X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsamplecommand.cpp;h=a89d191a9127065922c3d498edce5cab41030f27;hb=89cfcfcc9e648d2f956f2ff419e64ba7907106d2;hp=4128191598d22e8e7280f403dca79494e61da948;hpb=67ea6ccd74dbd64828d31b952808255f206364ff;p=mothur.git

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 4128191..a89d191 100644
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -273,7 +273,7 @@ SubSampleCommand::SubSampleCommand(string option) {
 			else if (countfile == "not found") { countfile = "";  }	
 			else {
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile);
+                ct.readTable(countfile, true, false);
             }
             
             if ((namefile != "") && (countfile != "")) {
@@ -552,7 +552,7 @@ int SubSampleCommand::getSubSampleFasta() {
                     else{
                         itGroupCounts = groupCounts.find(group);
                         if (itGroupCounts != groupCounts.end()) {
-                            if (groupCounts[group] < size) {	subset.insert(names[j]); 	groupCounts[group]++; }
+                            if (itGroupCounts->second < size) {	subset.insert(names[j]); 	(itGroupCounts->second)++; }
                         }
                     }				
                 }
@@ -947,7 +947,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
 	try {
 		
 		//save mothurOut's binLabels to restore for next label
-		vector<string> saveBinLabels = m->currentBinLabels;
+		vector<string> saveBinLabels = m->currentSharedBinLabels;
 		
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(sharedfile);  }
@@ -965,7 +965,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
 		m->openOutputFile(outputFileName, out);
 		outputTypes["shared"].push_back(outputFileName);  outputNames.push_back(outputFileName);
 		
-        m->currentBinLabels = subsampledLabels;
+        m->currentSharedBinLabels = subsampledLabels;
         
 		thislookup[0]->printHeaders(out);
 		
@@ -977,7 +977,7 @@ int SubSampleCommand::processShared(vector<SharedRAbundVector*>& thislookup) {
         
         
         //save mothurOut's binLabels to restore for next label
-		m->currentBinLabels = saveBinLabels;
+		m->currentSharedBinLabels = saveBinLabels;
 		
 		return 0;