added tempdefault to set.dir and fixed bug with padding type in sffinfo.

[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
index 6db61bd82cbfe30fd2b8c5d48e43f83b3df266b3..7c4934470f448e8fee497fbbdafe5f5cda57115e 100644 (file)
--- a/chimeracheckcommand.h
+++ b/chimeracheckcommand.h
@@ -28,9 +28,9 @@ 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 +46,10 @@ private:
        string fastafile, templatefile, namefile, outputDir;
        int processors, increment, ksize, numSeqs, templateSeqsLength;
        Chimera* chimera;
-       
-       
+       vector<string> fastaFileNames;
+       vector<string> nameFileNames;
+       vector<string> outputNames;
+               
 };
 
 /***********************************************************/