From: pschloss <pschloss>
Date: Wed, 27 Apr 2011 10:22:58 +0000 (+0000)
Subject: tracking down chimera.slayer issue
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=77ac47e1ea0b5a0c6f55eb25e6bc7d7494ed3ad2

tracking down chimera.slayer issue
---

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 40e074c..cf21995 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -27,7 +27,7 @@ vector<string> ChimeraSlayerCommand::setParameters(){
 		CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
 		CommandParameter psearch("search", "Multiple", "kmer-blast-distance", "distance", "", "", "",false,false); parameters.push_back(psearch);
 		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter prealign("realign", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prealign);
+		CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(prealign);
 		CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
 		CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit);
 		CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted);
@@ -342,7 +342,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 			temp = validParameter.validFile(parameters, "parents", false);			if (temp == "not found") { temp = "3"; }
 			convert(temp, parents); 
 			
-			temp = validParameter.validFile(parameters, "realign", false);			if (temp == "not found") { temp = "f"; }
+			temp = validParameter.validFile(parameters, "realign", true);			if (temp == "not found") { temp = "t"; }
 			realign = m->isTrue(temp); 
 			
 			temp = validParameter.validFile(parameters, "trim", false);				if (temp == "not found") { temp = "f"; }
diff --git a/decalc.cpp b/decalc.cpp
index 6725871..2a1736a 100644
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -867,12 +867,14 @@ vector<Sequence*> DeCalculator::findClosest(Sequence* querySeq, vector<Sequence*
 //cout << numWanted << endl;
 		for (int i = 0; i < numWanted; i++) {
 //			cout << db[dists[i].index]->getName() << '\t' << dists[i].dist << endl;
+
 			if (db[dists[i].index]->getName() != querySeq->getName()) {
 				Sequence* temp = new Sequence(db[dists[i].index]->getName(), db[dists[i].index]->getAligned()); //have to make a copy so you can trim and filter without stepping on eachother.
 			
 				seqsMatches.push_back(temp);
 				indexes.push_back(dists[i].index);
 			}
+
 		}
 		
 		return seqsMatches;
diff --git a/maligner.cpp b/maligner.cpp
index 5ea41fc..7d7145f 100644
--- a/maligner.cpp
+++ b/maligner.cpp
@@ -733,11 +733,13 @@ vector<Sequence*> Maligner::getBlastSeqs(Sequence* q, int num) {
 //cout << q->getName() << " merged results size = " << mergedResults.size() << '\t' << "numwanted = " << numWanted <<  endl;		
 		for (int i = 0; i < numWanted; i++) {
 //cout << db[mergedResults[i]]->getName()  << '\t' << mergedResults[i] << endl;	
-			//if (db[mergedResults[i]]->getName() != q->getName()) { 
+			
+			if (db[mergedResults[i]]->getName() != q->getName()) { 
 				Sequence* temp = new Sequence(db[mergedResults[i]]->getName(), db[mergedResults[i]]->getAligned());
 				refResults.push_back(temp);
 				indexes.push_back(mergedResults[i]);
-			//}
+			}
+			
 //cout << mergedResults[i] << endl;
 		}
 //cout << "done " << q->getName()  << endl;		
diff --git a/slayer.cpp b/slayer.cpp
index fab457b..ba1bf33 100644
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -56,7 +56,8 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
 					int numSNPSRight = snpsRight.size();
 					
 					//require at least 3 SNPs on each side of the break
-					if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
+//					if ((numSNPSLeft >= 3) && (numSNPSRight >= 3)) {
+					if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
 					
 						//removed in 12/09 version of chimeraSlayer
 						//int winSizeLeft = divs[k].winLEnd - divs[k].winLStart + 1;