update READMe

Author: NedaTavakoli

README.md

@@ -19,11 +19,6 @@ The project has the following folder structure:
 ```
 ```bash
 .
-├── .vscode
-│   ├── configurationCache.log
-│   ├── dryrun.log
-│   ├── settings.json
-│   └── targets.log
 ├── VF
 │   ├── examples
 │   │   └── README.md
@@ -104,7 +99,23 @@ The project has the following folder structure:
 │   ├── README.md
 │   └── dependencies.sh
 ├── .DS_Store
-├── README.md
-└── tree.txt
+└── README.md
 
-```
+```
+
+## Framework Overview
+
+## Variant Filtering (VF)
+VF is a prototype software implementation of our algorithms for variant filtering in variation graphs for the problems 1 to 4.
+
+## VF_Experiments
+VF_Experiments is a framework to establish a benchmark for datasets and tools needed to evaluate the VF experiments and the impact of read-to-graph mappers.
+
+## Havg (Haplotype-annotated Variation Graph)
+Havg is used to create a variation graph that corresponds to each chromosome, annotated with a list of haplotypes per edge when the graph only contains SNP variants. This annotated graph is then used in solving problems 5 and 6.
+
+## hg (Haplotype-aware Graphs)
+This repository constructs an ILP solution for haplotype-aware variant selection for genome graphs under Hamming distance for solving problems 5 and 6.
+
+## hged (Haplotype-aware Edit Distance)
+This repository constructs an ILP solution for haplotype-aware variant selection for genome graphs under Hamming distance for solving problems 7 and 8.