2da9964103135a26ecc753c4afbb33dea7a9324c
markd
  Tue May 5 19:52:29 2026 -0700
added for chainToMaf suggested by Hiram

diff --git src/hg/mouseStuff/chainToMaf/tests/makefile src/hg/mouseStuff/chainToMaf/tests/makefile
index fb129664d49..777ea867736 100644
--- src/hg/mouseStuff/chainToMaf/tests/makefile
+++ src/hg/mouseStuff/chainToMaf/tests/makefile
@@ -1,43 +1,59 @@
 kentSrc = ../../../..
 include ${kentSrc}/inc/common.mk
 
 chainToMaf = ${DESTBINDIR}/chainToMaf
+chainToAxt = ${DESTBINDIR}/chainToAxt
+axtToMaf = ${DESTBINDIR}/axtToMaf
+twoBitInfo = ${DESTBINDIR}/twoBitInfo
 
 hg38TwoBit = /gbdb/hg38/hg38.2bit
 mm10TwoBit = /gbdb/mm10/mm10.2bit
 hg38TwoBitUrl = https://hgdownload.gi.ucsc.edu/gbdb/hg38/hg38.2bit
 mm10TwoBitUrl = https://hgdownload.gi.ucsc.edu/gbdb/mm10/mm10.2bit
 
 all:
 
-test: localNoPrefix localPrefix urlPrefix rescorePrefix
+test: localNoPrefix localPrefix urlPrefix rescorePrefix viaAxt
 	${MAKE} clean
 
 # basic local 2bit test, no prefixes
 localNoPrefix: mkdirs
 	${chainToMaf} input/hg38.mm10.test.chain ${hg38TwoBit} ${mm10TwoBit} output/$@.maf
 	diff -u expected/$@.maf output/$@.maf
 
 # local 2bit with target/query prefixes
 localPrefix: mkdirs
 	${chainToMaf} -tPrefix=hg38. -qPrefix=mm10. \
 	    input/hg38.mm10.test.chain ${hg38TwoBit} ${mm10TwoBit} output/$@.maf
 	diff -u expected/$@.maf output/$@.maf
 
 # remote 2bit URLs with prefixes
 urlPrefix: mkdirs
 	${chainToMaf} -tPrefix=hg38. -qPrefix=mm10. \
 	    input/hg38.mm10.test.chain ${hg38TwoBitUrl} ${mm10TwoBitUrl} output/$@.maf
 	diff -u expected/$@.maf output/$@.maf
 
 # rescore with prefixes
 rescorePrefix: mkdirs
 	${chainToMaf} -score -tPrefix=hg38. -qPrefix=mm10. \
 	    input/hg38.mm10.test.chain ${hg38TwoBit} ${mm10TwoBit} output/$@.maf
 	diff -u expected/$@.maf output/$@.maf
 
+# verify chainToMaf output matches the chainToAxt | axtToMaf pipeline.
+# uses the same input chain and 2bits as localNoPrefix.
+viaAxt: mkdirs
+	${twoBitInfo} ${hg38TwoBit} output/hg38.sizes
+	${twoBitInfo} ${mm10TwoBit} output/mm10.sizes
+	${chainToAxt} input/hg38.mm10.test.chain ${hg38TwoBit} ${mm10TwoBit} \
+	    output/$@.axt
+	${axtToMaf} output/$@.axt output/hg38.sizes output/mm10.sizes \
+	    output/$@.viaPipe.maf
+	${chainToMaf} input/hg38.mm10.test.chain ${hg38TwoBit} ${mm10TwoBit} \
+	    output/$@.direct.maf
+	diff -u output/$@.viaPipe.maf output/$@.direct.maf
+
 clean::
 	rm -rf output
 
 mkdirs:
 	@${MKDIR} output