sens.spec changes

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index f225d50a15670d23f4b3d484901cfb7e30cd2c29..7226f9ddac16e61ebc2239ff4d868474b990ec25 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -228,9 +228,9 @@ int SeqSummaryCommand::execute(){
                                if(processors == 1){
                                        ifstream inFASTA;
                                        openInputFile(fastafile, inFASTA);
-                                       numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
-                                       inFASTA.close();
-                                       
+                                       getNumSeqs(inFASTA, numSeqs);
+                                       inFASTA.close();        
+                                               
                                        lines.push_back(new linePair(0, numSeqs));
                                        
                                        driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
@@ -250,7 +250,7 @@ int SeqSummaryCommand::execute(){
                #else
                                ifstream inFASTA;
                                openInputFile(fastafile, inFASTA);
-                               numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numSeqs));
@@ -334,6 +334,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
                        if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
                                        
                        Sequence current(in);
+       
                        if (current.getName() != "") {
                                startPosition.push_back(current.getStartPos());
                                endPosition.push_back(current.getEndPos());