started work on classify.seqs command. changed the database class so that it does...

[mothur.git] / chimeracheckrdp.cpp

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index acc3aa2eb62554743105b2847e2a682389d21b40..07fb8ab65019b9a45d7556fbd75d50310c5c0b98 100644 (file)
--- a/chimeracheckrdp.cpp
+++ b/chimeracheckrdp.cpp
@@ -77,11 +77,13 @@ void ChimeraCheckRDP::getChimeras() {
        try {
                
                //read in query sequences and subject sequences
-               mothurOut("Reading sequences and template file... "); cout.flush();
+               mothurOutEndLine();
+               mothurOut("Reading query sequences... "); cout.flush();
                querySeqs = readSeqs(fastafile);
+               mothurOut("Done."); 
                //templateSeqs = readSeqs(templateFile);
-               templateDB = new KmerDB(templateFile, kmerSize);
-               mothurOut("Done."); mothurOutEndLine();
+               templateDB = new AlignmentDB(templateFile, "kmer", kmerSize, 0,0,0,0);
+               mothurOutEndLine();
                
                int numSeqs = querySeqs.size();