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/expected/testDot.bed src/hg/utils/mafToBigMafSummary/tests/expected/testDot.bed
new file mode 100644
index 00000000000..860a3540e2a
--- /dev/null
+++ src/hg/utils/mafToBigMafSummary/tests/expected/testDot.bed
@@ -0,0 +1,17 @@
+chrY	2781479	2790761	GCA_018505835.1	0.972344	N	C
+chrY	2781479	2790761	GCA_018470435.1	0.972415	N	C
+chrY	2781479	2790761	GCA_018472705.1	0.972415	N	C
+chrY	2781479	2790761	GCA_018472575.1	0.972695	N	C
+chrY	2781479	2790761	GCA_018467005.1	0.972415	N	C
+chrY	2781479	2790761	GCA_018472835.1	0.972415	N	C
+chrY	2781479	2790761	GCA_018472585.1	0.972415	N	C
+chrY	2781479	2790761	GCA_018505855.1	0.972415	N	C
+chrY	2781479	2790761	GCA_018471555.1	0.972695	N	C
+chrY	2781479	2790761	GCA_018504645.1	0.972415	N	I
+chrY	2781479	2790761	GCA_018506155.1	0.972304	N	C
+chrY	2781479	2790761	GCA_018469965.1	0.972415	N	C
+chrY	2781479	2790761	GCA_018471075.1	0.97235	N	I
+chrY	2781479	2790761	GCA_018470425.1	0.972415	N	C
+chrY	2781479	2790761	GCA_018852595.1	0.972695	N	C
+chrY	2781479	2790761	GCA_018469675.1	0.972294	N	C
+chrY	2781479	2790761	GCA_018504045.1	0.972415	N	C