pat's slight modifications to trim.seqs

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 6db61bd82cbfe30fd2b8c5d48e43f83b3df266b3..89dc6aa7144175a6130743fe97fec9eac466c350 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "command.hpp"
 #include "chimera.h"
+#include "chimeracheckrdp.h"
 
 
 /***********************************************************/
@@ -28,9 +29,9 @@ public:
 private:
 
        struct linePair {
-               int start;
+               unsigned long int start;
                int numSeqs;
-               linePair(long int i, int j) : start(i), numSeqs(j) {}
+               linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
        };
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
@@ -46,8 +47,10 @@ private:
        string fastafile, templatefile, namefile, outputDir;
        int processors, increment, ksize, numSeqs, templateSeqsLength;
        Chimera* chimera;
-       
-       
+       vector<string> fastaFileNames;
+       vector<string> nameFileNames;
+       vector<string> outputNames;
+               
 };
 
 /***********************************************************/