From: pschloss <pschloss>
Date: Thu, 3 Mar 2011 22:41:20 +0000 (+0000)
Subject: modified reportfile class
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=24083a26340293cb3a0e44bcf79edbc9b31f41db

modified reportfile class
---

diff --git a/mothur.h b/mothur.h
index 97a1043..190254a 100644
--- a/mothur.h
+++ b/mothur.h
@@ -239,5 +239,15 @@ string toString(const T&x, int i){
 }
 //**********************************************************************************************************************
 
+template<class T>
+T fromString(const string& s){
+	istringstream stream (s);
+	T t;
+	stream >> t;
+	return t;
+}
+
+//**********************************************************************************************************************
+
 #endif
 
diff --git a/qualityscores.cpp b/qualityscores.cpp
index fca3d9f..1ef074d 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -310,6 +310,7 @@ 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/reportfile.cpp b/reportfile.cpp
index f392ed9..8e3b746 100644
--- a/reportfile.cpp
+++ b/reportfile.cpp
@@ -7,6 +7,8 @@
  *
  */
 
+#include "mothur.h"
+#include "mothurout.h"
 #include "reportfile.h"
 
 /**************************************************************************************************/
@@ -49,7 +51,7 @@ ReportFile::ReportFile(ifstream& repFile){
 		repFile >> templateName;
 		repFile >> templateLength;
 		repFile >> searchMethod;
-		repFile >> searchScore;
+		repFile >> dummySearchScore;
 		repFile >> alignmentMethod;
 		repFile >> queryStart;
 		repFile >> queryEnd;
@@ -61,6 +63,14 @@ ReportFile::ReportFile(ifstream& repFile){
 		repFile >> longestInsert;
 		repFile >> simBtwnQueryAndTemplate;
 
+		if(dummySearchScore != "nan"){
+			istringstream stream(dummySearchScore);
+			stream >> searchScore;
+		}
+		else{
+			searchScore = 0;
+		}
+		
 		m->gobble(repFile);		
 	}
 	catch(exception& e) {
diff --git a/reportfile.h b/reportfile.h
index 1bd2c94..067dd14 100644
--- a/reportfile.h
+++ b/reportfile.h
@@ -11,8 +11,6 @@
  */
 
 
-#include "mothur.h"
-#include "mothurout.h"
 
 /**************************************************************************************************/
 
@@ -46,7 +44,7 @@ private:
 	
 	MothurOut* m;
 		
-	string queryName, templateName, searchMethod, alignmentMethod;
+	string queryName, templateName, searchMethod, alignmentMethod, dummySearchScore;
 	int queryLength, templateLength, queryStart, queryEnd, templateStart, templateEnd, pairwiseAlignmentLength, gapsInQuery, gapsInTemplate, longestInsert;
 	float searchScore, simBtwnQueryAndTemplate;
 	
diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 2e20c57..db3a4a9 100644
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -310,6 +310,7 @@ 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();
@@ -339,17 +340,23 @@ 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;
 				}
 			}			
 
@@ -367,6 +374,8 @@ int SeqErrorCommand::execute(){
 			}
 
 			index++;
+			cout << "end of loop:\t" << index << endl;
+			
 			if(index % 1000 == 0){	cout << index << endl;	}
 		}
 		queryFile.close();