forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / sequenceparser.cpp

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index 105e0a9c7411f14c6112a9b7cf5555f0701720b5..fd94b246a43217cc9cbfa131bfe4cd672955e001 100644 (file)
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -64,6 +64,7 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                string first, second;
                int countName = 0;
                set<string> thisnames1;
+               
                while(!inName.eof()) {
                        
                        if (m->control_pressed) { break; }
@@ -135,12 +136,14 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
                
                if (countName != (groupMap->getNumSeqs())) {
                        vector<string> groupseqsnames = groupMap->getNamesSeqs();
+                       
                        for (int i = 0; i < groupseqsnames.size(); i++) {
                                set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
                                if (itnamesfile == thisnames1.end()){
                                        cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
                                }
                        }
+                       
                        m->mothurOutEndLine();
                        m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
                        m->mothurOutEndLine();
@@ -313,6 +316,7 @@ int SequenceParser::getSeqs(string g, string filename, bool uchimeFormat=false){
                                }
                                
                        }else { 
+                //m->mothurOut("Group " + g +  " contains " + toString(seqForThisGroup.size()) + " unique seqs.\n");
                                for (int i = 0; i < seqForThisGroup.size(); i++) {
                                        
                                        if(m->control_pressed) { out.close(); m->mothurRemove(filename); return 1; }