added count file to trim.seqs, get.groups, get.lineage, get.seqs, heatmap.sim, list...

[mothur.git] / seqerrorcommand.cpp

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 8fd6368154773bcc38e2b950d7b170c88be2186e..5ec6cf2d1cc4778399d289ea2280c882f936b944 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -782,7 +782,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                                if (queryFile.eof()) { break; }
                        #endif
                        
-                       if(index % 100 == 0){   m->mothurOut(toString(index) + '\n');   }
+                       if(index % 100 == 0){   m->mothurOut(toString(index));  m->mothurOutEndLine(); }
                }
                queryFile.close();
                if(qFileName != "" && rFileName != ""){  reportFile.close(); qualFile.close(); }
@@ -790,7 +790,7 @@ int SeqErrorCommand::driver(string filename, string qFileName, string rFileName,
                errorSeqFile.close();
                
                //report progress
-               if(index % 100 != 0){   m->mothurOut(toString(index) + '\n');   }
+               if(index % 100 != 0){   m->mothurOut(toString(index));  m->mothurOutEndLine(); }
                
                return index;
        }
@@ -821,12 +821,16 @@ void SeqErrorCommand::getReferences(){
                                //
                                //                      int endPos = rdb->referenceSeqs[i].getEndPos();
                                //                      if(endPos < minEndPos)          {       minEndPos = endPos;             }                               
+                               if (rdb->referenceSeqs[i].getNumBases() == 0) {
+                    m->mothurOut("[WARNING]: " + rdb->referenceSeqs[i].getName() + " is blank, ignoring.");m->mothurOutEndLine(); 
+                }else {
+                    referenceSeqs.push_back(rdb->referenceSeqs[i]);
+                }
                                
-                               referenceSeqs.push_back(rdb->referenceSeqs[i]);
                        }
                        referenceFileName = rdb->getSavedReference();
                        
-                       m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  
+                       m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(referenceSeqs.size()) + " sequences.");m->mothurOutEndLine();  
                
                }else {
                        int start = time(NULL);
@@ -844,9 +848,12 @@ void SeqErrorCommand::getReferences(){
        //
        //                      int endPos = currentSeq.getEndPos();
        //                      if(endPos < minEndPos)          {       minEndPos = endPos;             }
-                               referenceSeqs.push_back(currentSeq);
-                               
-                               if (rdb->save) { rdb->referenceSeqs.push_back(currentSeq); }
+                if (currentSeq.getNumBases() == 0) {
+                    m->mothurOut("[WARNING]: " + currentSeq.getName() + " is blank, ignoring.");m->mothurOutEndLine(); 
+                }else {
+                    referenceSeqs.push_back(currentSeq);
+                    if (rdb->save) { rdb->referenceSeqs.push_back(currentSeq); }
+                }
                                        
                                m->gobble(referenceFile);
                        }
@@ -860,7 +867,7 @@ void SeqErrorCommand::getReferences(){
                for(int i=0;i<numRefs;i++){
                        referenceSeqs[i].padToPos(maxStartPos);
                        referenceSeqs[i].padFromPos(minEndPos);
-               }
+        }
                
                if(numAmbigSeqs != 0){
                        m->mothurOut("Warning: " + toString(numAmbigSeqs) + " reference sequences have ambiguous bases, these bases will be ignored\n");
@@ -964,7 +971,6 @@ int SeqErrorCommand::getErrors(Sequence query, Sequence reference, Compare& erro
                errors.errorRate = (double)(errors.total-errors.matches) / (double)errors.total;
                errors.queryName = query.getName();
                errors.refName = reference.getName();
-               
                //return errors;
         return 0;
        }