r1208: reverted RMQ gap coefficient

Such that minimap2 can give the same alignment in other modes
2026-10-05 02:48:11 +08:00 · 2024-03-27 08:48:10 -04:00
parent 119bdc6029
commit e3d8c708ac
4 changed files with 8 additions and 3 deletions
@@ -268,6 +268,11 @@ or more of the shorter chain [0.5]
 Use the minigraph chaining algorithm [no]. The minigraph algorithm is better
 for aligning contigs through long INDELs.
 .TP
+.BI --rmq-inner \ NUM
+Apply full dynamic programming for anchors within distance
+.I NUM
+[1000].
+.TP
 .B --hard-mask-level
 Honor option
 .B -M