Fixes to SWIG bindings

* Fix vector and namespace error in `nucmer.i`. Only seem to occur with
recent version of SWIG.`

swig/nucmer.i

@@ -1,8 +1,12 @@
 %{
+#include <vector>
+#include <string>
 #include <sstream>
 %}
 
-%template(LongVector) ::std::vector<long>;
+%include <std_vector.i>
+
+%template(LongVector) std::vector<long>;
 
 namespace mummer {
 
@@ -14,7 +18,7 @@ struct Alignment   {
   //-- An alignment object between two sequences A and B
   signed char         dirB;     // the query sequence direction
   long int            sA, sB, eA, eB; // the start in A, B and the end in A, B
-  ::std::vector<long> delta;    // the delta values, with NO zero at the end
+  std::vector<long>   delta;    // the delta values, with NO zero at the end
   long int            deltaApos; // sum of abs(deltas) - #of negative deltas
   long int            Errors, SimErrors, NonAlphas; // errors, similarity errors, nonalphas
   double identity() const;
@@ -29,9 +33,11 @@ struct Alignment   {
     }
   }
 };
-%template(AlignmentVector) ::std::vector<mummer::postnuc::Alignment>;
 } // namespace postnuc
+} // namespace mummer
+%template(AlignmentVector) ::std::vector<mummer::postnuc::Alignment>;
 
+namespace mummer {
 namespace nucmer {
 struct Options {
   mummer::nucmer::Options& mum();
@@ -77,9 +83,8 @@ struct Options {
 };
 %apply (const char* STRING, size_t LENGTH) { (const char* reference, size_t reference_len) };
 %apply (const char* STRING, size_t LENGTH) { (const char* query, size_t query_len) };
-::std::vector<mummer::postnuc::Alignment> align_sequences(const char* reference, size_t reference_len,
-                                                          const char* query, size_t query_len,
-                                                          mummer::nucmer::Options opts = mummer::nucmer::Options());
+std::vector<mummer::postnuc::Alignment> align_sequences(const char* reference, size_t reference_len,
+                                                        const char* query, size_t query_len,
+                                                        mummer::nucmer::Options opts = mummer::nucmer::Options());
 } // namespace nucmer
 } // namespace mummer
-

tests/Makefile.am

@@ -17,7 +17,7 @@ EXTRA_DIST += %D%/testsh.in
 EXTRA_DIST += %D%/test_md5
 
 # Build generate_sequences, used to generage pseudo-random sequences.
-%C%_generate_sequences_SOURCES = %D%/generate_sequences.cc
+%C%_generate_sequences_SOURCES = %D%/generate_sequences.cc %D%/gcc10_uniform_dist.hpp
 %C%_generate_sequences_CPPFLAGS = $(CPPFLAGS) -I%D%
 YAGGO_BUILT += %D%/generate_sequences_cmdline.hpp