d99300bbd4e6250c0a72144745b3383a973adb14
markd
  Sun Mar 13 12:32:04 2022 -0700
drop querys not in repSizes file rather than generate an error

diff --git src/hg/utils/rmskAlignToPsl/tests/makefile src/hg/utils/rmskAlignToPsl/tests/makefile
index 075458c..8f75806 100644
--- src/hg/utils/rmskAlignToPsl/tests/makefile
+++ src/hg/utils/rmskAlignToPsl/tests/makefile
@@ -1,42 +1,43 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 rmskAlignToPsl = ${DESTBINDIR}/rmskAlignToPsl
 
 # input/hg38.fa.align.tsv is from Dfam_2.0
 
 pslCheck = pslCheck -verbose=0
 
 all::
 
 test:: hg38Test mm39Test mm39ProbTest hg38BigRmskTest wrongSizeTest
 
 hg38Test: mkout
 	${rmskAlignToPsl} input/hg38.align.tsv output/$@.psl
 	diff expected/$@.psl output/$@.psl
 
 mm39Test: mkout
 	${rmskAlignToPsl} input/mm39.align.tsv output/$@.psl
 	diff expected/$@.psl output/$@.psl
 
 mm39ProbTest: mkout
 	${rmskAlignToPsl} input/mm39.prob.align.tsv output/$@.psl >output/$@.err 2>&1
 	diff expected/$@.psl output/$@.psl
 	diff expected/$@.err output/$@.err
 	${pslCheck} output/$@.psl
 
 hg38BigRmskTest: mkout
 	${rmskAlignToPsl} -bigRmsk input/hg38.dfam_3.3.bigRmskIn output/$@.psl
 	diff expected/$@.psl output/$@.psl
 	${pslCheck} output/$@.psl
 
 wrongSizeTest: mkout
-	${rmskAlignToPsl} -repSizes=input/wrongSize.sizes -bigRmsk input/wrongSize.bigRmskIn output/$@.psl
+	${rmskAlignToPsl} -repSizes=input/wrongSize.sizes -bigRmsk input/wrongSize.bigRmskIn output/$@.psl 2> output/$@.out
 	diff expected/$@.psl output/$@.psl
+	diff expected/$@.out output/$@.out
 	${pslCheck} output/$@.psl
 
 mkout:
 	@mkdir -p output
 
 clean::
 	rm -rf output