X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.cpp;h=c352feb099a83879bae9e1aca0f35d5bfe56e691;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=49a821045e122b5097fde092a5845378e21afc60;hpb=65e21482d022d12f7a78a8d436fb51f322603e41;p=mothur.git

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 49a8210..c352feb 100644
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -234,7 +234,7 @@ SubSampleCommand::SubSampleCommand(string option) {
 			}
 			
 			string temp = validParameter.validFile(parameters, "size", false);		if (temp == "not found"){	temp = "0";		}
-			convert(temp, size);  
+			m->mothurConvert(temp, size);  
 			
 			temp = validParameter.validFile(parameters, "persample", false);		if (temp == "not found"){	temp = "f";		}
 			persample = m->isTrue(temp);
@@ -255,6 +255,10 @@ SubSampleCommand::SubSampleCommand(string option) {
 			if ((groupfile != "") && ((fastafile != "") && (listfile != ""))) { 
 				m->mothurOut("A new group file can only be made from the subsample of a listfile or fastafile, not both. Please correct."); m->mothurOutEndLine(); abort = true; }
 			
+			if ((fastafile != "") && (namefile == "")) {
+				vector<string> files; files.push_back(fastafile);
+				parser.getNameFile(files);
+			}
 		}
 
 	}
@@ -426,6 +430,7 @@ int SubSampleCommand::getSubSampleFasta() {
 		if (persample) {
 			//initialize counts
 			map<string, int> groupCounts;
+			map<string, int>::iterator itGroupCounts;
 			for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
 			
 			for (int j = 0; j < names.size(); j++) {
@@ -435,7 +440,10 @@ int SubSampleCommand::getSubSampleFasta() {
 				string group = groupMap->getGroup(names[j]);
 				if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 				else{
-					if (groupCounts[group] < size) {	subset.insert(names[j]); 	}
+					itGroupCounts = groupCounts.find(group);
+					if (itGroupCounts != groupCounts.end()) {
+						if (groupCounts[group] < size) {	subset.insert(names[j]); 	groupCounts[group]++; }
+					}
 				}				
 			}
 		}else {
@@ -1025,6 +1033,7 @@ int SubSampleCommand::getSubSampleList() {
 		if (persample) {
 			//initialize counts
 			map<string, int> groupCounts;
+			map<string, int>::iterator itGroupCounts;
 			for (int i = 0; i < Groups.size(); i++) { groupCounts[Groups[i]] = 0; }
 			
 			for (int j = 0; j < names.size(); j++) {
@@ -1034,7 +1043,10 @@ int SubSampleCommand::getSubSampleList() {
 				string group = groupMap->getGroup(names[j]);
 				if (group == "not found") { m->mothurOut("[ERROR]: " + names[j] + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
 				else{
-					if (groupCounts[group] < size) {	subset.insert(names[j]); 	}
+					itGroupCounts = groupCounts.find(group);
+					if (itGroupCounts != groupCounts.end()) {
+						if (groupCounts[group] < size) {	subset.insert(names[j]); 	groupCounts[group]++; }
+					}
 				}				
 			}
 		}else{