X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckrdp.cpp;fp=chimeracheckrdp.cpp;h=07fb8ab65019b9a45d7556fbd75d50310c5c0b98;hb=63e089e0b3aad1741bab60119ed7ccc784dce347;hp=acc3aa2eb62554743105b2847e2a682389d21b40;hpb=f5023c911c377e5320c5110c78af98dd8841ef58;p=mothur.git

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index acc3aa2..07fb8ab 100644
--- 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();