From: pschloss <pschloss>
Date: Thu, 21 Apr 2011 20:08:54 +0000 (+0000)
Subject: small things with chimera.slayer
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5f07b42548368731cedeb92cbf3e79f630b4e20f;p=mothur.git

small things with chimera.slayer
---

diff --git a/blastdb.cpp b/blastdb.cpp
index 6cfa3c6..14a1fa3 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -116,6 +116,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
 		vector<int> topMatches;
 		
 		ofstream queryFile;
+
 		m->openOutputFile((queryFileName+seq->getName()), queryFile);
 		queryFile << '>' << seq->getName() << endl;
 		queryFile << seq->getUnaligned() << endl;
@@ -154,7 +155,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
 		return topMatches;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "BlastDB", "findClosest");
+		m->errorOut(e, "BlastDB", "findClosestMegaBlast");
 		exit(1);
 	}
 }
diff --git a/maligner.cpp b/maligner.cpp
index b3cb991..18f7409 100644
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -628,13 +628,13 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
 		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()+"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);
-			
+		vector<int> tempIndexesRight = databaseLeft->findClosestMegaBlast(queryRight, 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;