fix trim.seqs / qualscores bug

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 865f078d99ea2504c19c97befe28ead0d6a2254e..78246b671e9d7f5b510565d0cb4650795fb4482f 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -1625,7 +1625,7 @@
                        attributes = {
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
-                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
+                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
                        compatibilityVersion = "Xcode 3.1";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
@@ -2049,7 +2049,7 @@
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
-               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB928A08733DD80010E9CD /* Debug */,

diff --git a/qualityscores.cpp b/qualityscores.cpp
index e26a4ffc74c54cba4c8a7ac9da4f0ba3a6ed6e5c..0641d3b7bf4ed8abc588467b946d0678766c5fb0 100644 (file)
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -44,7 +44,6 @@ QualityScores::QualityScores(ifstream& qFile){
                else{
                        seqName = seqName.substr(1);
                }
-               cout << seqName << endl;
                string qScoreString = m->getline(qFile);
                while(qFile.peek() != '>' && qFile.peek() != EOF){
                        qScoreString += ' ' + m->getline(qFile);
@@ -56,7 +55,6 @@ QualityScores::QualityScores(ifstream& qFile){
                        if (m->control_pressed) { break; }
                        qScoreStringStream >> score;
                        qScores.push_back(score);
-                       cout << score << '\t' << count << endl;
                        count++;
                }
                qScores.pop_back();

diff --git a/qualityscores.h b/qualityscores.h
index 4453145f690b9a8be8b8da1bbf78fd5626d5fa71..e522938ec91895aceb4cf11a4b7acd9ec2239822 100644 (file)
--- a/qualityscores.h
+++ b/qualityscores.h
@@ -22,6 +22,7 @@ public:
        QualityScores();
        QualityScores(ifstream&);
        string getName();
+       
        vector<int> getQualityScores() { return qScores; }
        void printQScores(ofstream&);
        void trimQScores(int, int);

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6aea7d827b5a3acab51a330958fb62bacaaa16d0..49aca824ea46fb18c5845e4caa5bab0aca5db305 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -406,10 +406,10 @@ int TrimSeqsCommand::execute(){
                //output group counts
                m->mothurOutEndLine();
                int total = 0;
-               for (int i = 0; i < barcodeNameVector.size(); i++) {
-                       if ((barcodeNameVector[i] != "") && (groupCounts[i] != 0)) { total += groupCounts[i]; m->mothurOut("Group " + barcodeNameVector[i] + " contains " + toString(groupCounts[i]) + " sequences."); m->mothurOutEndLine(); }
-               }
-               if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
+//             for (int i = 0; i < barcodeNameVector.size(); i++) {
+//                     if ((barcodeNameVector[i] != "") && (groupCounts[i] != 0)) { total += groupCounts[i]; m->mothurOut("Group " + barcodeNameVector[i] + " contains " + toString(groupCounts[i]) + " sequences."); m->mothurOutEndLine(); }
+//             }
+//             if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
                
                        if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } return 0;     }