better and more informative output

Author: sfchen

src/common.h

@@ -1,7 +1,7 @@
 #ifndef COMMON_H
 #define COMMON_H
 
-#define MUTSCAN_VER "1.11.0"
+#define MUTSCAN_VER "1.11.1"
 
 typedef long int64;
 typedef unsigned long uint64;

src/htmlreporter.cpp

@@ -30,12 +30,13 @@ void HtmlReporter::printHelper() {
         mFile << "<div id='logo' style='text-align:center;'> <span style='font-size:30px;font-weight:bold;'> MutScan </span> <span style='font-size:20px;'> " << MUTSCAN_VER << " Report </span> </div>";
     mFile << "<div style='text-align:center;font-size:13;color:#0366d6;padding-top:5px;'><a href='javascript:window.print();'>Print</a></div>";
     mFile << "<div id='helper'><p>Helpful tips:</p><ul>";
-    mFile << "<li> Base color indicates quality: <font color='#78C6B9'>extremely high (Q40+)</font>, <font color='#33BBE2'>high (Q30~Q39) </font>, <font color='#666666'>moderate (Q20~Q29)</font>, <font color='#E99E5B'>low (Q15~Q19)</font>, <font color='#FF0000'>extremely low (0~Q14)</font> </li>";
-    mFile << "<li> Move mouse over the base, it will show the quality value</li>";
+    mFile << "<li> Mutation point is in the center of the table.</li>";
+    mFile << "<li> Base color indicates quality: <font color='#78C6B9'>extremely high (Q40+)</font>, <font color='#33BBE2'>high (Q30~Q39) </font>, <font color='#666666'>moderate (Q20~Q29)</font>, <font color='#E99E5B'>low (Q15~Q19)</font>, <font color='#FF0000'>extremely low (0~Q14).</font> </li>";
+    mFile << "<li> Move mouse over the base, it will show the quality value.</li>";
     if(GlobalSettings::outputOriginalReads)
-        mFile << "<li> Click on any row, the original read/pair will be displayed</li>";
-    mFile << "<li> In first column, <i>d</i> means the edit distance of match, and --> means forward, <-- means reverse </li>";
-    mFile << "<li> For pair-end sequencing, MutScan tries to merge each pair, and the overlapped bases will be assigned higher qualities </li>";
+        mFile << "<li> Click on any row, the original read/pair will be displayed.</li>";
+    mFile << "<li> In first column, <i>d</i> means the edit distance of match, and --> means forward, <-- means reverse. </li>";
+    mFile << "<li> For pair-end sequencing, MutScan tries to merge each pair, and the overlapped bases will be assigned higher qualities. </li>";
     mFile << "</ul></div>";
 }
 

src/multihtmlreporter.cpp

@@ -64,26 +64,33 @@ void MultiHtmlReporter::printMainPage() {
 }
 
 void MultiHtmlReporter::printAllChromosomeLink(ofstream& file) {
+    bool found = false;
     map<string, int>::iterator iter;
     file << "<ul id='menu'>";
     file << "<div style='font-size:12px;padding-top:20px;text-align:left;color:#aaaaaa'>Mutations found of all chromosomes:</div>";
     for(int m=0; m<mMutationList.size(); m++) {
         vector<Match*> matches = mMutationMatches[m];
         if(matches.size()>=GlobalSettings::minReadSupport) {
+            found = true;
             string chr = mMutationList[m].mChr;
             string filename = chr + "/" + to_string(m) + ".html";
             file << "<li class='menu_item'><a href='" << filename << "'>" << mMutationList[m].mName;
             file<< " (" << matches.size() << " reads support, " << Match::countUnique(matches) << " unique)" 
             << " </a></li>";
         }
     }
+    if(!found) {
+        file << "<span style='size:28px;font-weight:bold;color:blue;line-height:30px;'>MutScan didn't find any mutation</span>";
+    }
     file << "</ul>";
 }
 
 void MultiHtmlReporter::printChrLink(ofstream& file, string chr) {
+    bool found = false;
     for(int m=0; m<mMutationList.size(); m++) {
         vector<Match*> matches = mMutationMatches[m];
         if(matches.size()>=GlobalSettings::minReadSupport) {
+            found = true;
             if(chr == mMutationList[m].mChr) {
                 string filename = chr + "/" + to_string(m) + ".html";
                 file << "<li class='menu_item'><a href='" << filename << "'>" << mMutationList[m].mName;
@@ -92,6 +99,9 @@ void MultiHtmlReporter::printChrLink(ofstream& file, string chr) {
             }
         }
     }
+    if(!found) {
+        file << "<span style='size:28px;font-weight:bold;color:blue;line-height:30px;'>MutScan didn't find any mutation</span>";
+    }
 }
 
 void MultiHtmlReporter::printMutationHtml() {

src/mutation.cpp

@@ -263,7 +263,6 @@ vector<Mutation> Mutation::parseVcf(string vcfFile, string refFile) {
         int lengthDiff = abs((int)v.ref.length() - (int)v.alt.length());
         if(lengthDiff>=1 && lengthDiff<=2 )
             mut.setSmallIndel(true);
-        cerr << name << ", " << left << ", " << center << ", " << right << ", " << chrom << endl;
         mutations.push_back(mut);
     }
     if(mutations.size() <= 0){

src/pescanner.cpp

@@ -282,9 +282,11 @@ void PairEndScanner::consumerTask()
 
 void PairEndScanner::textReport(vector<Mutation>& mutationList, vector<Match*> *mutationMatches) {
     //output result
+    bool found = false;
     for(int i=0;i<mutationList.size();i++){
         vector<Match*> matches = mutationMatches[i];
         if(matches.size()>=GlobalSettings::minReadSupport){
+            found = true;
             cout<<endl<<"---------------"<<endl;
             mutationList[i].print();
             for(int m=0; m<matches.size(); m++){
@@ -293,6 +295,9 @@ void PairEndScanner::textReport(vector<Mutation>& mutationList, vector<Match*> *
             }
         }
     }
+    if(found == false) {
+        cout << "MutScan didn't find any mutation" << endl;
+    }
 }
 
 void PairEndScanner::htmlReport(vector<Mutation>& mutationList, vector<Match*> *mutationMatches) {

src/sescanner.cpp

@@ -254,9 +254,11 @@ void SingleEndScanner::consumerTask()
 
 void SingleEndScanner::textReport(vector<Mutation>& mutationList, vector<Match*> *mutationMatches) {
     //output result
+    bool found = false;
     for(int i=0;i<mutationList.size();i++){
         vector<Match*> matches = mutationMatches[i];
         if(matches.size()>=GlobalSettings::minReadSupport){
+            found = true;
             cout<<endl<<"---------------"<<endl;
             mutationList[i].print();
             for(int m=0; m<matches.size(); m++){
@@ -265,6 +267,9 @@ void SingleEndScanner::textReport(vector<Mutation>& mutationList, vector<Match*>
             }
         }
     }
+    if(found == false) {
+        cout << "MutScan didn't find any mutation" << endl;
+    }
 }
 
 void SingleEndScanner::htmlReport(vector<Mutation>& mutationList, vector<Match*> *mutationMatches) {