added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error...

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 5d714fd1ee88ff18a00619e96ae253847883a151..57528b4026e538f4b9ad85b706182e162bca2567 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -44,6 +44,7 @@ int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int num
        }
 }
 //***************************************************************************************************************
+//template=self
 ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, int>& prior, string mode, int k, int ms, int mms, int win, float div, 
                                                         int minsim, int mincov, int minbs, int minsnp, int par, int it, int inc, int numw, bool r) : Chimera()  {      
        try {
@@ -256,6 +257,11 @@ vector<Sequence*> ChimeraSlayer::getTemplate(Sequence q, vector<Sequence*>& user
                        }
                }
                
+               //avoids nuisance error from formatdb for making blank blast database
+               if (userTemplate.size() == 0) {
+                       return userTemplate;
+               }
+               
                string  kmerDBNameLeft;
                string  kmerDBNameRight;
                
@@ -749,7 +755,6 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                else {  thisTemplate = getTemplate(*query, thisFilteredTemplate);  } //fills this template and creates the databases
                
                if (m->control_pressed) {  return 0;  }
-               
                if (thisTemplate.size() == 0) {  return 0; } //not chimeric
                
                //moved this out of maligner - 4/29/11