From: pschloss <pschloss>
Date: Fri, 6 May 2011 16:14:31 +0000 (+0000)
Subject: working on search=dist in chimera.slayer
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;ds=sidebyside;h=3871623415af21ae17f71d0f12e06811ed30c38f;p=mothur.git

working on search=dist in chimera.slayer
---

diff --git a/blastdb.cpp b/blastdb.cpp
index 2d17139..d227bc6 100644
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -123,7 +123,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		queryFile << '>' << seq->getName() << endl;
 		queryFile << seq->getUnaligned() << endl;
 		queryFile.close();
-		cout << seq->getUnaligned() << endl;
+//		cout << seq->getUnaligned() << endl;
 		//	the goal here is to quickly survey the database to find the closest match.  To do this we are using the default
 		//	wordsize used in megablast.  I'm sure we're sacrificing accuracy for speed, but anyother way would take way too
 		//	long.  With this setting, it seems comparable in speed to the suffix tree approach.
@@ -142,7 +142,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		
 		while(!m8FileHandle.eof()){
 			m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
-			cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
+//			cout << dummy << '\t' << templateAccession << '\t' << searchScore << '\t' << numBases << '\t' << mismatch << '\t' << gap << '\t' << startQuery << '\t' << endQuery << '\t' << startRef << '\t' << endRef << '\t' << eScore << '\t' << score << endl; 
 			
 			//get rest of junk in line
 			//while (!m8FileHandle.eof())	{	char c = m8FileHandle.get(); if (c == 10 || c == 13){	break;	}else{ cout << c; }	} //
@@ -157,7 +157,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n, int minPerID) {
 		m8FileHandle.close();
 		remove((queryFileName+seq->getName()).c_str());
 		remove((blastFileName+seq->getName()).c_str());
-cout << "\n" ;		
+//cout << "\n" ;		
 		return topMatches;
 	}
 	catch(exception& e) {
diff --git a/slayer.cpp b/slayer.cpp
index 61b7b63..8e17f87 100644
--- a/slayer.cpp
+++ b/slayer.cpp
@@ -61,16 +61,16 @@ string Slayer::getResults(Sequence* query, vector<Sequence*> refSeqs) {
 						
 						
 						//are we within 10 points of the bootstrap cutoff?
-						if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
-							bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
-								
-							if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
-								
-							divs[k].bsa = BS_A;
-							divs[k].bsb = BS_B;
-							divs[k].bsMax = max(BS_A, BS_B);
-							divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
-						}
+//						if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
+//							bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
+//								
+//							if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
+//								
+//							divs[k].bsa = BS_A;
+//							divs[k].bsb = BS_B;
+//							divs[k].bsMax = max(BS_A, BS_B);
+//							divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
+//						}
 						
 						//so results reflect orignal alignment
 						divs[k].winLStart = spots[divs[k].winLStart];