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

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index c41e026497191d8218f90ef8ddb5754aa92cfee0..004cfb0c9e1124cd5ad78c542c6df3815bd4541d 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -292,7 +292,6 @@ int ChimeraSlayerCommand::execute(){
                                int startIndex =  pid * numSeqsPerProcessor;
                                if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
                                
-                               
                                //align your part
                                driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
                                
@@ -330,7 +329,7 @@ int ChimeraSlayerCommand::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));
@@ -377,7 +376,6 @@ int ChimeraSlayerCommand::execute(){
                                        lines.push_back(new linePair(startPos, numSeqsPerProcessor));
                                }
                                
-                               
                                createProcesses(outputFileName, fastafile, accnosFileName); 
                        
                                rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
@@ -419,7 +417,7 @@ int ChimeraSlayerCommand::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));