X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=pairwiseseqscommand.h;fp=pairwiseseqscommand.h;h=06dbad975bc6f6b3035024f1260108e65470db64;hb=14cddf859d97118481161bf3e85a647976020758;hp=33fcfca0b6d0207ed1f282a36061893805745203;hpb=4b54ce99af7db8019ea907cd7c2edf789369ada9;p=mothur.git

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index 33fcfca..06dbad9 100644
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -128,7 +128,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
 		outFile.setf(ios::fixed, ios::showpoint);
 		outFile << setprecision(4);
 		
-		pDataArray->count = pDataArray->end;
+		pDataArray->count = 0;
         
         int startTime = time(NULL);
         
@@ -162,6 +162,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
         if(pDataArray->start == 0){	outFile << pDataArray->alignDB.getNumSeqs() << endl;	}
 		
 		for(int i=pDataArray->start;i<pDataArray->end;i++){
+            pDataArray->count++;
             
 			string name = pDataArray->alignDB.get(i).getName();
 			//pad with spaces to make compatible
@@ -201,7 +202,7 @@ static DWORD WINAPI MyPairwiseSquareThreadFunction(LPVOID lpParam){
 			}
 			
 		}
-		pDataArray->m->mothurOut(toString(pDataArray->end-1) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
+		pDataArray->m->mothurOut(toString(pDataArray->count) + "\t" + toString(time(NULL) - startTime)); pDataArray->m->mothurOutEndLine();
 		
 		outFile.close();
         delete alignment;