a8b15f82bbcff0d7953bae0da7df49363939f85a
lrnassar
  Wed Aug 5 16:59:54 2026 -0700
Add tests for every maf sequence-name form, and describe the splitting in the usage messages. refs #37928

The existing testDot and testPipe inputs are identical copies of each other and both use
pipe-form query names, so the dot path was never exercised in either tool. That is how
the break in ae63ce5 shipped even though a test suite existed, and why the suite could
not have caught the mafToBigMafSummary divergence either.

New inputs in both tests directories cover an ordinary db.chrom, a species name with a
dotted chrom, both GenArk accession forms, a GenArk accession with no chrom after the
version, a pipe with a dotted chrom, a name with no separator, a reference assembly
whose own name contains a dot, and a name where the reference db is a strict prefix of
another assembly. Every rule in the splitter is now load-bearing: breaking any one of
them fails a target.

Also adds mafToBigMafSummary to TEST_DIRS in hg/utils, since nothing above the directory
was running its suite, and adds a short note to both usage messages describing how a
sequence name is split into assembly and sequence.

diff --git src/hg/utils/makefile src/hg/utils/makefile
index 64c6e86f8fd..8c1951dac1f 100644
--- src/hg/utils/makefile
+++ src/hg/utils/makefile
@@ -1,162 +1,163 @@
 # Build all directories in utils
 # test comment
 # 	$Id: makefile,v 1.21 2010/06/04 00:12:42 larrym Exp $
 
 kentSrc = ../..
 
 include ${kentSrc}/inc/localEnvironment.mk
 include ${kentSrc}/inc/common.mk
 
 # to check for Mac OSX Darwin specifics:
 UNAME_S := $(shell uname -s)
 
 # can not build this on Mac OSX - has functions not supported
 ifeq ($(UNAME_S),Darwin)
   buildRefresh=
 else
   buildRefresh=refreshNamedSessionCustomTracks
 endif
 
 # List of directories to build for userApps
 UTILS_APPLIST = \
 	bedExtendRanges \
 	bedToPsl \
 	bedWeedOverlapping \
 	bedMergeAdjacent \
 	bedPartition \
 	bigChainBreaks \
 	bigChainToChain \
 	bigGenePredToGenePred \
 	bigMafToMaf \
 	bigPslToPsl \
 	binFromRange \
 	chainToBigChain \
 	chromGraphFromBin \
 	chromGraphToBin \
 	crTreeIndexBed \
 	crTreeSearchBed \
 	faToVcf \
 	gapToLift \
 	genePredFilter \
 	genePredToBigGenePred \
 	genePredToProt \
 	gencodeVersionForGenes \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	hicInfo \
 	hgvsToVcf \
 	hubCheck \
 	hubClone \
 	hubPublicCheck \
 	mafToBigMaf \
 	mafToBigMafSummary \
 	makeTableList \
 	oligoMatch \
 	overlapSelect \
 	positionalTblCheck \
 	pslLiftSubrangeBlat \
 	pslToBigPsl \
 	raSqlQuery \
 	rmskAlignToPsl \
 	tdbQuery \
 	transMapPslToGenePred \
 	twoBitMask \
 	vcfToBed \
 	fixTrackDb
 
 USER_APP_SCRIPTS = \
 	vai.pl
 
 SCRIPT_FILES = \
 	archiveTracks.sh \
 	dbNsfpToBed.pl \
 	dumpDb.pl \
 	mergeOverlapBed4.pl \
 	mergeSortedBed3Plus.pl \
 	mysqlRowSizes.pl \
 	${USER_APP_SCRIPTS}
 
 APP_SCRIPTS = ${SCRIPT_FILES}
 
 # List of directories to build of interest only at UCSC
 DIRS = ${buildRefresh} \
 	automation \
 	rts \
 	blatServersCheck \
 	buildReleaseLog \
 	checkUrlsInTable \
 	geoMirrorNode \
 	hubCrawl \
 	makeTrackIndex \
 	mysqlSecurityCheck \
 	phyloRenameAndPrune \
 	pslFixCdsJoinGap \
 	pslMismatchGapToBed \
 	pslUniq \
 	refSeqGet \
 	safePush \
 	scaffoldFaToAgp \
 	toDev64 \
 	vcfRenameAndPrune \
 	vcfToHgvs \
 	wigBedToStep
 
 TEST_DIRS = \
 	bedMergeAdjacent \
 	bedPartition \
 	genePredFilter \
 	genePredToProt \
 	gff3ToGenePred \
 	gff3ToPsl \
 	gtfToGenePred \
 	hgvsToVcf \
 	hubCheck \
+	mafToBigMafSummary \
 	overlapSelect \
 	pslToBigPsl \
 	refSeqGet \
 	transMapPslToGenePred \
 	vcfToHgvs
 
 APPS = $(DIRS) $(UTILS_APPLIST)
 
 all:: utils
 
 utils: $(APPS:%=%.utils) $(APP_SCRIPTS:%=%.appScript)
 # tolerate missing directories, as some were removed in kent-core
 %.utils:
 	if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi
 %.appScript:
 	chmod +x $*
 	rm -f ${DESTDIR}${SCRIPTS}/$*
 	cp -p $* ${DESTDIR}${SCRIPTS}/$*
 
 userApps: $(UTILS_APPLIST:%=%.userApp) $(USER_APP_SCRIPTS:%=%.userAppScript)
 %.userApp:
 	if test -d $* ; then cd $* && echo $* && $(MAKE) ; fi
 %.userAppScript:
 	chmod +x $*
 	rm -f ${DESTDIR}${BINDIR}/$*
 	cp -p $* ${DESTDIR}${BINDIR}/$*
 
 scripts: $(SCRIPT_FILES:%=%.scripts)
 %.scripts:
 	chmod +x $*
 	rm -f ${SCRIPTS}/$*
 	cp -p $* ${SCRIPTS}/$*
 
 alpha: scripts all
 
 test::	${TEST_DIRS:%=%.test}
 %.test:
 	(cd $* && ${MAKE} test)
 
 clean:: $(APPS:%=%.clean)
 	- find . -name '*.o' -exec rm {} \;
 %.clean:
 	(if test -d $* ; then cd $* && echo $* && $(MAKE) clean; fi)
 
 compile:: $(APPS:%=%.compile)
 	- find . -name '*.o' -exec rm {} \;
 %.compile:
 	(cd $* && ${MAKE} compile)