl
 
 # range genePred with headers
 chrRangeGenePredColHeaders: mkdirs
 	${hgGetAnn} -colHeaders ${DB} refGene ${CHR_RANGE} stdout | sort > output/$@.gp
 	sort expected/$@.gp | diff - output/$@.gp
 
 # range genePred with tsv headers
 chrRangeGenePredTsvHeaders: mkdirs
 	${hgGetAnn} -tsvHeaders ${DB} refGene ${CHR_RANGE} stdout | sort > output/$@.gp
 	sort expected/$@.gp | diff - output/$@.gp
 
 ###
 # acc, name and textual queries
 ###
 textTests: geneNameQuery geneAccQuery mrnaAccQuery keywordQuery multSameLoc
 
 geneNameQuery:
-	${hgGetAnn} ${DB} refGene CLOCK output/$@.gp
-	diff expected/$@.gp output/$@.gp
+	${hgGetAnn} ${DB} refGene CLOCK stdout | sort > output/$@.gp
+	sort expected/$@.gp | diff - output/$@.gp
 
 # aligns in 9 places
 geneAccQuery:
-	${hgGetAnn} ${DB} refGene NM_005083 output/$@.gp
-	diff expected/$@.gp output/$@.gp
+	${hgGetAnn} ${DB} refGene NM_005083 stdout | sort > output/$@.gp
+	sort expected/$@.gp | diff - output/$@.gp
 
 # aligns in 10 places
 mrnaAccQuery:
-	${hgGetAnn} ${DB} mrna AB062075  output/$@.psl
-	diff expected/$@.psl output/$@.psl
+	${hgGetAnn} ${DB} mrna AB062075 stdout | sort > output/$@.psl
+	sort expected/$@.psl | diff - output/$@.psl
 
 # hits multiple mRNAs
 keywordQuery::
-	${hgGetAnn} ${DB} mrna "breast cancer early onset" output/$@.psl
-	diff expected/$@.psl output/$@.psl
+	${hgGetAnn} ${DB} mrna "breast cancer early onset" stdout | sort > output/$@.psl
+	sort expected/$@.psl | diff - output/$@.psl
 
 # acc query were there are multiple genes with same start/stop
 multSameLoc:
-	${hgGetAnn} ${DB} refGene NM_005522 output/$@.gp
-	diff expected/$@.gp output/$@.gp
+	${hgGetAnn} ${DB} refGene NM_005522 stdout | sort > output/$@.gp
+	sort expected/$@.gp | diff - output/$@.gp
 
 
 clean::
 	rm -rf output
 
 mkdirs:
 	@${MKDIR} output