57d31ee9aede2bf610907285b05af8d9cbfe9bec
markd
  Sun Mar 13 10:45:03 2022 -0700
added ability to override incorrect sizes often found in RepeatMaster alignments

diff --git src/hg/utils/rmskAlignToPsl/tests/makefile src/hg/utils/rmskAlignToPsl/tests/makefile
index e5a6c0a..a11c73f 100644
--- src/hg/utils/rmskAlignToPsl/tests/makefile
+++ src/hg/utils/rmskAlignToPsl/tests/makefile
@@ -1,34 +1,38 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 rmskAlignToPsl = ${DESTBINDIR}/rmskAlignToPsl
 
 # input/hg38.fa.align.tsv is from Dfam_2.0
 
 
 all::
 
-test:: hg38Test mm39Test mm39ProbTest hg38BigRmskTest
+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
 
 hg38BigRmskTest: mkout
 	${rmskAlignToPsl} -bigRmsk input/hg38.dfam_3.3.bigRmskIn output/$@.psl
 	diff expected/$@.psl output/$@.psl
 
+wrongSizeTest: mkout
+	${rmskAlignToPsl} -repSizes=input/wrongSize.sizes -bigRmsk input/wrongSize.bigRmskIn output/$@.psl
+	diff expected/$@.psl output/$@.psl
+
 mkout:
 	@mkdir -p output
 
 clean::
 	rm -rf output