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/makefile src/hg/utils/mafToBigMafSummary/makefile
new file mode 100644
index 00000000000..5c4e1c0f951
--- /dev/null
+++ src/hg/utils/mafToBigMafSummary/makefile
@@ -0,0 +1,3 @@
+kentSrc = ../../..
+A = mafToBigMafSummary
+include $(kentSrc)/inc/userApp.mk