2f032b790bd3d0354f1d61de5dcadb2e469c1817
braney
  Tue Mar 10 17:42:42 2026 -0700
Add unit tests for mafFrag tool

Add test suite with 5 tests covering basic extraction, reverse strand,
custom outName, small region, and larger multi-block region using
hg38 multiz100way. Replace broken old test target that referenced
a missing expected.maf file.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

diff --git src/hg/ratStuff/mafFrag/tests/makefile src/hg/ratStuff/mafFrag/tests/makefile
new file mode 100644
index 00000000000..d532137a413
--- /dev/null
+++ src/hg/ratStuff/mafFrag/tests/makefile
@@ -0,0 +1,35 @@
+kentSrc = ../../../..
+include ${kentSrc}/inc/common.mk
+
+MAFFRAG = ${DESTDIR}${BINDIR}/mafFrag
+
+all::
+
+test:: basicTest revStrandTest outNameTest smallTest largerTest
+	@echo "All mafFrag tests passed."
+
+mkdirs:
+	@${MKDIR} output
+
+basicTest: mkdirs
+	${MAFFRAG} hg38 multiz100way chr1 11000 11100 + output/$@.maf
+	diff expected/basic.maf output/$@.maf
+
+revStrandTest: mkdirs
+	${MAFFRAG} hg38 multiz100way chr1 11000 11100 - output/$@.maf
+	diff expected/revStrand.maf output/$@.maf
+
+outNameTest: mkdirs
+	${MAFFRAG} hg38 multiz100way chr1 11000 11100 + -outName=testSeq output/$@.maf
+	diff expected/outName.maf output/$@.maf
+
+smallTest: mkdirs
+	${MAFFRAG} hg38 multiz100way chr1 11000 11010 + output/$@.maf
+	diff expected/small.maf output/$@.maf
+
+largerTest: mkdirs
+	${MAFFRAG} hg38 multiz100way chr1 100000 100500 + output/$@.maf
+	diff expected/larger.maf output/$@.maf
+
+clean::
+	rm -rf output