X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.cpp;h=88478a10ec86f97802a1b5b152fcf434c7e6dc14;hb=a89c6295ae9a35fcaaab7fa50dcb68360dd543b0;hp=e6b037b6bcafafa6c7ccf5aafa9731de3d7ba864;hpb=4283eb0248ca6e7e3e3344647f16166da0e14147;p=mothur.git

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index e6b037b..88478a1 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -203,7 +203,7 @@ int SeqSummaryCommand::execute(){
 		if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile, false);
+            ct.readTable(countfile, false, false);
             nameMap = ct.getNameMap();
         }
 		
@@ -376,7 +376,7 @@ int SeqSummaryCommand::execute(){
                 
         double meanstartPosition, meanendPosition, meanseqLength, meanambigBases, meanlongHomoPolymer;
                 
-		meanstartPosition /= (double) size; meanendPosition /= (double) size; meanlongHomoPolymer /= (double) size; meanseqLength /= (double) size; meanambigBases /= (double) size;
+		meanstartPosition = meanStartPosition / (double) size; meanendPosition = meanEndPosition /(double) size; meanlongHomoPolymer = meanLongHomoPolymer / (double) size; meanseqLength = meanSeqLength / (double) size; meanambigBases = meanAmbigBases /(double) size;
 				
 		int ptile0_25	= int(size * 0.025);
 		int ptile25		= int(size * 0.250);
@@ -449,7 +449,8 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 
 		bool done = false;
 		int count = 0;
-       
+        
+        
 		while (!done) {
 				
 			if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
@@ -479,7 +480,6 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 					ambigBases.push_back(current.getAmbigBases());
 					longHomoPolymer.push_back(current.getLongHomoPolymer());
 				}
-				
 				count++;
 				outSummary << current.getName() << '\t';
 				outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
@@ -584,17 +584,17 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
 		
 		//loop through and create all the processes you want
 		while (process != processors) {
-			int pid = fork();
+			pid_t pid = fork();
 			
 			if (pid > 0) {
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
-				num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
+				num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + m->mothurGetpid(process) + ".temp", lines[process]);
 				
 				//pass numSeqs to parent
 				ofstream out;
-				string tempFile = fastafile + toString(getpid()) + ".num.temp";
+				string tempFile = fastafile + m->mothurGetpid(process) + ".num.temp";
 				m->openOutputFile(tempFile, out);
 				
 				out << num << endl;