make rolling hash mode as default, and use --legacy to support old mode

README.md

@@ -37,7 +37,7 @@ options:
   -h, --html        filename of html report, no html report if not specified (string [=])
   -t, --thread      worker thread number, default is 4 (int [=4])
   -k, --mark        when mutation file is a vcf file, --mark means only process the records with FILTER column is M
-  -f, --fast        use fast mode, with stricter matching
+  -l, --legacy      use legacy mode, usually much slower but may be able to find a little more reads in certain case
   -?, --help        print this message
 ```
 The plain text result, contains the detected mutations and their support reads, will be printed directly. You can use `>` to redirect output to a file, like:

src/globalsettings.cpp

@@ -1,4 +1,4 @@
 #include "globalsettings.h"
 
 bool GlobalSettings::markedOnlyForVCF = false;
-bool GlobalSettings::fastMode = false;
+bool GlobalSettings::legacyMode = false;

src/globalsettings.h

@@ -15,13 +15,13 @@ class GlobalSettings{
     inline static void setMarkedOnlyForVCF(bool flag){
         markedOnlyForVCF = flag;
     }
-    inline static void setFastMode(bool flag){
-        fastMode = flag;
+    inline static void setLegacyMode(bool flag){
+        legacyMode = flag;
     }
 
 public:
     static bool markedOnlyForVCF;
-    static bool fastMode;
+    static bool legacyMode;
 };
 
 

src/main.cpp

@@ -24,7 +24,7 @@ int main(int argc, char* argv[]){
     cmd.add<string>("html", 'h', "filename of html report, no html report if not specified", false, "");
     cmd.add<int>("thread", 't', "worker thread number, default is 4", false, 4);
     cmd.add("mark", 'k', "when mutation file is a vcf file, --mark means only process the records with FILTER column is M");
-    cmd.add("fast", 'f', "use fast mode, with stricter matching");
+    cmd.add("legacy", 'l', "use legacy mode, usually much slower but may be able to find a little more reads in certain case");
     cmd.parse_check(argc, argv);
     string r1file = cmd.get<string>("read1");
     string r2file = cmd.get<string>("read2");
@@ -41,8 +41,8 @@ int main(int argc, char* argv[]){
     bool markedOnlyForVCF = cmd.exist("mark");
     GlobalSettings::setMarkedOnlyForVCF(markedOnlyForVCF);
 
-    bool fastMode = cmd.exist("fast");
-    GlobalSettings::setFastMode(fastMode);
+    bool legacyMode = cmd.exist("legacy");
+    GlobalSettings::setLegacyMode(legacyMode);
 
     stringstream ss;
     for(int i=0;i<argc;i++){

src/pescanner.cpp

@@ -39,7 +39,7 @@ bool PairEndScanner::scan(){
     else
         mutationList = Mutation::parseBuiltIn();
 
-    if(GlobalSettings::fastMode){
+    if(!GlobalSettings::legacyMode){
         mRollingHash = new RollingHash();
         mRollingHash->initMutations(mutationList);
     }
@@ -130,7 +130,7 @@ bool PairEndScanner::scanPairEnd(ReadPairPack* pack){
 }
 
 bool PairEndScanner::scanRead(Read* r, ReadPair* originalPair, bool reversed) {
-    if(GlobalSettings::fastMode){
+    if(!GlobalSettings::legacyMode){
         vector<int> targets = mRollingHash->hitTargets(r->mSeq.mStr);
         for(int t=0; t<targets.size(); t++) {
             Match* match = mutationList[targets[t]].searchInRead(r);

src/sescanner.cpp

@@ -37,7 +37,7 @@ bool SingleEndScanner::scan(){
     else
         mutationList = Mutation::parseBuiltIn();
 
-    if(GlobalSettings::fastMode){
+    if(!GlobalSettings::legacyMode){
         mRollingHash = new RollingHash();
         mRollingHash->initMutations(mutationList);
     }
@@ -102,7 +102,7 @@ bool SingleEndScanner::scanSingleEnd(ReadPack* pack){
 }
 
 bool SingleEndScanner::scanRead(Read* r, Read* originalRead, bool reversed) {
-    if(GlobalSettings::fastMode){
+    if(!GlobalSettings::legacyMode){
         vector<int> targets = mRollingHash->hitTargets(r->mSeq.mStr);
         for(int t=0; t<targets.size(); t++) {
             Match* match = mutationList[targets[t]].searchInRead(r);