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A703FE941194645F002C397E /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makegroupcommand.cpp; sourceTree = SOURCE_ROOT; };
+ A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = degapseqscommand.h; sourceTree = "<group>"; };
+ A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = degapseqscommand.cpp; sourceTree = "<group>"; };
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A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
A7DA2032113FECD400BF472F /* consensuscommand.h */,
+ A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */,
+ A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */,
A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
A7DA203B113FECD400BF472F /* deconvolutecommand.h */,
A7DA203E113FECD400BF472F /* distancecommand.cpp */,
#include "splitabundcommand.h"
#include "clustersplitcommand.h"
#include "classifyotucommand.h"
+#include "degapseqscommand.h"
/*******************************************************/
commands["split.abund"] = "split.abund";
commands["cluster.split"] = "cluster.split";
commands["classify.otu"] = "classify.otu";
+ commands["degap.seqs"] = "degap.seqs";
commands["classify.seqs"] = "MPIEnabled";
commands["dist.seqs"] = "MPIEnabled";
commands["filter.seqs"] = "MPIEnabled";
else if(commandName == "split.abund") { command = new SplitAbundCommand(optionString); }
else if(commandName == "cluster.split") { command = new ClusterSplitCommand(optionString); }
else if(commandName == "classify.otu") { command = new ClassifyOtuCommand(optionString); }
+ else if(commandName == "degap.seqs") { command = new DegapSeqsCommand(optionString); }
else { command = new NoCommand(optionString); }
return command;
// ...at some point should added some additional type checking...
string temp;
+ hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
+ else if (hard == "not open") { hard = ""; abort = true; }
+
temp = validParameter.validFile(parameters, "trump", false); if (temp == "not found") { temp = "*"; }
trump = temp[0];
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
convert(temp, processors);
- hard = validParameter.validFile(parameters, "hard", true); if (hard == "not found") { hard = ""; }
- else if (hard == "not open") { abort = true; }
-
- vertical = validParameter.validFile(parameters, "vertical", false); if (vertical == "not found") { vertical = "T"; }
+ vertical = validParameter.validFile(parameters, "vertical", false);
+ if (vertical == "not found") {
+ if ((hard == "") && (trump == '*')) { vertical = "T"; } //you have not given a hard file or set the trump char.
+ else { vertical = "F"; }
+ }
numSeqs = 0;
-
}
}
m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
m->mothurOut("The trump parameter .... The default is ...\n");
m->mothurOut("The soft parameter .... The default is ....\n");
- m->mothurOut("The hard parameter .... The default is ....\n");
- m->mothurOut("The vertical parameter .... The default is T.\n");
+ m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
+ m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
m->mothurOut("The filter.seqs command should be in the following format: \n");
- m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
- m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
+ m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
+ m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
}
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
- //char* outFilename = new char[filteredFasta.length()];
- //memcpy(outFilename, filteredFasta.c_str(), filteredFasta.length());
-
char outFilename[1024];
strcpy(outFilename, filteredFasta.c_str());
-
- //char* inFileName = new char[fastafileNames[s].length()];
- //memcpy(inFileName, fastafileNames[s].c_str(), fastafileNames[s].length());
-
+
char inFileName[1024];
strcpy(inFileName, fastafileNames[s].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);
-
- //delete inFileName;
- //delete outFilename;
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }