finished chimera.slayer adding trim parameter, added persample parameter to sub.sampl...

[mothur.git] / chimeraslayer.cpp

diff --git a/chimeraslayer.cpp b/chimeraslayer.cpp
index 020b8a6efc1edd7a581ba938be968908024cba4a..38f7abe49bfc7266e6eb4acd123ff057b8780c42 100644 (file)
--- a/chimeraslayer.cpp
+++ b/chimeraslayer.cpp
@@ -419,7 +419,7 @@ void ChimeraSlayer::printHeader(ostream& out) {
 Sequence* ChimeraSlayer::print(ostream& out, ostream& outAcc) {
        try {
                Sequence* trim = NULL;
-               if (trimChimera) { trim = new Sequence(trimQuery->getName(), trimQuery->getAligned()); }
+               if (trimChimera) { trim = trimQuery; }
                
                if (chimeraFlags == "yes") {
                        string chimeraFlag = "no";
@@ -472,7 +472,7 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
                string outputString = "";
                
                Sequence* trim = NULL;
-               if (trimChimera) { trim = new Sequence(trimQuery->getName(), trimQuery->getAligned()); }
+               if (trimChimera) { trim = trimQuery; }
                
                if (chimeraFlags == "yes") {
                        string chimeraFlag = "no";
@@ -546,7 +546,7 @@ Sequence* ChimeraSlayer::print(MPI_File& out, MPI_File& outAcc) {
 //***************************************************************************************************************
 int ChimeraSlayer::getChimeras(Sequence* query) {
        try {
-               trimQuery = query;
+               if (trimChimera) { trimQuery = new Sequence(query->getName(), query->getAligned());  }
                
                chimeraFlags = "no";