allow mismatches in words

src/RadiantDB.cpp

 #include "RadiantDB.hpp"
+#include <bitset> 
 
 using namespace std;
 namespace fs = boost::filesystem;
@@ -52,6 +53,25 @@ RadiantDB::build(const fs::path &inPath, bool forward, const fs::path &outPath)
  	fout.close();*/
 }
 
+short
+char_diff(SuffixType val1, SuffixType val2)
+{
+	SuffixType val = val1^val2;
+	short counter = 0;
+	for (short i=0; i< 10; ++i)
+	{
+		for (short j=0; j<3; ++j)
+		{
+			short n = i*3+j;
+			if (val & (1<<n))
+			{
+				++counter;
+				break;
+			}
+		}
+	}
+	return counter;
+}
 
 short
 RadiantDB::getDomID(const PrefixType &prefix, const CodedSuffix &suffix, bool &position) const
@@ -72,6 +92,7 @@ RadiantDB::getDomID(const PrefixType &prefix, const CodedSuffix &suffix, bool &p
 			else
 			{
 				auto tmp = it2->accession;
+				auto x = it2->suffix.suffix;
 				if (it2 != it->second.begin())
 				{
 					--it2;
@@ -79,11 +100,22 @@ RadiantDB::getDomID(const PrefixType &prefix, const CodedSuffix &suffix, bool &p
 					{
 						position = it2->suffix.position;
 						return tmp;
-						//assignment.emplace(l-(multiplyer*j), std::pair<unsigned short, bool>(tmp, +it2->suffix.position));
+					}
+					else
+					{
+						short threshold = 2;
+						auto diff1 = char_diff(x, suffix.suffix);
+						auto diff2 = char_diff(it2->suffix.suffix, suffix.suffix);
+						if ((diff1 < diff2) && (diff1 <= threshold))
+							return tmp;
+						else
+							if (diff2 <= threshold)
+								return it2->accession;
 					}
 				}
 			}
 		}
+
 	}
 	return 0;
 }

src/makeRadiantDb.hpp

@@ -92,7 +92,7 @@ cleanSuffixe(D &db)
 		auto currIt = nextIt++;
 		while (nextIt != endIt)
 		{
-			if (((currIt->second==0) && (prevIt->second==0)) || ((currIt->second == prevIt->second) && (currIt->second == nextIt->second)) || ((currIt->second != prevIt->second) && (currIt->second != nextIt->second) && (prevIt->second != nextIt->second)))
+			if (((currIt->second==0) && (prevIt->second==0)) || ((currIt->second == prevIt->second) && (currIt->second == nextIt->second))) //|| ((currIt->second != prevIt->second) && (currIt->second != nextIt->second) && (prevIt->second != nextIt->second)))
 				currIt = db.erase(currIt);
 			else
 			{
@@ -103,7 +103,7 @@ cleanSuffixe(D &db)
 		}
 	}
 
-
+/*
 	// remove first/last suffix if differnt from next/previous
 	if (db.size() > 1)
 	{
@@ -124,7 +124,7 @@ cleanSuffixe(D &db)
 	// if only one element left its most liklely not very useful and can be removed
 	if (db.size() == 1)
 		db.clear();
-
+*/
 	// test cleaning
 	if (db.size() > 1)
 	{