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Changes minlength=10 in screen.seqs
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#160
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@mothur-westcott
mothur-westcott committed Feb 29, 2016
1 parent 1919138 commit 24d445d
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Showing 2 changed files with 10 additions and 9 deletions.
17 changes: 9 additions & 8 deletions source/commands/screenseqscommand.cpp
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Expand Up @@ -27,7 +27,7 @@ vector<string> ScreenSeqsCommand::setParameters(){
CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false,true); parameters.push_back(pend);
CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxambig);
CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxhomop);
CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pminlength);
CommandParameter pminlength("minlength", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pminlength);
CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pmaxlength);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "","",false,false); parameters.push_back(pcriteria);
Expand Down Expand Up @@ -72,7 +72,7 @@ string ScreenSeqsCommand::getHelpString(){
helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1.\n";
helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
helpString += "The minlength parameter allows you to set and minimum sequence length. Default=10.\n";
helpString += "The maxn parameter allows you to set and maximum number of N's allowed in a sequence. \n";
helpString += "The minoverlap parameter allows you to set and minimum overlap. The default is -1. \n";
helpString += "The ostart parameter is used to set an overlap position the \"good\" sequences must start by. The default is -1. \n";
Expand Down Expand Up @@ -335,7 +335,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) {
temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found") { temp = "-1"; }
m->mothurConvert(temp, maxHomoP);

temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "-1"; }
temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "10"; }
m->mothurConvert(temp, minLength);

temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "-1"; }
Expand Down Expand Up @@ -824,7 +824,7 @@ int ScreenSeqsCommand::screenSummary(map<string, string>& badSeqNames){
if(endPos != -1 && endPos > end) { goodSeq = 0; trashCode += "end|"; }
if(maxAmbig != -1 && maxAmbig < ambigs) { goodSeq = 0; trashCode += "ambig|"; }
if(maxHomoP != -1 && maxHomoP < polymer) { goodSeq = 0; trashCode += "homop|"; }
if(minLength != -1 && minLength > length) { goodSeq = 0; trashCode += "<length|"; }
if(minLength > length) { goodSeq = 0; trashCode += "<length|"; }
if(maxLength != -1 && maxLength < length) { goodSeq = 0; trashCode += ">length|"; }

if(goodSeq == 1){
Expand Down Expand Up @@ -1088,7 +1088,7 @@ int ScreenSeqsCommand::getSummaryReport(){
else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100)); endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); if (minLength < 0) { m->control_pressed = true; } }
else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
}

Expand Down Expand Up @@ -1779,11 +1779,12 @@ int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100)); endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); if (minLength < 0) { m->control_pressed = true; } }
else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
else if (optimize[i] == "maxn") { maxN = numNs[criteriaPercentile]; m->mothurOut("Optimizing maxn to " + toString(maxN) + "."); m->mothurOutEndLine(); }
}



return 0;
}
catch(exception& e) {
Expand Down Expand Up @@ -2332,7 +2333,7 @@ int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccn
if(endPos != -1 && endPos > currSeq.getEndPos()) { goodSeq = 0; trashCode += "end|";}
if(maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; trashCode += "ambig|";}
if(maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; trashCode += "homop|";}
if(minLength != -1 && minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "<length|";}
if(minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "<length|";}
if(maxLength != -1 && maxLength < currSeq.getNumBases()) { goodSeq = 0; trashCode += ">length|";}
}

Expand Down
2 changes: 1 addition & 1 deletion source/commands/screenseqscommand.h
View file
Expand Up @@ -422,7 +422,7 @@ static DWORD WINAPI MySumScreenThreadFunction(LPVOID lpParam){
if(pDataArray->endPos != -1 && pDataArray->endPos > currSeq.getEndPos()) { goodSeq = 0; trashCode += "end|"; }
if(pDataArray->maxAmbig != -1 && pDataArray->maxAmbig < currSeq.getAmbigBases()) { goodSeq = 0; trashCode += "ambig|"; }
if(pDataArray->maxHomoP != -1 && pDataArray->maxHomoP < currSeq.getLongHomoPolymer()) { goodSeq = 0; trashCode += "homop|"; }
if(pDataArray->minLength != -1 && pDataArray->minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "<length|"; }
if(pDataArray->minLength > currSeq.getNumBases()) { goodSeq = 0; trashCode += "<length|"; }
if(pDataArray->maxLength != -1 && pDataArray->maxLength < currSeq.getNumBases()) { goodSeq = 0; trashCode += ">length|"; }
}
if (pDataArray->contigsreport == "") { //contigs report includes this so no need to check again
Expand Down

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