else if (countfile == "not open") { abort = true; countfile = ""; }
else {
m->setCountTableFile(countfile);
- ct.readTable(countfile);
+ ct.readTable(countfile, true);
if (ct.hasGroupInfo()) { hasGroups = true; }
}
-
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { groupfile = ""; abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else { m->setGroupFile(groupfile); }
+
method = validParameter.validFile(parameters, "method", false); if (method == "not found"){ method = "distance"; }
if ((method != "distance") && (method != "abundance")) {
m->mothurOut(method + " is not a valid option for the method parameter. The only options are: distance and abundance, aborting."); m->mothurOutEndLine(); abort = true;
else { allLines = 1; }
}
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { groupfile = ""; abort = true; }
- else if (groupfile == "not found") { groupfile = ""; }
- else { m->setGroupFile(groupfile); }
-
+
sorted = validParameter.validFile(parameters, "sorted", false); if (sorted == "not found"){ sorted = ""; }
if (sorted == "none") { sorted=""; }
if ((sorted != "") && (sorted != "name") && (sorted != "bin") && (sorted != "size") && (sorted != "group")) {
CountTable thisCt;
if (countfile != "") {
- thisCt.readTable(countfile);
+ thisCt.readTable(countfile, true);
if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
}
CountTable thisCt;
if (countfile != "") {
- thisCt.readTable(countfile);
+ thisCt.readTable(countfile, true);
if (tempGroup != "noGroup") { out2 << "Representative_Sequence\ttotal\t" << tempGroup << endl; }
}