algo: Remove compilation warnings due to signed/unsigned comparisons

algo/cgi/similarity.cpp

@@ -117,7 +117,7 @@ int main(int argc, char* argv[])
       reads = fa.getAll();
       
       list<string> labels;
-      for (int i=0; i < reads.size(); i++) {
+      for (size_t i=0; i < reads.size(); i++) {
         labels.push_back(fa.label(i));
       }
       

algo/core/fasta.cpp

@@ -39,7 +39,7 @@ unsigned long long filesize(const char* filename)
     return in.tellg();
 }
 
-void Fasta::init(int extract_field, string extract_separator, int mark_pos)
+void Fasta::init(int extract_field, string extract_separator, size_t mark_pos)
 {
   this -> extract_field = extract_field ;
   this -> extract_separator = extract_separator ; 
@@ -108,7 +108,7 @@ void Fasta::add(Sequence seq) {
 }
 
 int Fasta::size() const{ return (int)reads.size(); }
-int Fasta::totalSize() const { return total_size ; }
+size_t Fasta::totalSize() const { return total_size ; }
 
 list<Sequence> Fasta::getAll() const {
   list<Sequence> reads;
@@ -235,7 +235,7 @@ void OnlineFasta::addLineToCurrentSequence(string line)
       current.sequence += c;
 
       if (mark_pos) {
-        if (current.sequence.length() + current_gaps == mark_pos)
+        if ((int) current.sequence.length() + current_gaps == mark_pos)
           current.marked_pos = current.sequence.length();
       }
     }

algo/core/fasta.h

@@ -17,7 +17,7 @@ typedef struct read_t
   string sequence; // Sequence: original string representation
   string quality;
   int*   seq;      // Sequence: seq representation
-  int    marked_pos; // Some marked position in the sequence
+  size_t    marked_pos; // Some marked position in the sequence
 } Sequence;
 
 typedef enum {
@@ -32,9 +32,9 @@ unsigned long long filesize(const char* filename);
 
 class Fasta
 {
-        void init(int extract_field, string extract_separator, int mark_pos=0);
+        void init(int extract_field, string extract_separator, size_t mark_pos=0);
 
-        int total_size;
+        size_t total_size;
         int extract_field;
         int mark_pos;
 	string extract_separator;
@@ -59,7 +59,7 @@ public:
         string name;
         string basename;
 	int size() const;
-        int totalSize() const;
+        size_t totalSize() const;
 
         /**
          * Get all the sequences from the FASTA file

algo/core/kmerstore.h

@@ -44,7 +44,7 @@ protected:
   int s; // span of the seed (s >= k)
   string seed ;
   size_t nb_kmers_inserted;
-  int max_size_indexing;
+  size_t max_size_indexing;
 
 public:
 

algo/core/segment.cpp

@@ -103,7 +103,7 @@ string AlignBox::refToString(int from, int to) {
     if (i == start)
       s << color;
 
-    if (j > 0 && j <= ref.size())
+    if (j > 0 && (size_t)j <= ref.size())
       s << ref[j-1] ;
     else
       s << ".";
@@ -684,7 +684,7 @@ string check_and_resolve_overlap(string seq, int seq_begin, int seq_end,
       int trim_l[overlap+1];
       int trim_r[overlap+1];
 
-      for(int i=0; i<=overlap; i++) {
+      for(size_t i=0; i<=(size_t)overlap; i++) {
         score_l[i] = i < seq_left.size()  ? dp_l.best_score_on_i(seq_left.size()  - i, trim_l + i) : MINUS_INF ;
         score_r[i] = i < seq_right.size() ? dp_r.best_score_on_i(seq_right.size() - i, trim_r + i) : MINUS_INF ;
       }

algo/core/tools.cpp

@@ -139,7 +139,7 @@ int dna_to_int(const string &word, int size) {
 string nuc_to_aa(const string &word) {
   string aa;
   int index_word = 0;
-  int i = 0;
+  size_t i = 0;
 
   for (; i < word.length() ; i++) {
     index_word = (index_word << 2) | nuc_to_int(word[i]);