For VCF scanning, output no-detected mutations to STDERR

Author: sfchen

src/common.h

@@ -1,7 +1,7 @@
 #ifndef COMMON_H
 #define COMMON_H
 
-#define MUTSCAN_VER "1.11.2"
+#define MUTSCAN_VER "1.12.0"
 
 typedef long int64;
 typedef unsigned long uint64;

src/globalsettings.cpp

@@ -4,4 +4,5 @@ bool GlobalSettings::markedOnlyForVCF = false;
 bool GlobalSettings::legacyMode = false;
 bool GlobalSettings::outputOriginalReads = true;
 bool GlobalSettings::standaloneHtml = false;
-int GlobalSettings::minReadSupport = 2;
+int GlobalSettings::minReadSupport = 2;
+bool GlobalSettings::processingVCF = false;

src/globalsettings.h

@@ -27,13 +27,17 @@ class GlobalSettings{
     inline static void setMinReadSupport(int val){
         minReadSupport = val;
     }
+    inline static void setProcessingVCF(bool flag){
+        processingVCF = flag;
+    }
 
 public:
     static bool markedOnlyForVCF;
     static bool legacyMode;
     static bool outputOriginalReads;
     static bool standaloneHtml;
     static int minReadSupport;
+    static bool processingVCF;
 };
 
 

src/main.cpp

@@ -71,6 +71,7 @@ int main(int argc, char* argv[]){
         check_file_valid(refFile);
     // if the mutation file is a vcf, then the reference should be provided
     if(ends_with(mutationFile, ".vcf") || ends_with(mutationFile, ".VCF") || ends_with(mutationFile, ".Vcf")){
+        GlobalSettings::setProcessingVCF(true);
         if(refFile == "") {
             cerr << "You should specify the reference fasta file by -r <ref.fa>, because your mutation file (-m) is a VCF"<<endl;
             exit(-1);

src/pescanner.cpp

@@ -298,6 +298,17 @@ void PairEndScanner::textReport(vector<Mutation>& mutationList, vector<Match*> *
     if(found == false) {
         cout << "MutScan didn't find any mutation" << endl;
     }
+    // if processing VCF, output those with no supporting reads found
+    if(GlobalSettings::processingVCF) {
+        cerr << "Following mutations are not detected" << endl;
+        for(int i=0;i<mutationList.size();i++){
+            vector<Match*> matches = mutationMatches[i];
+            if(matches.size()<GlobalSettings::minReadSupport){
+                Mutation m = mutationList[i];
+                cerr <<m.mChr << " " <<m.mName<<" "<<m.mLeft<<" "<<m.mCenter<<" "<<m.mRight <<endl;
+            }
+        }
+    }
 }
 
 void PairEndScanner::htmlReport(vector<Mutation>& mutationList, vector<Match*> *mutationMatches) {

src/sescanner.cpp

@@ -270,6 +270,17 @@ void SingleEndScanner::textReport(vector<Mutation>& mutationList, vector<Match*>
     if(found == false) {
         cout << "MutScan didn't find any mutation" << endl;
     }
+    // if processing VCF, output those with no supporting reads found
+    if(GlobalSettings::processingVCF) {
+        cerr << "Following mutations are not detected" << endl;
+        for(int i=0;i<mutationList.size();i++){
+            vector<Match*> matches = mutationMatches[i];
+            if(matches.size()<GlobalSettings::minReadSupport){
+                Mutation m = mutationList[i];
+                cerr <<m.mChr << " " <<m.mName<<" "<<m.mLeft<<" "<<m.mCenter<<" "<<m.mRight <<endl;
+            }
+        }
+    }
 }
 
 void SingleEndScanner::htmlReport(vector<Mutation>& mutationList, vector<Match*> *mutationMatches) {