CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig);
CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pminlength("minlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pminlength);
+ CommandParameter pminlength("minlength", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pminlength);
CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pmaxlength);
CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "0"; }
m->mothurConvert(temp, maxHomoP);
- temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
+ temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "1"; }
m->mothurConvert(temp, minLength);
temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
if (countfile != "") {
CountTable ct;
- ct.readTable(countfile);
+ ct.readTable(countfile, true);
nameCount = ct.getNameMap();
outputNames.push_back(trimCountFile);
outputNames.push_back(scrapCountFile);
if (countfile != "") { //create countfile with group info included
CountTable* ct = new CountTable();
- ct->readTable(trimCountFile);
+ ct->readTable(trimCountFile, true);
map<string, int> justTrimmedNames = ct->getNameMap();
delete ct;
int currentSeqsDiffs = 0;
Sequence currSeq(inFASTA); m->gobble(inFASTA);
- //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
QualityScores currQual; QualityScores savedQual;
}
else{ currentSeqsDiffs += success; }
}
-
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned() << endl;
if(numSpacers != 0){
success = trimOligos->stripSpacer(currSeq, currQual);
if(success > sdiffs) { trashCode += 's'; }
int thisBarcodeIndex = 0;
int thisPrimerIndex = 0;
-
+ //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl;
if(numBarcodes != 0){
thisSuccess = rtrimOligos->stripBarcode(savedSeq, savedQual, thisBarcodeIndex);
if(thisSuccess > bdiffs) { thisTrashCode += "b"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
-
+ //cout << currSeq.getName() << '\t' << savedSeq.getUnaligned() << endl;
if(numFPrimers != 0){
thisSuccess = rtrimOligos->stripForward(savedSeq, savedQual, thisPrimerIndex, keepforward);
if(thisSuccess > pdiffs) { thisTrashCode += "f"; }
string sname = ""; nameStream >> sname;
sname = sname.substr(1);
- for (int i = 0; i < sname.length(); i++) {
- if (sname[i] == ':') { sname[i] = '_'; m->changedSeqNames = true; }
- }
+ m->checkName(sname);
map<string, int>::iterator it = firstSeqNames.find(sname);