From ecb6c5c36cce03f756b8366652937997540d99b9 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 23 Oct 2018 10:00:21 -0400
Subject: [PATCH] Document --no-pairing (#256)

---
 minimap2.1 | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/minimap2.1 b/minimap2.1
index 879ef44..0cdf6d8 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -274,6 +274,10 @@ Only map to the reverse complement strand of the reference sequences.
 .BR --heap-sort = no | yes
 If yes, sort anchors with heap merge, instead of radix sort. Heap merge is
 faster for short reads, but slower for long reads. [no]
+.TP
+.B --no-pairing
+Treat two reads in a pair as independent reads. The mate related fields in SAM
+are still properly populated.
 .SS Alignment options
 .TP 10
 .BI -A \ INT