From 1e72e3f39b4173231fa1ad4ca30c419e3220c8c8 Mon Sep 17 00:00:00 2001
From: Todd J Treangen <treangen@gmail.com>
Date: Sat, 7 Feb 2015 17:04:32 -0500
Subject: [PATCH] update to v1.2

---
 docs/content/harvest/quickstart.rst | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/docs/content/harvest/quickstart.rst b/docs/content/harvest/quickstart.rst
index c83d11a..b15fb1a 100644
--- a/docs/content/harvest/quickstart.rst
+++ b/docs/content/harvest/quickstart.rst
@@ -19,14 +19,14 @@ harvest-tools is distributed as a precompiled binary. The three steps below repr
 
 On OSX:
 """""""
-  1. wget https://github.com/marbl/harvest-tools/releases/download/v1.0.1/harvesttools-OSX64-v1.0.1.tar.gz
-  2. tar -xvf harvesttools-OSX64-v1.0.1.tar.gz
+  1. wget https://github.com/marbl/harvest-tools/releases/download/v1.2/harvesttools-OSX64-v1.2.zip
+  2. tar -xvf harvesttools-OSX64-v1.2.tar.gz
 
 On Linux:
 """""""""
 
-  1. wget https://github.com/marbl/harvest-tools/releases/download/v1.0.1/harvesttools-Linux64-v1.0.1.tar.gz
-  2. tar -xvf harvesttools-Linux64-v1.0.1.tar.gz
+  1. wget https://github.com/marbl/harvest-tools/releases/download/v1.2/harvesttools-Linux64-v1.2.tar.gz
+  2. tar -xvf harvesttools-Linux64-v1.2.tar.gz
 
 Basic usage:
 """"""""""""
@@ -54,25 +54,27 @@ With harvest-tools file as input, fasta formatted SNP file as output::
 
 Command-line parameters:
 """""""""""""""""""""""""
+   - -i <Gingr input>
    - -b <bed filter intervals>,<filter name>,"<description>"
    - -B <output backbone intervals>
    - -f <reference fasta>
    - -F <reference fasta out>
    - -g <reference genbank>
-   - -h (show this help)
-   - -i <harvest input>
+   - -a <MAF alignment input>
    - -m <multi-fasta alignment input>
    - -M <multi-fasta alignment output (concatenated LCBs)>
    - -n <Newick tree input>
    - -N <Newick tree output>
    - --midpoint-reroot (reroot the tree at its midpoint after loading)
-   - -o <hvt output>
-   - -q (quiet mode)
+   - -o <Gingr output>
    - -S <output for multi-fasta SNPs>
+   - -u 0/1 (update the branch values to reflect genome length)
    - -v <VCF input>
    - -V <VCF output>
    - -x <xmfa alignment file>
    - -X <output xmfa alignment file>
+   - -h (show this help)
+   - -q (quiet mode)
 
 Primary output files
 -------------