another attempt to fix sffinfo

[mothur.git] / chimeraslayercommand.cpp

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index ae98ff3075e691e0db5c5fcedd288f10da14cb9f..1dd3d4221975a33bf52e5e6031029c97d66e0ca5 100644 (file)
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -29,7 +29,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        OptionParser parser(option);
                        map<string,string> parameters = parser.getParameters();
                        
-                       ValidParameters validParameter;
+                       ValidParameters validParameter("chimera.slayer");
                        map<string,string>::iterator it;
                        
                        //check to make sure all parameters are valid for command
@@ -77,7 +77,17 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                                                if (pid == 0) {
                                        #endif
 
-                                       ableToOpen = openInputFile(fastaFileNames[i], in);
+                                       ableToOpen = openInputFile(fastaFileNames[i], in, "noerror");
+                               
+                                       //if you can't open it, try default location
+                                       if (ableToOpen == 1) {
+                                               if (m->getDefaultPath() != "") { //default path is set
+                                                       string tryPath = m->getDefaultPath() + getSimpleName(fastaFileNames[i]);
+                                                       m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+                                                       ableToOpen = openInputFile(tryPath, in, "noerror");
+                                                       fastaFileNames[i] = tryPath;
+                                               }
+                                       }
                                        in.close();
                                        
                                        #ifdef USE_MPI  
@@ -92,7 +102,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                                        #endif
 
                                        if (ableToOpen == 1) { 
-                                               m->mothurOut(fastaFileNames[i] + " will be disregarded."); m->mothurOutEndLine(); 
+                                               m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); 
                                                //erase from file list
                                                fastaFileNames.erase(fastaFileNames.begin()+i);
                                                i--;
@@ -140,7 +150,7 @@ ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
                        temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
                        convert(temp, minBS);
                        
-                       temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "10"; }
+                       temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "100"; }
                        convert(temp, minSNP);
 
                        temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
@@ -195,7 +205,7 @@ void ChimeraSlayerCommand::help(){
                m->mothurOut("The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n");
                m->mothurOut("The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n");
                m->mothurOut("The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n");
-               m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n");
+               m->mothurOut("The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n");
                m->mothurOut("The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n");
                m->mothurOut("The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false.  \n");
                m->mothurOut("The chimera.slayer command should be in the following format: \n");
@@ -243,7 +253,7 @@ int ChimeraSlayerCommand::execute(){
                #ifdef USE_MPI  
                        int pid, end, numSeqsPerProcessor; 
                                int tag = 2001;
-                               vector<long> MPIPos;
+                               vector<unsigned long int> MPIPos;
                                
                                MPI_Status status; 
                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
@@ -357,7 +367,7 @@ int ChimeraSlayerCommand::execute(){
                                        }
                                        
                                }else{
-                                       vector<int> positions;
+                                       vector<unsigned long int> positions;
                                        processIDS.resize(0);
                                        
                                        ifstream inFASTA;
@@ -367,7 +377,7 @@ int ChimeraSlayerCommand::execute(){
                                        while(!inFASTA.eof()){
                                                input = getline(inFASTA);
                                                if (input.length() != 0) {
-                                                       if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
+                                                       if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
                                                }
                                        }
                                        inFASTA.close();
@@ -377,7 +387,7 @@ int ChimeraSlayerCommand::execute(){
                                        int numSeqsPerProcessor = numSeqs / processors;
                                        
                                        for (int i = 0; i < processors; i++) {
-                                               long int startPos = positions[ i * numSeqsPerProcessor ];
+                                               unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
                                                if(i == processors - 1){
                                                        numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor;
                                                }
@@ -519,7 +529,7 @@ int ChimeraSlayerCommand::driver(linePair* line, string outputFName, string file
 }
 //**********************************************************************************************************************
 #ifdef USE_MPI
-int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<long>& MPIPos){
+int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, vector<unsigned long int>& MPIPos){
        try {                           
                MPI_Status status; 
                int pid;