diff --git a/balanced.go b/balanced.go
index 7cf247e..073e39d 100644
--- a/balanced.go
+++ b/balanced.go
@@ -1,4 +1,3 @@
-
 // BalancedGo - A research prototype to compute structural decompositions of Conjunctive Queries and CSPs
 // via the use of Balanced Separators with a focus on parallelism using the programming language Go.
 //
@@ -32,7 +31,7 @@ import (
 	"time"
 
 	jsoniter "github.com/json-iterator/go"
-	
+
 	algo "github.com/cem-okulmus/BalancedGo/algorithms"
 	"github.com/cem-okulmus/BalancedGo/lib"
 )
@@ -130,7 +129,6 @@ func outputStanza(algorithm string, decomp Decomp, times []labelTime, graph Grap
 	}
 }
 
-
 func main() {
 
 	// ==============================================
diff --git a/lib/graph.go b/lib/graph.go
index ab1164f..743271a 100644
--- a/lib/graph.go
+++ b/lib/graph.go
@@ -108,9 +108,11 @@ func (g Graph) GetComponents(sep Edges, vertices map[int]*disjoint.Element) ([]G
 	var compsSp = make(map[*disjoint.Element][]Edges)
 
 	balsepVert := sep.Vertices()
-	balSepCache := make(map[int]bool, len(balsepVert))
+	// var balSepCache
+
+	balSepCache := make([]bool, encode)
 	for _, v := range balsepVert {
-		balSepCache[v] = true
+		balSepCache[v-1] = true
 	}
 
 	//  Set up the disjoint sets for each node
@@ -125,11 +127,11 @@ func (g Graph) GetComponents(sep Edges, vertices map[int]*disjoint.Element) ([]G
 	// Merge together the connected components
 	for k := range g.Edges.Slice() {
 		for i := 0; i < len(g.Edges.Slice()[k].Vertices); i++ {
-			if balSepCache[g.Edges.Slice()[k].Vertices[i]] {
+			if balSepCache[g.Edges.Slice()[k].Vertices[i]-1] {
 				continue
 			}
 			for j := i + 1; j < len(g.Edges.Slice()[k].Vertices); j++ {
-				if balSepCache[g.Edges.Slice()[k].Vertices[j]] {
+				if balSepCache[g.Edges.Slice()[k].Vertices[j]-1] {
 					continue
 				}
 
@@ -142,11 +144,11 @@ func (g Graph) GetComponents(sep Edges, vertices map[int]*disjoint.Element) ([]G
 
 	for k := range g.Special {
 		for i := 0; i < len(g.Special[k].Vertices())-1; i++ {
-			if balSepCache[g.Special[k].Vertices()[i]] {
+			if balSepCache[g.Special[k].Vertices()[i]-1] {
 				continue
 			}
 			for j := i + 1; j < len(g.Special[k].Vertices()); j++ {
-				if balSepCache[g.Special[k].Vertices()[j]] {
+				if balSepCache[g.Special[k].Vertices()[j]-1] {
 					continue
 				}
 				disjoint.Union(vertices[g.Special[k].Vertices()[i]], vertices[g.Special[k].Vertices()[j]])
@@ -163,7 +165,7 @@ func (g Graph) GetComponents(sep Edges, vertices map[int]*disjoint.Element) ([]G
 		var vertexRep int
 		found := false
 		for _, v := range g.Edges.Slice()[i].Vertices {
-			if balSepCache[v] {
+			if balSepCache[v-1] {
 				continue
 			}
 			vertexRep = v
@@ -190,7 +192,7 @@ func (g Graph) GetComponents(sep Edges, vertices map[int]*disjoint.Element) ([]G
 		var vertexRep int
 		found := false
 		for _, v := range g.Special[i].Vertices() {
-			if balSepCache[v] {
+			if balSepCache[v-1] {
 				continue
 			}
 			vertexRep = v
diff --git a/lib/parser.go b/lib/parser.go
index 5e3964f..8ca0d95 100644
--- a/lib/parser.go
+++ b/lib/parser.go
@@ -10,7 +10,7 @@ import (
 	"sync"
 
 	jsoniter "github.com/json-iterator/go"
-	
+
 	"github.com/alecthomas/participle"
 	"github.com/alecthomas/participle/lexer"
 	"github.com/alecthomas/participle/lexer/ebnf"
@@ -33,6 +33,14 @@ type ParseGraph struct {
 	Encoding map[string]int
 }
 
+// TransparentEncoding will overwrite the encoding map in order to print out the exact underlying integer encoding.
+// Needs to be called after GetGraph to be effective.
+func TransparentEncoding() {
+	for i := 0; i < encode; i++ {
+		m[i] = strconv.Itoa(i)
+	}
+}
+
 // GetGraph parses a string in HyperBench format into a graph
 func GetGraph(s string) (Graph, ParseGraph) {
 
@@ -61,34 +69,47 @@ func GetGraph(s string) (Graph, ParseGraph) {
 	}
 	encoding := make(map[int]string)
 	encode = 1 // initialize to 1
-
 	pgraph.Encoding = make(map[string]int)
-	//fix first numbers for edge names
+
+	// first fix the encoding, starting with vertices
+	for _, e := range pgraph.Edges {
+		for _, n := range e.Vertices {
+			_, ok := pgraph.Encoding[n]
+			if !ok {
+				pgraph.Encoding[n] = encode
+				encoding[encode] = n
+				encode++
+			}
+		}
+
+	}
 	for _, e := range pgraph.Edges {
 		_, ok := pgraph.Encoding[e.Name]
 		if ok {
-			log.Panicln("Edge names not unique, not a vald hypergraph!")
+			log.Panicln("Edge names not unique, not a valid hypergraph!")
 		}
 
 		pgraph.Encoding[e.Name] = encode
 		encoding[encode] = e.Name
 		encode++
 	}
+
+	// now create the edges
 	for _, e := range pgraph.Edges {
 		var outputEdges []int
 		for _, n := range e.Vertices {
 			i, ok := pgraph.Encoding[n]
-			if ok {
-				outputEdges = append(outputEdges, i)
-			} else {
-				pgraph.Encoding[n] = encode
-				encoding[encode] = n
-				outputEdges = append(outputEdges, encode)
-				encode++
+			if !ok {
+				log.Panicln("Vertex not properly encoded, something went wrong with the parsing process!")
 			}
+			outputEdges = append(outputEdges, i)
+
 		}
 		edges = append(edges, Edge{Name: pgraph.Encoding[e.Name], Vertices: outputEdges})
 	}
+
+	encode = encode + len(pgraph.Edges)
+
 	output.Edges = NewEdges(edges)
 	m = encoding
 	return output, pgraph
@@ -267,7 +288,6 @@ func (n Node) IntoJson() NodeJson {
 		output.Children = append(output.Children, n.Children[i].IntoJson())
 	}
 
-
 	return output
 }
 
@@ -295,7 +315,6 @@ func (n NodeJson) IntoNode(graph Graph, encoding map[string]int) Node {
 	}
 	output.Cover = NewEdges(cover)
 
-
 	for i := range n.Children {
 		output.Children = append(output.Children, n.Children[i].IntoNode(graph, encoding))
 	}