updated readme; removed the instruction to run the intersect etc, now its done automatically

README.md

 # GrAnnoT
 
-GrAnnoT is an annotation transfer tool for pangenome graphs. It can transfer genome annotations to a pangenome graph containing the genome, and also transfer the pangenome graph's annotations on the genomes it contains. 
+GrAnnoT is an annotation transfer tool for pangenome graphs. It can transfer genome annotations to a pangenome graph containing the genome, and also transfer the pangenome graph's annotations on the genomes it contains. It also outputs complementary information such as the alignments of the transfered genes, or a presence-absence matrix.
+
 This project is young and in development, some errors will be corrected, improvements will be made and new features will appear in the near future.
 
 ## Usage
+
 GrAnnoT requires the graph to be in GFA format with W-lines that describe the walks of the input genomes. For example minigraph-cactus gives that kind of output. 
 
-You first need to extract from the GFA the positions of the segments of the graph on the genomes it contains. For this you need to run the script getSegmentsCoordinates.py with the GFA file as input. 
-Then you will need to run the following command using the segments coordinates on the reference genome (for the annotation), and the annotation file in GFF/GTF format : 
-```
-bedtools intersect -wo -a segmentsCoordinatesOnReferenceGenome.bed -b annotationFile.gff > intersectFile.bed
-```
-
-You can then finally run GrAnnoT itself via the script main.py with the following arguments : 
-- intersect file
-- GFA file  with walks
-- bed file with coordinates of the segments on the target genome
-- the name of the target genome path in the GFA file.
-
-It will output the following files :
-- a GFF and a GAF file with the annotation of the graph
-- the GFF file with the annotation of the target genome
-- a text file with the details of the variations within the annotated regions.
+It also takes as input an annotation file in GFF format, and the name of the genome related to the annotation (must be contained in the walks of the graph that correspond to this genome).
+
+To run GrAnnoT you need to execute the file 'main.py'. The option '-h' will then descripe the inputs, outputs, and options available.