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

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index c5407ca345a2ff7bdec2ed47089f7e10d1df1fc3..1f93068d6451d701d6587b7b913bcc0e0856fd90 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -373,7 +373,7 @@ int AlignCommand::execute(){
                        if(processors == 1){
                                ifstream inFASTA;
                                openInputFile(candidateFileNames[s], inFASTA);
-                               numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numFastaSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numFastaSeqs));
@@ -472,7 +472,7 @@ int AlignCommand::execute(){
        #else
                        ifstream inFASTA;
                        openInputFile(candidateFileNames[s], inFASTA);
-                       numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                       getNumSeqs(inFASTA, numFastaSeqs);
                        inFASTA.close();
                        
                        lines.push_back(new linePair(0, numFastaSeqs));