From 328431ac8a3a2e3c5645ff0598301d8a85227f43 Mon Sep 17 00:00:00 2001
From: samuel hanot <smlhnt@gmail.com>
Date: Tue, 20 Feb 2018 11:36:29 +0100
Subject: [PATCH] update README

---
 README.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/README.md b/README.md
index 3b3953b..ae19549 100644
--- a/README.md
+++ b/README.md
@@ -18,16 +18,26 @@ gnuplot (www.gnuplot.info/)
 ```
 ${SRC_DIR}/recursive_gmconvert.sh -f map_filename -t threshold -n num_gaussians -N num_iterations [-i first_iteration] [-s]
 ```
+
 Required arguments:
+
 `-f map_filename`: the file name of the input EM map
+
 `-t threshold`: the density threshold
+
 `-n num_gaussians`: number of gaussians per sub-process
+
 `-N num_iterations`: number of recursion levels
+
 Optional arguments:
+
 `-i first_iteration`: initial recursion level (defaults to 1)
+
 `-s`: enable serial mode
+
 `-h`: display this message
 
+
 The script creates a sub-directory (called `i`) for each recursion level `i`, and the output files are called `i/i.gmm` and `i_imp.gmm`.
 `i/i.gmm` contains the gmm in `gmconvert` format, and `i_imp.gmm` contains the gmm in `IMP` format (the conversion is handeld by `gmconvert2imp.sh`), which can be read in IMP using `IMP.isd.gmm_tools.decorate_gmm_from_text` function.
 
-- 
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