From e079b5d7a53cb39052b13b172db9ab0451474b9c Mon Sep 17 00:00:00 2001
From: Yoann Dufresne <yoann.dufresne0@gmail.com>
Date: Mon, 6 Aug 2018 09:56:03 +0200
Subject: [PATCH] update readme

---
 README.md | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 456c13a..1f37d18 100644
--- a/README.md
+++ b/README.md
@@ -37,11 +37,10 @@ The binary file also contains a bloom filter corresponding to the selected kmers
 
 ### Matching alleles on sequences:
 ```bash
-	./bin/bpm match -alleles <alleles.fasta> -bin <alleles.bin> -sequences <sequences.fasta>
+	./bin/bpm match -bin <alleles.bin> -sequences <sequences.fasta>
 ```
 Arguments:  
-* **-a** or **-alleles**: A fasta file containing all the alleles that you want to search.
-* **-b** or **-bin**: A binary file containing one kmer of size 32 (to be computed on 64 bits) that represent each allele and the offset inside the sequence. This file also contains a bloom filter corresponding to the selected kmers.
+* **-b** or **-bin**: A binary file generated by the indexing part. This file contains relevant kmers, a bloom filter and the allele sequences.  
 * **-s** of **-sequences**: A fasta file containing the sequence(s) where you want to find the alleles.
 
 ### Tests:
-- 
GitLab