From: westcott <westcott>
Date: Fri, 20 Aug 2010 17:17:35 +0000 (+0000)
Subject: pre.cluster
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=4a4ce519c1241b195b8a48919feba3ee9e30ea94;p=mothur.git

pre.cluster
---

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 0275648..5dc2f5a 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -134,39 +134,44 @@ int PreClusterCommand::execute(){
 
 		//sort seqs by number of identical seqs
 		alignSeqs.sort(comparePriority);
-	
+		
 		int count = 0;
 		int i = 0;
-
+		
 		//think about running through twice...
 		list<seqPNode>::iterator itList;
 		list<seqPNode>::iterator itList2;
-		for (itList = alignSeqs.begin(); itList != alignSeqs.end(); itList++) {			
+		for (itList = alignSeqs.begin(); itList != alignSeqs.end(); itList++) {
+			
 			//try to merge it with all smaller seqs
 			for (itList2 = alignSeqs.begin(); itList2 != alignSeqs.end(); itList2++) {
-					
+				
 				if (m->control_pressed) { outFasta.close(); outNames.close(); remove(newFastaFile.c_str()); remove(newNamesFile.c_str());  return 0; }
-					
-				if ((*itList).seq.getName() != (*itList2).seq.getName()) { //you don't want to merge with yourself
+				
+			
+				if (itList->seq.getName() != itList2->seq.getName()) { //you don't want to merge with yourself
 					//are you within "diff" bases
+					
 					int mismatch = calcMisMatches((*itList).seq.getAligned(), (*itList2).seq.getAligned());
-						
+									
 					if (mismatch <= diffs) {
 						//merge
 						(*itList).names += ',' + (*itList2).names;
 						(*itList).numIdentical += (*itList2).numIdentical;
+						
+						itList2 = alignSeqs.erase(itList2); 
 
-						alignSeqs.erase(itList2); itList2--;
 						count++;
 					}
 				}
+
 			}
-			
+
 			//ouptut this sequence
 			printData(outFasta, outNames, (*itList));
 			
 			//remove sequence
-			alignSeqs.erase(itList); itList--;
+			itList = alignSeqs.erase(itList); 
 			
 			i++;
 			
@@ -179,7 +184,6 @@ int PreClusterCommand::execute(){
 		outNames.close();
 		
 		if (m->control_pressed) {  remove(newFastaFile.c_str()); remove(newNamesFile.c_str());  return 0; }
-
 		
 		m->mothurOut("Total number of sequences before precluster was " + toString(numSeqs) + "."); m->mothurOutEndLine();
 		m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); 
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 4b2ee4e..daf0ece 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -476,7 +476,9 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 			
 			int success = 1;
 			
+
 			Sequence currSeq(inFASTA); gobble(inFASTA);
+
 			QualityScores currQual;
 			if(qFileName != ""){
 				currQual = QualityScores(qFile, currSeq.getNumBases());  gobble(qFile);