From 845ecc4769cf508edffbc30f773c83995660675d Mon Sep 17 00:00:00 2001
From: Jean-Francois Pombert <jpombert@iit.edu>
Date: Thu, 16 May 2024 07:33:48 -0400
Subject: [PATCH] + new cmdline options

---
 Examples/commands.conf | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/Examples/commands.conf b/Examples/commands.conf
index 7fb37a1..8478e48 100644
--- a/Examples/commands.conf
+++ b/Examples/commands.conf
@@ -26,9 +26,18 @@
 ### Minimum contig size (in bp) [Default: 1]; i.e. investigates all contigs
 --minsize 1
 
+### Exclude contigs with names matching the regular expression(s); e.g. --exclude 
+# --exclude '^AUX'
+
+### Specify genome alignment tool: minimap or mashmap [Default: minimap]
+--aligner minimap
+
 ### Specify minimap2 max divergence preset (--asm 5, 10 or 20) [Default: off]
 # --asm 20
 
+### Specify mashmap percentage identity [Default: 85]
+--mpid 85
+
 ### Resume minimap2 computations (skip completed alignments)
 # --resume