X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summaryqualcommand.cpp;h=e1e626ea273a650840dd849442e43762e9a100cf;hp=ae5b652a3cbfa0e43aa74e495bb28eb16775d9d3;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index ae5b652..e1e626e 100644
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -196,7 +196,7 @@ int SummaryQualCommand::execute(){
 		if (namefile != "") { nameMap = m->readNames(namefile); }
 		else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             nameMap = ct.getNameMap();
         }
         
@@ -441,7 +441,10 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
 		
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
-			numSeqs += pDataArray[i]->count;
+			numSeqs += pDataArray[i]->numSeqs;
+            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; 
+            }
             int tempNum = pDataArray[i]->position.size();
             if (position.size() < tempNum) { position.resize(tempNum, 0); }
 			if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }