X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=maligner.cpp;h=6deeb8012c5f18937f65b889ad50e69852ece5c9;hb=03acfa01ede71b107817966fcf27cd728038b3c9;hp=5da4b9f9cece7a9e64dd4a5dd621477fc365e94e;hpb=813f0516e9c7533859f57ebe6d7b8854896bf009;p=mothur.git

diff --git a/maligner.cpp b/maligner.cpp
index 5da4b9f..6deeb80 100644
--- 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];
 			}
 		}
 		
@@ -502,13 +507,13 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
 		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);
+		Sequence* queryLeft = new Sequence(q->getName()+"left", leftQuery);
+		Sequence* queryRight = new Sequence(q->getName()+"right", rightQuery);
 		
 		vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, num+1);
 		vector<int> tempIndexesLeft = databaseLeft->findClosestMegaBlast(queryLeft, num+1);
-		
-		//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; }
+			
+		//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;