//**********************************************************************************************************************
vector<string> ChimeraSlayerCommand::getValidParameters(){
try {
- string AlignArray[] = {"fasta", "processors","trim","trimera", "name","window", "include","template","numwanted", "ksize", "match","mismatch",
+ string AlignArray[] = {"fasta", "processors","trim","split", "name","window", "include","template","numwanted", "ksize", "match","mismatch",
"divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
return myArray;
else {
//valid paramters for this command
- string Array[] = {"fasta", "processors","name", "include","trim", "trimera","window", "template","numwanted", "ksize", "match","mismatch",
+ string Array[] = {"fasta", "processors","name", "include","trim", "split","window", "template","numwanted", "ksize", "match","mismatch",
"divergence", "minsim","mincov","minbs", "minsnp","parents", "iters","outputdir","inputdir", "search","realign" };
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
trim = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "trimera", false); if (temp == "not found") { temp = "f"; }
+ temp = validParameter.validFile(parameters, "split", false); if (temp == "not found") { temp = "f"; }
trimera = m->isTrue(temp);
search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
m->mothurOut("When using MPI, the processors parameter is set to the number of MPI processes running. \n");
#endif
m->mothurOut("The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n");
- m->mothurOut("The trimera parameter allows you to check both peices of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n");
+ m->mothurOut("The split parameter allows you to check both pieces of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \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");