editdist mappability (deprecated)

src/dicey.cpp

@@ -17,7 +17,6 @@
 #include "hunter.h"
 #include "silica.h"
 #include "mapbam.h"
-#include "mappability.h"
 #include "padlock.h"
 
 using namespace dicey;
@@ -37,7 +36,6 @@ displayUsage() {
   std::cout << "Mappability:" << std::endl;
   std::cout << std::endl;
   std::cout << "    chop         chop reference into paired-end / single-end reads" << std::endl;
-  std::cout << "    mappability  mappability using read's edit distance (slow)" << std::endl;
   std::cout << "    mappability2 parse BAM from mapped chopped reads (requires chop + map before)" << std::endl;
   std::cout << "    blacklist    blacklist certain regions in mappability map" << std::endl;
   std::cout << std::endl;
@@ -82,9 +80,6 @@ int main(int argc, char **argv) {
   else if ((std::string(argv[1]) == "search")) {
     return silica(argc-1,argv+1);
   }
-  else if ((std::string(argv[1]) == "mappability")) {
-    return mappability(argc-1,argv+1);
-  }
   else if ((std::string(argv[1]) == "mappability2")) {
     return mapbam(argc-1,argv+1);
   }