working on pam

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index 5f2441515378031891c78d2fbb809c816e885cec..84fddcf263cfdeb572f72ff3bd658325f31271e0 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -111,7 +111,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                        }
                }else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
 
-                               
+       
                //read file
                while(!fileHandle.eof()){  
                
@@ -193,7 +193,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                         PDistCell value(itA->second, distance);
                                         matrix->addCell(it->first, value);
                                     }
-                                                               }else{
+                                }else{
                                                                        outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
                                                                }
                                                        }
@@ -348,7 +348,12 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                        //is this a new name?
                        if (name != prevName) {
                                prevName = name;
-                               nameMap->push_back(name);
+                
+                if (nameMap->get(name) != -1) { m->mothurOut("[ERROR]: trying to exact names from blast file, and I found dups.  Are you sequence names unique? quitting.\n"); m->control_pressed = true; }
+                else {
+                    nameMap->push_back(name);
+                }
+                //outName << name << '\t' << name << endl;
                                num++;
                        }
                }