}
//***************************************************************************************************************
-Pintail::Pintail(string filename, string temp) { fastafile = filename; templateFile = temp; }
+Pintail::Pintail(string filename, string temp, string o) { fastafile = filename; templateFile = temp; outputDir = o; }
//***************************************************************************************************************
Pintail::~Pintail() {
mothurOut("Getting conservation... "); cout.flush();
if (consfile == "") {
mothurOut("Calculating probability of conservation for your template sequences. This can take a while... I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command. Providing the .freq file will improve speed. "); cout.flush();
- probabilityProfile = decalc->calcFreq(templateSeqs, templateFile);
+ probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFile));
mothurOut("Done."); mothurOutEndLine();
}else { probabilityProfile = readFreq(); }
string noOutliers, outliers;
if ((!filter) && (seqMask == "")) {
- noOutliers = getRootName(templateFile) + "pintail.quan";
+ noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.quan";
}else if ((filter) && (seqMask == "")) {
- noOutliers = getRootName(templateFile) + "pintail.filtered.quan";
+ noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.filtered.quan";
}else if ((!filter) && (seqMask != "")) {
- noOutliers = getRootName(templateFile) + "pintail.masked.quan";
+ noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.masked.quan";
}else if ((filter) && (seqMask != "")) {
- noOutliers = getRootName(templateFile) + "pintail.filtered.masked.quan";
+ noOutliers = outputDir + getRootName(getSimpleName(templateFile)) + "pintail.filtered.masked.quan";
}
//outliers = getRootName(templateFile) + "pintail.quanYESOUTLIERS";