--- a
+++ b/neusomatic/include/SeqanUtils.h
@@ -0,0 +1,119 @@
+#ifndef SEQAN_UTILS_HPP
+#define SEQAN_UTILS_HPP
+
+#include <vector>
+#include<seqan/seq_io.h>
+#include<seqan/misc/interval_tree.h>
+#include<seqan/find.h>
+
+namespace neusomatic{ namespace bio{
+
+template<typename Base>
+std::string Base2String(const Base& base, const std::string& gap_symbol){
+
+    //std::cout<<static_cast<unsigned char>(base)<<" :static cast: ";
+    //std::cout<<(unsigned)seqan::ordValue(base)<<std::endl;
+    
+    switch((unsigned)seqan::ordValue(base))
+    {
+        case 0: return "A";
+        case 1: return "C";
+        case 2: return "G";
+        case 3: return "T";
+        default: return gap_symbol;
+    }
+    //should never reach here
+    return "";
+
+}
+
+template<>
+std::string Base2String<char>(const char& base, const std::string& gap_symbol) {
+  switch(base) {
+    case 'a':
+    case 'A': 
+    case 0:
+      return "A";
+
+    case 'c':
+    case 'C':
+    case 1:
+      return "C";
+
+    case 'g':
+    case 'G':
+    case 2:
+      return "G";
+    case 't':
+    case 'T':
+    case 3:
+      return "T";
+    default:
+      return gap_symbol;
+  }
+}
+
+template<typename Itr>
+std::string to_string(Itr b, Itr e, const std::string& gap_symbol = "N"){
+  std::string result;
+  auto it = b;
+  for(; it < e; ++it){
+    result += Base2String(*it, gap_symbol);
+  }
+  return result;
+}
+
+inline std::string to_string(const seqan::Dna5String& seq, const std::string& gap_symbol = "N"){
+  std::string result;
+  for (unsigned int i = 0; i < seqan::length(seq); ++i) {
+     result += Base2String(seq[i], gap_symbol); 
+  }
+  return result;
+}
+
+template<typename TInterval>
+inline decltype(auto) ToSeqanIntervals(const std::vector<TInterval>& invs){ 
+
+  typedef seqan::IntervalAndCargo<int, TInterval> TIntervalAndCargo;
+  std::vector<TIntervalAndCargo> seqan_intervals; 
+  for (auto it = invs.cbegin(); it != invs.cend(); ++it) {
+    TIntervalAndCargo i(it->left(), it->right(), *it);
+    seqan_intervals.push_back(i);
+  }
+  return seqan_intervals;
+}
+
+inline std::vector<seqan::CharString> SeqanSplit(seqan::CharString target, std::string splitter) {
+  /*
+    Return a vec of size 1 containing the intact target if splitter is not found in the target. 
+  */
+  if (seqan::length(target) == 0 || seqan::length(splitter) == 0) {
+    throw std::runtime_error("Invalid string and pattern to split.");
+  }
+  using TPos = typename seqan::Position<seqan::CharString>::Type;
+
+  std::vector<seqan::CharString> result;
+  seqan::Finder<seqan::CharString> finder(target);
+  seqan::Pattern<seqan::CharString, seqan::Horspool> pattern(splitter);
+  std::vector<std::pair<TPos, TPos>> searches;
+  while (seqan::find(finder, pattern)) {
+    searches.emplace_back(seqan::beginPosition(finder), seqan::endPosition(finder));
+  }
+
+  TPos lastp = 0;
+  for (auto const& p: searches) {
+    seqan::CharString unit = seqan::infix(target, lastp, p.first);
+    if (!seqan::empty(unit)) result.push_back(unit);
+    lastp = p.second;
+  }
+  if (lastp < seqan::length(target) - 1) {
+    seqan::CharString unit = seqan::infix(target, lastp, seqan::length(target));
+    result.push_back(unit);
+  }
+  return result;
+}
+
+}// namespace neusomatic
+}// namespace bio
+
+#endif /* SEQAN_UTILS_HPP */