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

[mothur.git] / chimeracheckcommand.cpp

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 66cf12fb8768bcc9c4995256544761e2d8baf820..4947dc97939b6b147718968bb70e544ca262cc00 100644 (file)
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -245,7 +245,7 @@ int ChimeraCheckCommand::execute(){
                        if(processors == 1){
                                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));
@@ -309,7 +309,7 @@ int ChimeraCheckCommand::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));