From 98a3aa1b39d56eb9ae83497468bca2660b5ec9b8 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Tue, 24 Oct 2023 09:52:39 -0400
Subject: [PATCH] document --secondary-seq in manpage

Resolve #1122
---
 minimap2.1 | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/minimap2.1 b/minimap2.1
index 9e33971..a88dc6c 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -506,6 +506,9 @@ Output =/X CIGAR operators for sequence match/mismatch.
 .B -Y
 In SAM output, use soft clipping for supplementary alignments.
 .TP
+.B --secondary-seq
+In SAM output, show query sequences for secondary alignments.
+.TP
 .BI --seed \ INT
 Integer seed for randomizing equally best hits. Minimap2 hashes
 .I INT