changed random forest output filename

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index a871244f4538881c8d285c2a1202597be319498d..f757a7920bb337883a2a7773f35ed533d2186c80 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -558,6 +558,7 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        if (m->control_pressed) {  break; }
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
+            cout  << candidateSeq->getAligned() << endl;
                        report.setCandidate(candidateSeq);
 
                        int origNumBases = candidateSeq->getNumBases();
@@ -644,11 +645,11 @@ int AlignCommand::driver(linePair* filePos, string alignFName, string reportFNam
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count) + "\n");               }
                        
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count) + "\n");               }
                
                delete alignment;
                alignmentFile.close();
@@ -965,6 +966,9 @@ int AlignCommand::createProcesses(string alignFileName, string reportFileName, s
                
                //Close all thread handles and free memory allocations.
                for(int i=0; i < pDataArray.size(); i++){
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
                        num += pDataArray[i]->count;
                        CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];