tracking down chimera.slayer issue

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 40e074c80c2d3a56136cb48f4fb20d95ebfd2456..cf219951f08e314f57ebb2e6c27985d3f5409167 100644 (file)
--- 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 67258714aa3b45cbdeaee2cf8d43576f2de4f446..2a1736a7344e312e4d2cdb4371fc943335d6970b 100644 (file)
--- 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 5ea41fcd867d291fe928f096cb7d90e03d4d19d4..7d7145f4ca6bd9fac7a316745ace4432e4c26fe0 100644 (file)
--- 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 fab457bc8f3e7948271190a55ac519ef0d1cd06d..ba1bf337d4084e58416b06c48cb6a359bb5b05b1 100644 (file)
--- 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;