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
@@ -100,30 +100,31 @@
 	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: