initial

src/naive_search.cpp

 #include <sstream>
 
+// #include <seqan/sequence.h>
+// #include <seqan/stream.h>
+
 #include <seqan3/alphabet/nucleotide/dna5.hpp>
 #include <seqan3/argument_parser/all.hpp>
 #include <seqan3/core/debug_stream.hpp>
@@ -7,9 +10,38 @@
 #include <seqan3/search/fm_index/fm_index.hpp>
 #include <seqan3/search/search.hpp>
 
+#include <iostream>
+#include <string>
+using namespace std;
+
 // prints out all occurences of query inside of ref
 void findOccurences(std::vector<seqan3::dna5> const& ref, std::vector<seqan3::dna5> const& query) {
     //!TODO ImplementMe
+    int m = query.vector::size();
+    int total_count = 0;
+    std::vector<int> occurances;  // number of occurences of pattern in referenc
+
+    for(int i=0; i<ref.vector::size(); i++){
+        
+        for(int j=0; j<m; j++){
+            if(ref.at(i+j) != query.at(j)){
+                break;
+            }else if(j=m-1)
+            {
+                std::cout << "Infix found at position: " << i <<std::endl;
+                // std::cout << i << std::endl;
+                // std::cout << "\n" << std::endl;
+                total_count+=1;
+                
+            }
+            
+           
+        }
+        if(total_count> 10){
+            break;
+        }
+
+	}
 }
 
 int main(int argc, char const* const* argv) {