diff --git a/minimap2.1 b/minimap2.1 index 67b61c9..bfd3f59 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -182,6 +182,11 @@ Maximum fragment length (aka insert size; effective with .BR -xsr / --frag) [800] .TP +.BI -M \ FLOAT +Mark as secondary a chain that overlaps with a better chain by +.I FLOAT +or more of the shorter chain [0.5] +.TP .BI --max-chain-skip \ INT A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming for chaining. The time complexity is quadratic in the number of seeds. This