From 0454e6be91ef355786d1cc1f3490653a5c23b216 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Thu, 18 Jan 2018 11:47:11 -0500
Subject: [PATCH] explain -M in the manpage

---
 minimap2.1 | 5 +++++
 1 file changed, 5 insertions(+)

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