X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=preclustercommand.h;h=2b93328e64a038695a3abbd10cfe9be1165b783d;hp=7be805f0083fca6819703f487d438257674d03df;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=e0c50fc42e953dbe258feb9bc1d1d7dc10fafff0

diff --git a/preclustercommand.h b/preclustercommand.h
index 7be805f..2b93328 100644
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -301,7 +301,7 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                         out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl;
                         
                     }//end if active i
-                    if(i % 100 == 0)	{ pDataArray->m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine();	}
+                    if(i % 100 == 0)	{ pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); 	}
                 }
                 
             }else {
@@ -329,7 +329,7 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                                 if (mismatch > pDataArray->diffs) { mismatch = length; break; } //to far to cluster
                             }
                             
-                            if (mismatch <= diffs) {
+                            if (mismatch <= pDataArray->diffs) {
                                 //merge
                                 alignSeqs[j].names += ',' + alignSeqs[i].names;
                                 alignSeqs[j].numIdentical += alignSeqs[i].numIdentical;
@@ -344,7 +344,7 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
                         }//end abundance check
                     }//end for loop j
                     
-                    if(i % 100 == 0)	{ pDataArray->m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine();	}
+                    if(i % 100 == 0)	{ pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); 	}
                 }
                 
                 for (int i = 0; i < numSeqs; i++) {