fixed outputName creator, added debugging to readblast

[mothur.git] / readblast.cpp

diff --git a/readblast.cpp b/readblast.cpp
index 5f2441515378031891c78d2fbb809c816e885cec..e98b69c68bfdb8f90fa841429cf4d607ba6fe1c3 100644 (file)
--- a/readblast.cpp
+++ b/readblast.cpp
@@ -110,8 +110,9 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                }
                        }
                }else { m->mothurOut("Error in your blast file, cannot read."); m->mothurOutEndLine(); exit(1); }
-
-                               
+string outDistFilem = "../kathryn/blastDist.dist";
+        ofstream outMDist;
+        m->openOutputFile(outDistFilem, outMDist);
                //read file
                while(!fileHandle.eof()){  
                
@@ -193,6 +194,7 @@ int ReadBlast::read(NameAssignment* nameMap) {
                                         PDistCell value(itA->second, distance);
                                         matrix->addCell(it->first, value);
                                     }
+                                    outMDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
                                                                }else{
                                                                        outDist << itA->first << '\t' << nameMap->get(it->first) << '\t' << distance << endl;
                                                                }
@@ -324,8 +326,8 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                ifstream in;
                m->openInputFile(blastfile, in);
                
-               //ofstream outName;
-               //m->openOutputFile((blastfile + ".tempOutNames"), outName);
+               ofstream outName;
+               m->openOutputFile((blastfile + ".tempOutNames"), outName);
                
                //read first line
                in >> prevName;
@@ -349,6 +351,7 @@ int ReadBlast::readNames(NameAssignment* nameMap) {
                        if (name != prevName) {
                                prevName = name;
                                nameMap->push_back(name);
+                outName << name << '\t' << name << endl;
                                num++;
                        }
                }