957b916c9cb686a1e2f21c8702db24369623cb85
hiram
  Tue Jun 2 12:33:46 2026 -0700
correct primate score matrix for lastz input refs #31811

diff --git src/hg/utils/otto/userRequests/kegAlignLastz.sh src/hg/utils/otto/userRequests/kegAlignLastz.sh
index af71984abd6..fb106bc4313 100755
--- src/hg/utils/otto/userRequests/kegAlignLastz.sh
+++ src/hg/utils/otto/userRequests/kegAlignLastz.sh
@@ -446,31 +446,40 @@
 # -356 -236 -330   90
 #     O=600 E=150
 # lastz options
 xdropX: 910
 ydropY: 15000
 stepZ: 1
 noTransitionT: false
 strand_selectorB: both
 # seeding_options.seed.seed_selector: 12of19 does not get into the process
 hspthreshK: 4500
 gappedthreshL: 4500
 innerH: 2000
 scoringMatrix:
   class: File
   filetype: txt
-  path: https://genome-test.gi.ucsc.edu/~hiram/galaxy/kegAlign/primate-primate.lastz.score.txt
+  path: https://genome-test.gi.ucsc.edu/~hiram/galaxy/kegAlign/kegAlign.primatePrimate.lastz.score.txt
+#
+# gap_open_penalty   = 600
+# gap_extend_penalty = 150
+#
+#    A    C    G    T
+# A   90 -330 -236 -356
+# C -330  100 -318 -236
+# G -236 -318  100 -330
+# T -356 -236 -330   90
 "
 
 export defString="# ${qOrgName} ${Query} vs. ${tOrgName} ${Target}
 BLASTZ=/cluster/bin/penn/lastz-distrib-1.04.03/bin/lastz
 BLASTZ_T=2
 BLASTZ_O=600
 BLASTZ_E=150
 BLASTZ_M=254
 BLASTZ_K=4500
 BLASTZ_Y=15000
 BLASTZ_Q=/hive/data/staging/data/blastz/human_chimp.v2.q
 #       A     C     G     T
 # A    90  -330  -236  -356
 # C  -330   100  -318  -236
 # G  -236  -318   100  -330