From 6da6af5c7f43f9f4f602d224af447805fb01c46c Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Mon, 7 Mar 2011 22:39:32 +0000
Subject: [PATCH] fix trim.seqs / qualscores bug

---
 Mothur.xcodeproj/project.pbxproj | 4 ++--
 qualityscores.cpp                | 2 --
 qualityscores.h                  | 1 +
 trimseqscommand.cpp              | 8 ++++----
 4 files changed, 7 insertions(+), 8 deletions(-)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 865f078..78246b6 100644
--- 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 e26a4ff..0641d3b 100644
--- 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 4453145..e522938 100644
--- 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 6aea7d8..49aca82 100644
--- 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;	}
 
-- 
2.39.2