X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraslayercommand.cpp;h=c41e026497191d8218f90ef8ddb5754aa92cfee0;hb=b8f3e71c8a0310e25261464d27e6fcfe891483b0;hp=1a5ae09df87ee9e37abbf81621b0da532a4549dd;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/chimeraslayercommand.cpp b/chimeraslayercommand.cpp
index 1a5ae09..c41e026 100644
--- a/chimeraslayercommand.cpp
+++ b/chimeraslayercommand.cpp
@@ -8,10 +8,6 @@
  */
 
 #include "chimeraslayercommand.h"
-#include "bellerophon.h"
-#include "pintail.h"
-#include "ccode.h"
-#include "chimeracheckrdp.h"
 #include "chimeraslayer.h"
 
 
@@ -141,14 +137,13 @@ void ChimeraSlayerCommand::help(){
 	
 		m->mothurOut("The chimera.slayer command reads a fastafile and templatefile and outputs potentially chimeric sequences.\n");
 		m->mothurOut("This command was modeled after the chimeraSlayer written by the Broad Institute.\n");
-		m->mothurOut("The chimera.slayer command parameters are fasta, template, filter, mask, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
+		m->mothurOut("The chimera.slayer command parameters are fasta, template, processors, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"); //realign,
 		m->mothurOut("The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required. \n");
 		m->mothurOut("The template parameter allows you to enter a template file containing known non-chimeric sequences, and is required. \n");
 		m->mothurOut("The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n");
 		#ifdef USE_MPI
 		m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
 		#endif
-		m->mothurOut("The mask parameter allows you to specify a file containing one sequence you wish to use as a mask for the your sequences. \n");
 		m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=50. \n");
 		m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n");
 		m->mothurOut("The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n");
@@ -164,7 +159,6 @@ void ChimeraSlayerCommand::help(){
 		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 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. Found to make results worse. \n");
-		m->mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
 		m->mothurOut("The chimera.slayer command should be in the following format: \n");
 		m->mothurOut("chimera.slayer(fasta=yourFastaFile, template=yourTemplate, search=yourSearch) \n");
 		m->mothurOut("Example: chimera.slayer(fasta=AD.align, template=core_set_aligned.imputed.fasta, search=kmer) \n");
@@ -220,22 +214,34 @@ int ChimeraSlayerCommand::execute(){
 			
 			int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
 			int inMode=MPI_MODE_RDONLY; 
-							
-			char outFilename[outputFileName.length()];
+			
+			//char* outFilename = new char[outputFileName.length()];
+			//memcpy(outFilename, outputFileName.c_str(), outputFileName.length());
+			
+			char outFilename[1024];
 			strcpy(outFilename, outputFileName.c_str());
 			
-			char outAccnosFilename[accnosFileName.length()];
+			//char* outAccnosFilename = new char[accnosFileName.length()];
+			//memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
+			
+			char outAccnosFilename[1024];
 			strcpy(outAccnosFilename, accnosFileName.c_str());
+
+			//char* inFileName = new char[fastafile.length()];
+			//memcpy(inFileName, fastafile.c_str(), fastafile.length());
 			
-			char inFileName[fastafile.length()];
+			char inFileName[1024];
 			strcpy(inFileName, fastafile.c_str());
 
 			MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 			MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 			MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 			
-			if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
+			//delete inFileName;
+			//delete outFilename;
+			//delete outAccnosFilename;
 
+			if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);   MPI_File_close(&outMPIAccnos);  delete chimera; return 0;  }
 		
 			if (pid == 0) { //you are the root process 
 				m->mothurOutEndLine();
@@ -246,20 +252,25 @@ int ChimeraSlayerCommand::execute(){
 				
 				//print header
 				int length = outTemp.length();
-				char buf2[length];
-				strcpy(buf2, outTemp.c_str()); 
+				char* buf2 = new char[length];
+				memcpy(buf2, outTemp.c_str(), length);
+
 				MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
-				
+				delete buf2;
+
 				MPIPos = setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 				
 				//send file positions to all processes
-				MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
-				MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos	
+				for(int i = 1; i < processors; i++) { 
+					MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
+					MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
+				}
 				
 				//figure out how many sequences you have to align
 				numSeqsPerProcessor = numSeqs / processors;
-				if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
 				int startIndex =  pid * numSeqsPerProcessor;
+				if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
+				
 			
 				//align your part
 				driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
@@ -272,14 +283,15 @@ int ChimeraSlayerCommand::execute(){
 					if (tempResult != 0) { MPIWroteAccnos = true; }
 				}
 			}else{ //you are a child process
-				MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
+				MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 				MPIPos.resize(numSeqs+1);
-				MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
+				MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 				
 				//figure out how many sequences you have to align
 				numSeqsPerProcessor = numSeqs / processors;
-				if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
 				int startIndex =  pid * numSeqsPerProcessor;
+				if(pid == (processors - 1)){	numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor; 	}
+				
 				
 				//align your part
 				driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, MPIPos);
@@ -293,6 +305,7 @@ int ChimeraSlayerCommand::execute(){
 			MPI_File_close(&inMPI);
 			MPI_File_close(&outMPI);
 			MPI_File_close(&outMPIAccnos);
+			MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 			
 			//delete accnos file if blank
 			if (pid == 0) {
@@ -425,7 +438,7 @@ int ChimeraSlayerCommand::execute(){
 			if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  hasAccnos = false; }
 		#endif
 		
-		appendFiles(tempHeader, outputFileName);
+		appendFiles(outputFileName, tempHeader);
 	
 		remove(outputFileName.c_str());
 		rename(tempHeader.c_str(), outputFileName.c_str());
@@ -508,8 +521,7 @@ 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){
-	try {
-				
+	try {				
 		MPI_Status status; 
 		int pid;
 		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
@@ -520,29 +532,33 @@ int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fil
 			
 			//read next sequence
 			int length = MPIPos[start+i+1] - MPIPos[start+i];
-	
-			char buf4[length];
+
+			char* buf4 = new char[length];
 			MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
-			
+	
 			string tempBuf = buf4;
 			if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 			istringstream iss (tempBuf,istringstream::in);
 
+			delete buf4;
+
 			Sequence* candidateSeq = new Sequence(iss);  gobble(iss);
-				
+		
 			if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 				
 				if (candidateSeq->getAligned().length() != templateSeqsLength) {  
 					m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 				}else{
+		
 					//find chimeras
 					chimera->getChimeras(candidateSeq);
-					
+			
 					if (m->control_pressed) {	delete candidateSeq; return 1;	}
-		
+		//cout << "about to print" << endl;
 					//print results
 					bool isChimeric = chimera->print(outMPI, outAccMPI);
 					if (isChimeric) { MPIWroteAccnos = true;  }
+	
 				}
 			}
 			delete candidateSeq;