sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / chimeracheckrdp.cpp

diff --git a/chimeracheckrdp.cpp b/chimeracheckrdp.cpp
index 51a3d9bbac0eaea545e1626682049db382a973ac..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() {
        }
 }      
 //***************************************************************************************************************
-int 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 @@ int ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
                        }
                }
                
-               return 0;
+               return *querySeq;
        }
        catch(exception& e) {
                m->errorOut(e, "ChimeraCheckRDP", "print");
@@ -81,7 +81,7 @@ int ChimeraCheckRDP::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
+Sequence ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
        try {
                
                cout << "Processing: " << querySeq->getName() << endl; 
@@ -97,11 +97,12 @@ int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
                
                MPI_Status status;
                int length = outString.length();
-               char buf[length];
-               strcpy(buf, outString.c_str()); 
+               char* buf = new char[length];
+               memcpy(buf, outString.c_str(), length);
                                
                MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
-               
+               delete buf;
+
                if (svg) {
                        if (name != "") { //if user has specific names
                                map<string, string>::iterator it = names.find(querySeq->getName());
@@ -114,7 +115,7 @@ int ChimeraCheckRDP::print(MPI_File& out, MPI_File& outAcc) {
                        }
                }
                
-               return 0;
+               return *querySeq;
        }
        catch(exception& e) {
                m->errorOut(e, "ChimeraCheckRDP", "print");
@@ -261,22 +262,28 @@ void ChimeraCheckRDP::readName(string namefile) {
                MPI_File inMPI;
                MPI_Offset size;
                MPI_Status status;
+
+               //char* inFileName = new char[namefile.length()];
+               //memcpy(inFileName, namefile.c_str(), namefile.length());
                
-               char inFileName[namefile.length()];
+               char inFileName[1024];
                strcpy(inFileName, namefile.c_str());
 
                MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  
                MPI_File_get_size(inMPI, &size);
 
-               char buffer[size];
+               //delete inFileName;
+
+               char* buffer = new char[size];
                MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 
                string tempBuf = buffer;
                if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
                istringstream iss (tempBuf,istringstream::in);
+               delete buffer;
                
                while(!iss.eof()) {
-                       iss >> name; gobble(iss);
+                       iss >> name; m->gobble(iss);
                        names[name] = name;
                }
        
@@ -285,10 +292,10 @@ void ChimeraCheckRDP::readName(string namefile) {
        #else   
        
                ifstream in;
-               openInputFile(namefile, in);
+               m->openInputFile(namefile, in);
                                
                while (!in.eof()) {
-                       in >> name; gobble(in);
+                       in >> name; m->gobble(in);
                        names[name] = name;
                }
                in.close();
@@ -308,25 +315,26 @@ int ChimeraCheckRDP::calcKmers(map<int, int> query, map<int, int> subject) {
        try{
                
                int common = 0;
-               map<int, int>::iterator small;
-               map<int, int>::iterator large;
                
+               map<int, int>::iterator smallone;
+               map<int, int>::iterator largeone;
+
                if (query.size() < subject.size()) {
                
-                       for (small = query.begin(); small != query.end(); small++) {
-                               large = subject.find(small->first);
+                       for (smallone = query.begin(); smallone != query.end(); smallone++) {
+                               largeone = subject.find(smallone->first);
                                
                                //if you found it they have that kmer in common
-                               if (large != subject.end()) {   common++;       }
+                               if (largeone != subject.end()) {        common++;       }
                        }
                        
                }else { 
                 
-                       for (small = subject.begin(); small != subject.end(); small++) {
-                               large = query.find(small->first);
+                       for (smallone = subject.begin(); smallone != subject.end(); smallone++) {
+                               largeone = query.find(smallone->first);
                                
                                //if you found it they have that kmer in common
-                               if (large != query.end()) {             common++;        }
+                               if (largeone != query.end()) {          common++;        }
                        }
                }
                
@@ -347,12 +355,17 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
                
                MPI_File outSVG;
                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
+
+               //char* FileName = new char[file.length()];
+               //memcpy(FileName, file.c_str(), file.length());
                
-               char FileName[file.length()];
+               char FileName[1024];
                strcpy(FileName, file.c_str());
-               
+
                MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outSVG);  //comm, filename, mode, info, filepointer
                
+               //delete FileName;
+
                int width = (info.size()*5) + 150;
                
                string outString = "";
@@ -398,10 +411,11 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
                
                MPI_Status status;
                int length = outString.length();
-               char buf2[length];
-               strcpy(buf2, outString.c_str()); 
+               char* buf2 = new char[length];
+               memcpy(buf2, outString.c_str(), length);
                                
                MPI_File_write(outSVG, buf2, length, MPI_CHAR, &status);
+               delete buf2;
                
                MPI_File_close(&outSVG);
 
@@ -418,7 +432,7 @@ void ChimeraCheckRDP::makeSVGpic(vector<sim> info) {
                
                string file = outputDir + querySeq->getName() + ".chimeracheck.svg";
                ofstream outsvg;
-               openOutputFile(file, outsvg);
+               m->openOutputFile(file, outsvg);
                
                int width = (info.size()*5) + 150;