fixed problem with class.fy.seqs where group totals did not add up. added constructo...

[mothur.git] / chimerapintailcommand.cpp

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 384c88513f06f9bdf8a738a62cb2a11cf6596661..adf060f485d862dc93797069a54bb58fbe25adfb 100644 (file)
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -147,7 +147,7 @@ void ChimeraPintailCommand::help(){
                #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 window parameter allows you to specify the window size for searching for chimeras, default=1/4 sequence length. \n");
+               m->mothurOut("The window parameter allows you to specify the window size for searching for chimeras, default=300. \n");
                m->mothurOut("The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=25.\n");
                m->mothurOut("The conservation parameter allows you to enter a frequency file containing the highest bases frequency at each place in the alignment.\n");
                m->mothurOut("The quantile parameter allows you to enter a file containing quantiles for a template files sequences, if you use the filter the quantile file generated becomes unique to the fasta file you used.\n");
@@ -175,12 +175,11 @@ int ChimeraPintailCommand::execute(){
                
                int start = time(NULL); 
                
-               chimera = new Pintail(fastafile, templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
-               
                //set user options
                if (maskfile == "default") { m->mothurOut("I am using the default 236627 EU009184.1 Shigella dysenteriae str. FBD013."); m->mothurOutEndLine();  }
                
-
+               chimera = new Pintail(fastafile, templatefile, filter, processors, maskfile, consfile, quanfile, window, increment, outputDir);
+               
                string outputFileName, accnosFileName;
                if (maskfile != "") {
                        outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + maskfile + ".pintail.chimeras";
@@ -255,8 +254,9 @@ int ChimeraPintailCommand::execute(){
                                
                                //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);
@@ -275,8 +275,9 @@ int ChimeraPintailCommand::execute(){
                                
                                //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);