Corrects size_t error with GFF coordinates

src/definitions.h

@@ -81,7 +81,7 @@ typedef std::vector<std::vector<size_t>> NodeColourVector;
 //a pair of start and end coordinates for an ORF across a node
 typedef std::pair<unsigned int, unsigned int> indexPair;
 // pair that describes the contig locations of an ORF, 1-indexed for contig id (first) and locations within contig (second)
-typedef std::pair<size_t, std::pair<size_t, size_t>> ContigLoc;
+typedef std::pair<size_t, std::pair<int, int>> ContigLoc;
 // tuple holding ORF path ID, nodes traversed, node coordinates, coordinates in path, 5p and 3p coordinates
 typedef std::pair<std::vector<int>, std::vector<indexPair>> ORFCoords;
 // tuple containing a vector of nodeIDs, a vector of start,stop and length coordinates, length of an ORF, relative strand and score and strings for protein/DNA

src/match_string.cpp

@@ -120,7 +120,7 @@ std::pair<ContigLoc, bool> get_ORF_coords(const std::string& query,
     if (query_loc >= 0)
     {
         // go through contig_locs to determine in which contig sequence sits
-        for (int i = 0; i < contig_locs.size(); i++)
+        for (size_t i = 0; i < contig_locs.size(); i++)
         {
             if (query_loc < contig_locs.at(i))
             {
@@ -131,7 +131,7 @@ std::pair<ContigLoc, bool> get_ORF_coords(const std::string& query,
                 } else
                 {
                     // account for 1-indexing
-                    size_t relative_loc = ((query_loc - 1) - contig_locs.at(i - 1));
+                    int relative_loc = ((query_loc - 1) - contig_locs.at(i - 1));
                     contig_loc = {i + 1, {(relative_loc - 1), relative_loc + query.size()}};
                 }
                 break;