433d9b4fce034247a83b60de96fea913fa4631d9
markd
  Thu Apr 30 08:40:54 2026 -0700
added chainToMaf command

diff --git src/hg/mouseStuff/chainToMaf/tests/makefile src/hg/mouseStuff/chainToMaf/tests/makefile
new file mode 100644
index 00000000000..fb129664d49
--- /dev/null
+++ src/hg/mouseStuff/chainToMaf/tests/makefile
@@ -0,0 +1,43 @@
+kentSrc = ../../../..
+include ${kentSrc}/inc/common.mk
+
+chainToMaf = ${DESTBINDIR}/chainToMaf
+
+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
+	${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
+
+clean::
+	rm -rf output
+
+mkdirs:
+	@${MKDIR} output