cc610239716fe32f9c774d98a71f75e8c6b5fba3
braney
  Tue Apr 21 17:23:50 2026 -0700
mafToBigMafSummary: new utility that emits bed3+4 input ready for bedToBigBed -as=mafSummary.as, replacing the hgLoadMafSummary -test / cut -f2- / sort hack documented in bigMaf.html. Companion to mafToBigMaf. The summary scoring/merging logic is intentionally duplicated from hgLoadMafSummary.c (see header comment) — that code is stable and refactoring would force retesting all the makedocs that call hgLoadMafSummary. Also fixes a bug in the duplicated copy of mafSplitSrcGetChrom: the original errAborts on plain 'hg38.chrY' style master src because of an inverted differentString check; rewritten with cleaner correct logic. Updates bigMaf.html and trackDb/trackDbLibrary.shtml to reference the new tool. refs #37404

diff --git src/hg/utils/makefile src/hg/utils/makefile
index a544dec2fc7..0302797e868 100644
--- src/hg/utils/makefile
+++ src/hg/utils/makefile
@@ -38,30 +38,31 @@
 	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 = \