From dab66140d8a86b6c5866539652801f5d90eea5dd Mon Sep 17 00:00:00 2001
From: Yu Sugihara <yu57th@gmail.com>
Date: Thu, 27 Feb 2020 09:44:06 +0900
Subject: [PATCH] change help message

---
 README.md          | 9 +++++----
 mutmap/__init__.py | 2 +-
 mutmap/params.py   | 3 ++-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 0345b8d..2ed2c09 100755
--- a/README.md
+++ b/README.md
@@ -1,5 +1,5 @@
 # MutMap User Guide
-#### version 2.1.5
+#### version 2.1.6
 
 ## Table of contents
 - [What is MutMap?](#What-is-MutMap)
@@ -74,7 +74,7 @@ $ mutmap -h
 usage: mutmap -r <FASTA> -c <BAM|FASTQ> -b <BAM|FASTQ>
               -n <INT> -o <OUT_DIR> [-T] [-e <DATABASE>]
 
-MutMap version 2.1.5
+MutMap version 2.1.6
 
 optional arguments:
   -h, --help         show this help message and exit
@@ -218,11 +218,12 @@ usage: mutplot -v <VCF> -o <OUT_DIR> -n <INT> [-w <INT>] [-s <INT>]
                [-D <INT>] [-d <INT>] [-N <INT>] [-m <FLOAT>]
                [-S <INT>] [-e <DATABASE>] [--igv] [--corr] [--indel]
 
-MutPlot version 2.1.5
+MutPlot version 2.1.6
 
 optional arguments:
   -h, --help            show this help message and exit
-  -v , --vcf            VCF which contains cultivar and mutant bulk.
+  -v , --vcf            VCF file which contains cultivar and mutant bulk.
+                        in this order. This VCF file must have AD field.
   -o , --out            Output directory. Specified name can exist.
   -n , --N-bulk         Number of individuals in mutant bulk.
   -w , --window         Window size (kb). [2000]
diff --git a/mutmap/__init__.py b/mutmap/__init__.py
index 0b167e6..edc60b3 100644
--- a/mutmap/__init__.py
+++ b/mutmap/__init__.py
@@ -1 +1 @@
-__version__ = "2.1.5"
+__version__ = "2.1.6"
diff --git a/mutmap/params.py b/mutmap/params.py
index 711882e..7aeb334 100755
--- a/mutmap/params.py
+++ b/mutmap/params.py
@@ -223,7 +223,8 @@ def mutplot_options(self):
                             action='store',
                             required=True,
                             type=str,
-                            help='VCF which contains cultivar and mutant bulk.',
+                            help=('VCF file which contains cultivar and mutant bulk.\n'
+                                  'in this order. This VCF file must have AD field.'),
                             metavar='')
 
         parser.add_argument('-o',