Re-activate pre-scoring = 1 if no reduction is used

Author: sarahet

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "seqan"]
 	path = include/seqan
-	url = git://github.com/seqan/seqan.git
+	url = ../../seqan/seqan.git

src/search_options.hpp

@@ -835,10 +835,9 @@ parseCommandLine(LambdaOptions & options, int argc, char const ** argv)
     // TODO always prescore 1
     getOptionValue(options.preScoring, parser, "pre-scoring");
 
-    //TODO reactivate
-//     if ((!isSet(parser, "pre-scoring")) &&
-//         (options.alphReduction == 0))
-//         options.preScoring = 1;
+    if ((!isSet(parser, "pre-scoring")) &&
+        (options.reducedAlphabet == options.transAlphabet))
+        options.preScoring = 1;
 
     getOptionValue(options.preScoringThresh, parser, "pre-scoring-threshold");
 //     if (options.preScoring == 0)

src/shared_misc.hpp

@@ -26,7 +26,10 @@
 #include <locale>
 #include <type_traits>
 #include <forward_list>
-#include <sys/sysctl.h>
+
+#if __has_include(<sys/sysctl.h>)
+    #include <sys/sysctl.h>
+#endif
 
 #include <seqan/basic.h>
 #include <seqan/sequence.h>