added ':' name check to seq. error and fastq.info. sffinfo now ignores clipQualRight...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 67e43aa0d4b7f6a6ff251bc45a8254ca49b8b162..0a6eae93df72e8556554bef32c5a52074a4d0a54 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -1381,6 +1381,10 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                                        
                                        string sname = "";  nameStream >> sname;
                                        sname = sname.substr(1);
+                    
+                    for (int i = 0; i < sname.length(); i++) {
+                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+                    }
                                        
                                        map<string, int>::iterator it = firstSeqNames.find(sname);
                                        
@@ -1441,6 +1445,10 @@ int SeqErrorCommand::setLines(string filename, string qfilename, string rfilenam
                     istringstream nameStream(input);
                     string sname = "";  nameStream >> sname;
                     
+                    for (int i = 0; i < sname.length(); i++) {
+                        if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
+                    }
+                    
                     map<string, int>::iterator it = firstSeqNamesReport.find(sname);
                 
                     if(it != firstSeqNamesReport.end()) { //this is the start of a new chunk