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

diff --git src/hg/mouseStuff/makefile src/hg/mouseStuff/makefile
index 9a9e942fb31..7a93b667c90 100644
--- src/hg/mouseStuff/makefile
+++ src/hg/mouseStuff/makefile
@@ -1,110 +1,112 @@
 # Build all directories in makeDb 
 
 kentSrc = ../..
 
 include ${kentSrc}/inc/localEnvironment.mk
 include ${kentSrc}/inc/common.mk
 
 BADDIRS = \
         correctEst
 
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	axtChain \
 	axtSort \
 	axtSwap \
 	axtToMaf \
 	axtToPsl \
 	bedCoverage \
 	chainAntiRepeat \
 	chainBridge \
 	chainCleaner \
 	chainFilter \
 	chainMergeSort \
 	chainNet \
 	chainPreNet \
 	chainScore \
 	chainSort \
 	chainSplit \
 	chainStitchId \
 	chainSwap \
 	chainToAxt \
+	chainToMaf \
 	chainToPsl \
 	chainToPslBasic \
 	lavToAxt \
 	lavToPsl \
 	mafCoverage \
 	mafFetch \
 	mafRanges \
 	mafNoAlign \
 	mafToAxt \
+	mafToChain \
 	mafToPsl \
 	netChainSubset \
 	netClass \
 	netFilter \
 	netSplit \
 	netSyntenic \
 	netToAxt \
 	netToBed \
 	pslMrnaCover
 
 # List of directories to build at UCSC
 DIRS = \
 	axtAndBed \
 	axtBest \
 	axtCalcMatrix \
 	axtDropOverlap \
 	axtDropSelf \
 	axtFilter \
 	axtIndex \
 	axtPretty \
 	axtQueryCount \
 	axtRecipBest \
 	axtRescore \
 	axtSplitByTarget \
 	axtToBed \
 	axtToChain \
 	calcGap \
 	chainDbToFile \
 	gcForBed \
 	knownVsBlat \
 	libScan \
 	mousePoster \
 	netStats \
 	netToBedWithId \
         orthologBySynteny \
 	phToPsl \
 	regionPicker \
 	rikenBestInCluster \
 	simpleChain \
 	splitSim \
 	subsetAxt \
 	subsetTraces \
 	whyConserved 
 
 # List of directories to build
 USE_DIRS = $(DIRS) $(UTILS_APPLIST)
 
 all: ${USE_DIRS:%=%.all}
 # kent-core doesn't contain all utils, so tolerate missing directories
 %.all:
 	if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi
 
 userApps: $(UTILS_APPLIST:%=%.userApp)
 # kent-core doesn't contain all utils, so tolerate missing directories
 %.userApp:
 	if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi
 
 clean:: $(USE_DIRS:%=%.cleanAll)
 %.cleanAll:
 	if test -d $* ; then cd $* && echo $* && $(MAKE) clean ; fi
 
 clean::
 	cd simpleChain && ${MAKE} clean
 
 testAll: $(USE_DIRS:%=%.testAll)
 
 %.testAll:
 	@test -s $*/tests/makefile && (echo $*; cd $* && $(MAKE) test) || true
 
 test:: testAll