CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepprimer);
+ CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pkeepdots);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
temp = validParameter.validFile(parameters, "keepprimer", false); if (temp == "not found") { temp = "f"; }
keepprimer = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "keepdots", false); if (temp == "not found") { temp = "t"; }
+ keepdots = m->isTrue(temp);
+
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligosfile = ""; }
else if(temp == "not open"){ oligosfile = ""; abort = true; }
if (m->control_pressed) { return 0; }
- writeAccnos(badNames);
+ //don't write or keep if blank
+ if (badNames.size() != 0) { writeAccnos(badNames); }
+ if (m->isBlank(badSeqFile)) { m->mothurRemove(badSeqFile); }
+
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (namefile != "") { readName(badNames); }
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
// Allocate memory for thread data.
- pcrData* tempPcr = new pcrData(filename, goodFileName+extension, badFileName+extension, m, oligosfile, ecolifile, primers, revPrimer, nomatch, keepprimer, start, end, length, lines[i].start, lines[i].end);
+ pcrData* tempPcr = new pcrData(filename, goodFileName+extension, badFileName+extension, m, oligosfile, ecolifile, primers, revPrimer, nomatch, keepprimer, keepdots, start, end, length, lines[i].start, lines[i].end);
pDataArray.push_back(tempPcr);
//default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
else{
//are you aligned
if (aligned) {
- if (!keepprimer) { currSeq.filterToPos(mapAligned[primerEnd]); }
- else { currSeq.filterToPos(mapAligned[primerStart]); }
+ if (!keepprimer) {
+ if (keepdots) { currSeq.filterToPos(mapAligned[primerEnd]); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerEnd])); }
+ }
+ else {
+ if (keepdots) { currSeq.filterToPos(mapAligned[primerStart]); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(mapAligned[primerStart])); }
+ }
}else {
if (!keepprimer) { currSeq.setAligned(currSeq.getUnaligned().substr(primerEnd)); }
else { currSeq.setAligned(currSeq.getUnaligned().substr(primerStart)); }
else{
//are you aligned
if (aligned) {
- if (!keepprimer) { currSeq.filterFromPos(mapAligned[primerStart]); }
- else { currSeq.filterFromPos(mapAligned[primerEnd]); }
+ if (!keepprimer) {
+ if (keepdots) { currSeq.filterFromPos(mapAligned[primerStart]); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerStart])); }
+ }
+ else {
+ if (keepdots) { currSeq.filterFromPos(mapAligned[primerEnd]); }
+ else { currSeq.setAligned(currSeq.getAligned().substr(0, mapAligned[primerEnd])); }
+ }
}
else {
if (!keepprimer) { currSeq.setAligned(currSeq.getUnaligned().substr(0, primerStart)); }
else if (currSeq.getAligned().length() != length) {
m->mothurOut("[ERROR]: seqs are not the same length as ecoli seq. When using ecoli option your sequences must be aligned and the same length as the ecoli sequence.\n"); m->control_pressed = true; break;
}else {
- currSeq.filterToPos(start);
- currSeq.filterFromPos(end);
+ if (keepdots) {
+ currSeq.filterToPos(start);
+ currSeq.filterFromPos(end);
+ }else {
+ string seqString = currSeq.getAligned().substr(0, end);
+ seqString = seqString.substr(start);
+ currSeq.setAligned(seqString);
+ }
}
}else{ //using start and end to trim
//make sure the seqs are aligned
lengths.insert(currSeq.getAligned().length());
if (lengths.size() > 1) { m->mothurOut("[ERROR]: seqs are not aligned. When using start and end your sequences must be aligned.\n"); m->control_pressed = true; break; }
else {
- if (start != -1) { currSeq.filterToPos(start); }
if (end != -1) {
if (end > currSeq.getAligned().length()) { m->mothurOut("[ERROR]: end is longer than your sequence length, aborting.\n"); m->control_pressed = true; break; }
else {
- currSeq.filterFromPos(end);
+ if (keepdots) { currSeq.filterFromPos(end); }
+ else {
+ string seqString = currSeq.getAligned().substr(0, end);
+ currSeq.setAligned(seqString);
+ }
+ }
+ }
+ if (start != -1) {
+ if (keepdots) { currSeq.filterToPos(start); }
+ else {
+ string seqString = currSeq.getAligned().substr(start);
+ currSeq.setAligned(seqString);
}
}
}