core/fasta.{h,cpp}: stores 'nb_sequences_max' and 'nth_only_sequence' in OnlineFasta

algo/core/fasta.cpp

@@ -107,14 +107,19 @@ const string& Fasta::sequence(int index) const{ return reads[index].sequence; }
 
 // OnlineFasta
 
-OnlineFasta::OnlineFasta(int extract_field, string extract_separator):
-  input(NULL), extract_field(extract_field), extract_separator(extract_separator){}
+OnlineFasta::OnlineFasta(int extract_field, string extract_separator,
+                         int nb_sequences_max, int only_nth_sequence):
+  input(NULL),
+  extract_field(extract_field), extract_separator(extract_separator),
+  nb_sequences_max(nb_sequences_max), only_nth_sequence(only_nth_sequence){}
 
 OnlineFasta::OnlineFasta(const string &input, 
-                         int extract_field, string extract_separator)
+                         int extract_field, string extract_separator,
+                         int nb_sequences_max, int only_nth_sequence)
   :input(new igzstream(input.c_str())),
   extract_field(extract_field), 
-  extract_separator(extract_separator)
+   extract_separator(extract_separator),
+   nb_sequences_max(nb_sequences_max), only_nth_sequence(only_nth_sequence)
 {
   if (this->input->fail()) {
     delete this->input;
@@ -127,9 +132,11 @@ OnlineFasta::OnlineFasta(const string &input,
 }
 
 OnlineFasta::OnlineFasta(istream &input, 
-                         int extract_field, string extract_separator)
+                         int extract_field, string extract_separator,
+                         int nb_sequences_max, int only_nth_sequence)
   :input(&input), extract_field(extract_field),
-  extract_separator(extract_separator)
+   extract_separator(extract_separator),
+   nb_sequences_max(nb_sequences_max), only_nth_sequence(only_nth_sequence)
 {
   input_allocated = false;
   init();

algo/core/fasta.h

@@ -97,12 +97,16 @@ class OnlineFasta {
   size_t line_nb;
   unsigned long long char_nb;
 
+  int nb_sequences_max;
+  int only_nth_sequence;
+
  public:
 
   /**
    * Default constructor
    */
-  OnlineFasta(int extract_field=0, string extract_separator="|");
+  OnlineFasta(int extract_field=0, string extract_separator="|",
+              int nb_sequences_max=NO_LIMIT_VALUE, int only_nth_sequence=1);
 
   /**
    * Open the file. No sequence is read at first.
@@ -112,10 +116,12 @@ class OnlineFasta {
    *         well-formed
    */
   OnlineFasta(const string &input, 
-              int extract_field=0, string extract_separator="|");
+              int extract_field=0, string extract_separator="|",
+              int nb_sequences_max=NO_LIMIT_VALUE, int only_nth_sequence=1);
 
   OnlineFasta(istream &input, 
-              int extract_field=0, string extract_separator="|");
+              int extract_field=0, string extract_separator="|",
+              int nb_sequences_max=NO_LIMIT_VALUE, int only_nth_sequence=1);
 
   ~OnlineFasta();