added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 8164e2714db5fc4c1f2c1d59f9593475717386b5..a4464692607df14d08384f3cfdf112a4e18debb8 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -33,7 +33,7 @@ vector<string> CountSeqsCommand::setParameters(){
 string CountSeqsCommand::getHelpString(){      
        try {
                string helpString = "";
-               helpString += "The count.seqs command reads a name file and outputs a .count.summary file.  You may also provide a group file to get the counts broken down by group.\n";
+               helpString += "The count.seqs command reads a name file and outputs a .seq.count file.  You may also provide a group file to get the counts broken down by group.\n";
                helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
                helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
                helpString += "The count.seqs command should be in the following format: count.seqs(name=yourNameFile).\n";
@@ -146,7 +146,7 @@ int CountSeqsCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ofstream out;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "count.summary";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + ".seq.count";
                m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
                out << "Representative Sequence\t total\t";