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

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 6cef8bbec330c3d345d332f772970ff33a988f79..c43dd38046f53fcf7422cfa920374365d374ec30 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -312,7 +312,7 @@ int ChimeraPintailCommand::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));
@@ -399,7 +399,7 @@ int ChimeraPintailCommand::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));