X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=screenseqscommand.cpp;h=1e6b5a36786a58ce9ca44de8703a620554d89732;hb=14cddf859d97118481161bf3e85a647976020758;hp=5a9c0c8320b7305834cdf4bb544effd515728417;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e;p=mothur.git

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index 5a9c0c8..1e6b5a3 100644
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -588,7 +588,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 		while(!inputNames.eof()){
 			if (m->control_pressed) { goodNameOut.close();  inputNames.close(); m->mothurRemove(goodNameFile);  return 0; }
 
-			inputNames >> seqName >> seqList;
+			inputNames >> seqName; m->gobble(inputNames); inputNames >> seqList;
 			it = badSeqNames.find(seqName);
 				
 			if(it != badSeqNames.end()){
@@ -636,7 +636,7 @@ int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 			while(!inputGroups.eof()){
 				if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile);  m->mothurRemove(goodGroupFile); return 0; }
 
-				inputGroups >> seqName >> group;
+				inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group;
 				
 				it = badSeqGroups.find(seqName);
 				
@@ -934,6 +934,9 @@ int ScreenSeqsCommand::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]);       }
@@ -970,7 +973,7 @@ int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 		while(!inputGroups.eof()){
 			if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; }
 
-			inputGroups >> seqName >> group;
+			inputGroups >> seqName; m->gobble(inputGroups); inputGroups >> group;
 			it = badSeqNames.find(seqName);
 			
 			if(it != badSeqNames.end()){
@@ -1157,7 +1160,7 @@ int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
 		while(!input.eof()){
 			if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
 			
-			input >> seqName >> tax;
+			input >> seqName; m->gobble(input); input >> tax;
 			it = badSeqNames.find(seqName);
 			
 			if(it != badSeqNames.end()){ badSeqNames.erase(it); }
@@ -1518,6 +1521,9 @@ int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, st
 		//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 (set<string>::iterator it = pDataArray[i]->badSeqNames.begin(); it != pDataArray[i]->badSeqNames.end(); it++) {	badSeqNames.insert(*it);       }
 			CloseHandle(hThreadArray[i]);
 			delete pDataArray[i];