CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch);
CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim);
CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov);
- CommandParameter pminsnp("minsnp", "Number", "", "100", "", "", "",false,false); parameters.push_back(pminsnp);
+ CommandParameter pminsnp("minsnp", "Number", "", "10", "", "", "",false,false); parameters.push_back(pminsnp);
CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
CommandParameter psearch("search", "Multiple", "kmer-blast-distance", "distance", "", "", "",false,false); parameters.push_back(psearch);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter prealign("realign", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prealign);
+ CommandParameter prealign("realign", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(prealign);
CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit);
CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted);
- CommandParameter piters("iters", "Number", "", "100", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence);
CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents);
CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
helpString += "The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n";
helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n";
helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n";
- helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n";
+ helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=1000.\n";
helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n";
helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n";
helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n";
- helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n";
+ helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 10) \n";
helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n";
helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default true. \n";
helpString += "The chimera.slayer command should be in the following format: \n";
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 = "100"; }
+ temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
convert(temp, minSNP);
temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
convert(temp, parents);
- temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "f"; }
+ temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; }
realign = m->isTrue(temp);
temp = validParameter.validFile(parameters, "trim", false); if (temp == "not found") { temp = "f"; }
search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "distance"; }
- temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
convert(temp, iters);
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; }
int ChimeraSlayerCommand::execute(){
try{
-
if (abort == true) { if (calledHelp) { return 0; } return 2; }
for (int s = 0; s < fastaFileNames.size(); s++) {