changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 71e5c9277af61fef9884f42b2c8e9d54a2796e12..3fd3ad1d8376125c5d2f85b6cf66078f0c083f2f 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -224,8 +224,9 @@ int TrimSeqsCommand::execute(){
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                if(processors == 1){
                                        ifstream inFASTA;
+                                       int numSeqs;
                                        openInputFile(fastaFile, inFASTA);
-                                       int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                                       getNumSeqs(inFASTA, numSeqs);
                                        inFASTA.close();
                                        
                                        lines.push_back(new linePair(0, numSeqs));
@@ -266,8 +267,9 @@ int TrimSeqsCommand::execute(){
                                if (m->control_pressed) {  return 0; }
                #else
                                ifstream inFASTA;
+                               int numSeqs;
                                openInputFile(fastaFile, inFASTA);
-                               int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numSeqs));