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

[mothur.git] / parsefastaqcommand.cpp

diff --git a/parsefastaqcommand.cpp b/parsefastaqcommand.cpp
index 89f97acf13ad45650a1f8294a3e88895beaa347c..704e752341320dd75b9f213658d74530583ec9cb 100644 (file)
--- a/parsefastaqcommand.cpp
+++ b/parsefastaqcommand.cpp
@@ -183,7 +183,10 @@ int ParseFastaQCommand::execute(){
                        string name = m->getline(in); m->gobble(in);
                        if (name == "") {  m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
-                       else { name = name.substr(1); }
+                       else { 
+                name = name.substr(1); 
+                for (int i = 0; i < name.length(); i++) { if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; } }
+            }
                        
                        //read sequence
                        string sequence = m->getline(in); m->gobble(in);
@@ -193,7 +196,10 @@ int ParseFastaQCommand::execute(){
                        string name2 = m->getline(in); m->gobble(in);
                        if (name2 == "") {  m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; break; }
                        else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; break; }
-                       else { name2 = name2.substr(1);  }
+                       else { 
+                name2 = name2.substr(1);  
+                for (int i = 0; i < name2.length(); i++) { if (name2[i] == ':') { name2[i] = '_'; m->changedSeqNames = true; } }
+            }
                        
                        //read quality scores
                        string quality = m->getline(in); m->gobble(in);