misc. changes

hts_utils.cpp

@@ -22,6 +22,7 @@
 */
 
 #include "hts_utils.h"
+#include "Rmath/Rmath.h"
 
 /********
  *General

hts_utils.h

@@ -34,7 +34,6 @@
 #include "htslib/faidx.h"
 #include "htslib/tbx.h"
 #include "htslib/hfile.h"
-#include "Rmath/Rmath.h"
 #include "utils.h"
 
 /**********

needle.cpp

@@ -25,6 +25,7 @@
 
 #include <algorithm>
 #include <iostream>
+#include <fstream>
 #include <string>
 
 NeedlemanWunsch::NeedlemanWunsch(bool debug)

normalize.cpp

@@ -332,7 +332,7 @@ class Igor : Program
     void print_options()
     {
         if (!print) return;
-
+    
         std::clog << "normalize v" << version << "\n";
         std::clog << "\n";
         std::clog << "options:     input VCF file                                  " << input_vcf_file << "\n";
@@ -395,6 +395,6 @@ bool normalize(int argc, char ** argv)
     igor.initialize();
     igor.normalize();
     igor.print_stats();
-
+    
     return igor.print;
 };

program.h

@@ -24,6 +24,8 @@
 #ifndef PROGRAM_H
 #define PROGRAM_H
 
+#include <fstream>
+#include <iostream>
 #include <typeinfo>
 #include "tclap/CmdLine.h"
 #include "tclap/Arg.h"
@@ -58,6 +60,7 @@ class Program
     public:
 
     std::string version;
+    std::ofstream out;
 
     /**
      * Process arguments.
@@ -90,15 +93,15 @@ class Program
      * @filter_string - comma delimited filters in a string
      * @n             - ensure that filters vector had n filters.
      *                  if there are less, just pad with empty strings
-     *                  if there are more, thrown an error. 
+     *                  if there are more, thrown an error.
      *                  if n is 0, ignore the previous contraints.
      * @pad           - if there are less than expected variant expressions
      *                      when true, the remaining filter expressions are padded with the empty string.
      *                      when false and only one expression is observed, the remaining filter expressions
      *                      duplicated with that filter expression.
      */
     void parse_filters(std::vector<std::string>& filters, std::string filter_string, int32_t n=0, bool pad=false);
-        
+
     /**
      * Parse a list of strings delimited by commas.
      *