fixed sub.sample so that it will eliminate samples with abundances that are less...

[mothur.git] / maligner.cpp

diff --git a/maligner.cpp b/maligner.cpp
index f06884fcad747a84e8c3d8ae673a5eabf839f2ec..7f0cd0a85ffded74edea865c2d2d9378d53d9dd8 100644 (file)
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -71,6 +71,9 @@ string Maligner::chimeraMaligner(int chimeraPenalty, DeCalculator* decalc) {
                
                //trims seqs to first non gap char in all seqs and last non gap char in all seqs
                spotMap = decalc->trimSeqs(query, refSeqs);
+               
+               //you trimmed the whole sequence, skip
+               if (query->getAligned() == "") { return "no"; }
 
                vector<Sequence*> temp = refSeqs;
                temp.push_back(query);
@@ -175,6 +178,8 @@ vector<Sequence*> Maligner::minCoverageFilter(vector<Sequence*> ref){
                        //if coverage above minimum
                        if (coverage > minCoverage) {
                                newRefs.push_back(ref[i]);
+                       }else {
+                               delete ref[i];
                        }
                }
                
@@ -496,24 +501,19 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
        try {   
                indexes.clear();
                vector<Sequence*> refResults;
-               //generate blastdb
-               Database* database = new BlastDB(-2.0, -1.0, matchScore, misMatchPenalty);
-               for (int i = 0; i < db.size(); i++) {   database->addSequence(*db[i]);  }
-               database->generateDB();
-               database->setNumSeqs(db.size());
-               
+                               
                //get parts of query
                string queryUnAligned = q->getUnaligned();
                string leftQuery = queryUnAligned.substr(0, int(queryUnAligned.length() * 0.33)); //first 1/3 of the sequence
                string rightQuery = queryUnAligned.substr(int(queryUnAligned.length() * 0.66)); //last 1/3 of the sequence
 
-               Sequence* queryLeft = new Sequence(q->getName(), leftQuery);
-               Sequence* queryRight = new Sequence(q->getName(), rightQuery);
-               
-               vector<int> tempIndexesRight = database->findClosestMegaBlast(queryRight, num+1);
-               vector<int> tempIndexesLeft = database->findClosestMegaBlast(queryLeft, num+1);
+               Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
+               Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
                
-               //if ((tempIndexesRight.size() != (num+1)) || (tempIndexesLeft.size() != (num+1)))  {  m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to porcess sequence " + q->getName()); m->mothurOutEndLine(); return refResults; }
+               vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
+               vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
+                       
+               //if ((tempIndexesRight.size() == 0) && (tempIndexesLeft.size() == 0))  {  m->mothurOut("megablast returned " + toString(tempIndexesRight.size()) + " results for the right end, and " + toString(tempIndexesLeft.size()) + " for the left end. Needed " + toString(num+1) + ". Unable to process sequence " + q->getName()); m->mothurOutEndLine(); return refResults; }
                
                vector<int> smaller;
                vector<int> larger;
@@ -551,9 +551,9 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
                }
                
                if (mergedResults.size() < numWanted) { numWanted = mergedResults.size(); }
-//cout << q->getName() <<  endl;               
+//cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted <<  endl;           
                for (int i = 0; i < numWanted; i++) {
-//cout << db[mergedResults[i]]->getName() << endl;     
+//cout << db[mergedResults[i]]->getName()  << '\t' << mergedResults[i] << endl;        
                        if (db[mergedResults[i]]->getName() != q->getName()) { 
                                Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
                                refResults.push_back(temp);
@@ -561,11 +561,10 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
                        }
 //cout << mergedResults[i] << endl;
                }
-//cout << endl;                
+//cout << "done " << q->getName()  << endl;            
                delete queryRight;
                delete queryLeft;
-               delete database;
-               
+                       
                return refResults;
        }
        catch(exception& e) {
@@ -625,7 +624,7 @@ vector<Sequence*> Maligner::getKmerSeqs(Sequence* q, int num) {
                return refResults;
        }
        catch(exception& e) {
-               m->errorOut(e, "Maligner", "getBlastSeqs");
+               m->errorOut(e, "Maligner", "getKmerSeqs");
                exit(1);
        }
 }