X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sequenceparser.cpp;h=fd94b246a43217cc9cbfa131bfe4cd672955e001;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=e60f19b0df0034de0c1a693d7c5a55c59ef0ef82;hpb=c47e480b743d1c242b8c527b6d12f992c68b8c2c;p=mothur.git

diff --git a/sequenceparser.cpp b/sequenceparser.cpp
index e60f19b..fd94b24 100644
--- a/sequenceparser.cpp
+++ b/sequenceparser.cpp
@@ -7,7 +7,7 @@
  *
  */
 
-#include "sequenceParser.h"
+#include "sequenceparser.h"
 
 
 /************************************************************/
@@ -63,6 +63,8 @@ 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; }
@@ -94,10 +96,12 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
 					it = splitMap.find(group);
 					if (it != splitMap.end()) { //adding seqs to this group
 						(it->second) += "," + names[i];
+						thisnames1.insert(names[i]);
 						countName++;
 					}else { //first sighting of this group
 						splitMap[group] = names[i];
 						countName++;
+						thisnames1.insert(names[i]);
 						
 						//is this seq in the fasta file?
 						if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
@@ -131,6 +135,15 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
 		if (error == 1) { m->control_pressed = true; }
 		
 		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();
@@ -303,6 +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; }