X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.cpp;h=e9002bd7c12781eb6fd2fdb284da2ea06e65c4fa;hb=feb0fbef36b8a681efc04e9b5e3efb1647b99021;hp=8f27b8c7beaf797775f680bdef5c34bcf7f980c8;hpb=deba0af0ccdcb6005ed5b2b82649b137c63fbdf7;p=mothur.git

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 8f27b8c..e9002bd 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -415,6 +415,13 @@ int SeqSummaryCommand::execute(){
 			}
 		#endif
 
+        //set fasta file as new current fastafile
+		string current = "";
+		itTypes = outputTypes.find("summary");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSummaryFile(current); }
+		}
+        
 		return 0;
 	}
 	catch(exception& e) {
@@ -675,6 +682,9 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
 			num += pDataArray[i]->count;
+            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; 
+            }
             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {	startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 			for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {	endPosition.push_back(pDataArray[i]->endPosition[k]);       }
             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) {	seqLength.push_back(pDataArray[i]->seqLength[k]);       }