sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / chimeracheckrdp.cpp

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index 16d5f9242f2379465a285b866f6359a5d376215e..42b531282c5f020664277a9e907699a3bf227658 100644 (file)
--- a/chimeracheckrdp.cpp
+++ b/chimeracheckrdp.cpp
@@ -20,7 +20,7 @@ ChimeraCheckRDP::ChimeraCheckRDP(string filename, string temp, string n, bool s,
                kmerSize = k;
                outputDir = o; 
                
-               templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0);
+               templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand());
                m->mothurOutEndLine();
                
                kmer = new Kmer(kmerSize);
@@ -47,7 +47,7 @@ ChimeraCheckRDP::~ChimeraCheckRDP() {
        }
 }      
 //***************************************************************************************************************
-Sequence* ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
+Sequence ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
        try {
                
                m->mothurOut("Processing: " + querySeq->getName()); m->mothurOutEndLine();
@@ -72,7 +72,7 @@ Sequence* ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
                        }
                }
                
-               return NULL;
+               return *querySeq;
        }
        catch(exception& e) {
                m->errorOut(e, "ChimeraCheckRDP", "print");
@@ -81,7 +81,7 @@ Sequence* ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-Sequence* ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
+Sequence ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
        try {
                
                cout << "Processing: " << querySeq->getName() << endl; 
@@ -115,7 +115,7 @@ Sequence* ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
                        }
                }
                
-               return NULL;
+               return *querySeq;
        }
        catch(exception& e) {
                m->errorOut(e, "ChimeraCheckRDP", "print");