X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=bayesian.cpp;h=8278afb32e1d2c028a83ffdece17ed9910a78e20;hp=6eaab6f2f974f8e1036561c2f76d9587d6dd0399;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a

diff --git a/bayesian.cpp b/bayesian.cpp
index 6eaab6f..8278afb 100644
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -145,6 +145,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
 
 				//for each word
 				for (int i = 0; i < numKmers; i++) {
+                    //m->mothurOut("[DEBUG]: kmer = " + toString(i) + "\n");
+                    
 					if (m->control_pressed) {  break; }
 					
 					#ifdef USE_MPI
@@ -239,7 +241,9 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
 			}
 		}
 		
+        if (m->debug) { m->mothurOut("[DEBUG]: about to generateWordPairDiffArr\n"); }
 		generateWordPairDiffArr();
+        if (m->debug) { m->mothurOut("[DEBUG]: done generateWordPairDiffArr\n"); }
 		
 		//save probabilities
 		if (rdb->save) { rdb->wordGenusProb = wordGenusProb; rdb->WordPairDiffArr = WordPairDiffArr; }
@@ -298,7 +302,7 @@ string Bayesian::getTaxonomy(Sequence* seq) {
 			}  
 		}
 		
-		if (queryKmers.size() == 0) {  m->mothurOut(seq->getName() + "is bad."); m->mothurOutEndLine(); simpleTax = "unknown;";  return "unknown;"; }
+		if (queryKmers.size() == 0) {  m->mothurOut(seq->getName() + " is bad. It has no kmers of length " + toString(kmerSize) + "."); m->mothurOutEndLine(); simpleTax = "unknown;";  return "unknown;"; }
 		
 		
 		int index = getMostProbableTaxonomy(queryKmers);