From 55b750c49231bcad5a86dfd97785ca0c6d4b861a Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Thu, 11 Jul 2019 11:13:22 +0200
Subject: [PATCH] Updated README, that was a copy of another one.

---
 README.md | 29 ++++++++++++++++++++++++-----
 1 file changed, 24 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index b92ab58..1af164b 100644
--- a/README.md
+++ b/README.md
@@ -1,13 +1,32 @@
-# Utilities to generate stats and graphs from reads.
-
-This is a very preliminary version, with very few utilities.
+# Utilities to collapse reads in bam files to their 5' end.
 
 
 ## Installing
 
-Get the source using `git clone git@gitlab.pasteur.fr:bli/libreads.git`, `cd` into it and run `python3 -m pip install .`
+Get the source using `git clone git@gitlab.pasteur.fr:bli/bam25prime.git`, `cd` into it and run `python3 -m pip install .`
 
 It might also work directly:
 
-    python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/libreads.git
+    python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/bam25prime.git
+
+## Usage
+
+This package provides a `bam25prime`.
+Its help can be obtained using option `-h` or `--help`.
+
+```
+$ bam25prime --help
+usage: bam25prime [-h] -b BAMFILE -o OUT_BED
+
+When executed, this module collapses reads in a bam file to their 5-prime end
+(reducing them to length 1) and writes the result in bed format.
 
+optional arguments:
+  -h, --help            show this help message and exit
+  -b BAMFILE, --bamfile BAMFILE
+                        Sorted and indexed bam file containing the aligned
+                        reads. (default: None)
+  -o OUT_BED, --out_bed OUT_BED
+                        Bed file in which the results should be written.
+                        (default: None)
+```
-- 
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