pre.cluster

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 0275648066b99c55533e4aaacdcde5bb21edad5f..5dc2f5a79e006e947791042c9296fd3e646448a1 100644 (file)
--- 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 4b2ee4eee99d3d38c2e5cd4f77ad2c0b90af4b81..daf0ecea2efe53fafa907518cc347444da651b6f 100644 (file)
--- 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);