if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}else if (fastaFile == "not open") { abort = true; }
+ else { m->setFastaFile(fastaFile); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found"){ oligoFile = ""; }
else if(temp == "not open"){ abort = true; }
- else { oligoFile = temp; }
+ else { oligoFile = temp; m->setOligosFile(oligoFile); }
temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
temp = validParameter.validFile(parameters, "qfile", true);
if (temp == "not found") { qFileName = ""; }
else if(temp == "not open") { abort = true; }
- else { qFileName = temp; }
+ else { qFileName = temp; m->setQualFile(qFileName); }
temp = validParameter.validFile(parameters, "name", true);
if (temp == "not found") { nameFile = ""; }
else if(temp == "not open") { nameFile = ""; abort = true; }
- else { nameFile = temp; }
+ else { nameFile = temp; m->setNameFile(nameFile); }
temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
convert(temp, qThreshold);
if(qFileName != ""){
currQual = QualityScores(qFile); m->gobble(qFile);
}
-
+ //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
string origSeq = currSeq.getUnaligned();
if (origSeq != "") {
if (alignment != NULL) { delete alignment; }
}
-
+
return success;
}