else { m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
}
else if (queryFileName == "not open") { abort = true; }
+ else { m->setFastaFile(queryFileName); }
referenceFileName = validParameter.validFile(parameters, "reference", true);
if (referenceFileName == "not found") { m->mothurOut("reference is a required parameter for the seq.error command."); m->mothurOutEndLine(); abort = true; }
namesFileName = validParameter.validFile(parameters, "name", true);
if(namesFileName == "not found"){ namesFileName = ""; }
else if (namesFileName == "not open") { namesFileName = ""; abort = true; }
+ else { m->setNameFile(namesFileName); }
qualFileName = validParameter.validFile(parameters, "qfile", true);
if(qualFileName == "not found"){ qualFileName = ""; }
else if (qualFileName == "not open") { qualFileName = ""; abort = true; }
-
+ else { m->setQualFile(qualFileName); }
+
reportFileName = validParameter.validFile(parameters, "report", true);
if(reportFileName == "not found"){ reportFileName = ""; }
else if (reportFileName == "not open") { reportFileName = ""; abort = true; }