Merge branch 'deltaEncoding' of...

Merge branch 'deltaEncoding' of https://gitlab.cristal.univ-lille.fr/lvandamm/indexkmertoread into deltaEncoding

README.md

@@ -3,8 +3,10 @@
 ## Compilation
 
 git clone https://gitlab.cristal.univ-lille.fr/lvandamm/indexkmertoread
+git submodule init
+git submodule update
 
-make
+make -j
 
 ## Launch 
 
@@ -12,6 +14,8 @@ make
 
 - Fasta file (reads) : path to the fasta file containing reads
 - K-mer length
+- BitVector Size
+- Compressed or not (-c or -nc)
 
 Used to create the index.
 
@@ -22,13 +26,13 @@ Used to create the index.
 - Fasta file (containing a list of sequences, to search and count all the kmers in the index)
 
 <code>
-./index [Fasta file (reads)] [Kmer length] -k [Fasta file (1 kmer)] -s [Fasta file (1 sequence)] -f [Fasta file (several sequences)]
+./index [Fasta file (reads)] [Kmer length] [Bitvector Size] [Compressed (-c or -nc)] -k [Fasta file (1 kmer)] -s [Fasta file (1 sequence)] -f [Fasta file (several sequences)]
 </code>
 
-<br/>Example :
+<br/>Example to create the index :
 
 <code>
-./index input_files/phage_5kb_10percent.fa 15 -k input_files/kmer.fa -s input_files/sequence.fa
+make clean && make -j && ./index input_files/phage/phage_hifi.fa 15 26 -c
 </code>
 
 <br/>