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/mafToBigMafSummary/tests/makefile src/hg/utils/mafToBigMafSummary/tests/makefile
new file mode 100644
index 00000000000..a0f94792058
--- /dev/null
+++ src/hg/utils/mafToBigMafSummary/tests/makefile
@@ -0,0 +1,20 @@
+kentSrc = ../../../..
+include ../../../../inc/common.mk
+
+mafToBigMafSummary = ${DESTBINDIR}/mafToBigMafSummary
+
+test: testdot testpipe clean
+
+testdot: init
+	${mafToBigMafSummary} hg38 input/testDot.maf output/testDot.bed
+	diff expected/testDot.bed output/testDot.bed
+
+testpipe: init
+	${mafToBigMafSummary} hg38 input/testPipe.maf output/testPipe.bed
+	diff expected/testPipe.bed output/testPipe.bed
+
+init:
+	${MKDIR} output
+
+clean:
+	rm -fr output