From 6973be461c47c057531f447de22003a30cabc193 Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Thu, 3 Mar 2011 22:43:48 +0000
Subject: [PATCH] took out couts

---
 qualityscores.cpp   |  3 +--
 seqerrorcommand.cpp | 10 +---------
 2 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 1ef074d..8b8e4ec 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -194,7 +194,6 @@ bool QualityScores::stripQualRollingAverage(Sequence& sequence, double qThreshol
 			
 			if(rollingSum / (double)(i+1) < qThreshold){
 				end = i;
-//				cout << i+1 << '\t' << seqName << '\t' << rollingSum / (double)(i+1) << endl;
 				break;
 			}
 		}
@@ -310,7 +309,7 @@ void QualityScores::updateQScoreErrorMap(map<char, vector<int> >& qualErrorMap,
 		int seqLength = errorSeq.size();
 		
 		int qIndex = start - 1;
-		cout << start << '\t' << stop << '\t' << seqLength << endl;
+
 		for(int i=0;i<seqLength;i++){
 			
 			if(errorSeq[i] == 'm')		{	qualErrorMap['m'][qScores[qIndex]] += weight;	}
diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index db3a4a9..407850f 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -310,7 +310,6 @@ int SeqErrorCommand::execute(){
 			if (m->control_pressed) { errorSummaryFile.close();	errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 		
 			Sequence query(queryFile);
-			cout << "gotQuery" << endl;
 			
 			int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned());
 			int closestRefIndex = chimeraTest.getClosestRefIndex();
@@ -340,23 +339,17 @@ int SeqErrorCommand::execute(){
 
 			if(qualFileName != "" && reportFileName != ""){
 				report = ReportFile(reportFile);
-				cout << "gotReport" << endl;
 				
 //				int origLength = report.getQueryLength();
 				int startBase = report.getQueryStart();
 				int endBase = report.getQueryEnd();
 
 				quality = QualityScores(qualFile);
-				cout << "gotQuality" << endl;
 
 				if(!ignoreSeq){
-					cout << "not ignoring" << endl;
 					quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
-					cout << "updateQScoreErrorMap" << endl;
 					quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
-					cout << "updateForwardMap" << endl;
 					quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
-					cout << "updateReverseMap" << endl;
 				}
 			}			
 
@@ -374,9 +367,8 @@ int SeqErrorCommand::execute(){
 			}
 
 			index++;
-			cout << "end of loop:\t" << index << endl;
 			
-			if(index % 1000 == 0){	cout << index << endl;	}
+			if(index % 1000 == 0){	m->mothurOut(toString(index) + '\n');	}
 		}
 		queryFile.close();
 		errorSummaryFile.close();	
-- 
2.39.2