working on slayer bug

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 73037c783be84270a28b0dacf1795c51a3668d0e..7aa7cd4271f0ccbdcb443ae580b7ddd046b255cf 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -85,22 +85,22 @@ ChimeraSlayer::ChimeraSlayer(string file, string temp, bool trim, map<string, in
 //***************************************************************************************************************
 int ChimeraSlayer::doPrep() {
        try {
+               if (searchMethod == "distance") { 
+                       //read in all query seqs
+                       vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
                
-               //read in all query seqs
-               vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
+                       vector<Sequence*> temp = templateSeqs;
+                       for (int i = 0; i < tempQuerySeqs.size(); i++) {  temp.push_back(tempQuerySeqs[i]);  }
                
-               vector<Sequence*> temp = templateSeqs;
-               for (int i = 0; i < tempQuerySeqs.size(); i++) {  temp.push_back(tempQuerySeqs[i]);  }
+                       createFilter(temp, 0.0); //just removed columns where all seqs have a gap
                
-               createFilter(temp, 0.0); //just removed columns where all seqs have a gap
+                       for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
                
-               for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
-               
-               if (m->control_pressed) {  return 0; } 
-               
-               //run filter on template
-               for (int i = 0; i < templateSeqs.size(); i++) {  if (m->control_pressed) {  return 0; }  runFilter(templateSeqs[i]);  }
+                       if (m->control_pressed) {  return 0; } 
                
+                       //run filter on template
+                       for (int i = 0; i < templateSeqs.size(); i++) {  if (m->control_pressed) {  return 0; }  runFilter(templateSeqs[i]);  }
+               }
                string  kmerDBNameLeft;
                string  kmerDBNameRight;
        
@@ -751,7 +751,12 @@ int ChimeraSlayer::getChimeras(Sequence* query) {
                if (m->control_pressed) {  return 0;  }
                
                vector<results> Results = maligner.getOutput();
-
+               
+               //cout << query->getName() << endl;
+               //for (int i = 0; i < Results.size(); i++) {
+                       //cout << Results[i].parent << '\t' << Results[i].regionStart << '\t' << Results[i].regionEnd << '\t' << Results[i].nastRegionStart << '\t' << Results[i].nastRegionEnd << '\t' << Results[i].queryToParent << '\t' << Results[i].queryToParentLocal << endl;
+               //}
+               //cout << "done\n" << endl;
                if (chimeraFlag == "yes") {
                        
                        if (realign) {