classify.seqs allows sequences to be in taxonomy file that are not in template. ...

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
index 474951a9feaee7d497417cf2a03f206367056241..e26e751032402cd39dac933acf3f57814ab2fc0f 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -34,13 +34,15 @@ class RemoveSeqsCommand : public Command {
        
        private:
                set<string> names;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               string accnosfile, fastafile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
                vector<string> outputNames;
+        map<string, string> uniqueMap;
                
                int readFasta();
                int readName();
                int readGroup();
+        int readCount();
                int readAlign();
                int readList();
                int readTax();