changed defaults for filter.seqs()

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 5e93a5c10dab67d52494b36675f38a71f63b29ae..ddec9d1ca4ef463972b4c43899364474114f422f 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -273,13 +273,13 @@ void ValidParameters::initCommandParameters() {
                string vennArray[] =  {"groups","line","label","calc"};
                commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
                
-               string binseqsArray[] =  {"fasta","line","label","name"};
+               string binseqsArray[] =  {"fasta","line","label","name", "group"};
                commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
                
-               string getrepseqsArray[] =  {"fasta","line","label","name", "group"};
-               commandParameters["get.repseqs"] = addParameters(getrepseqsArray, sizeof(getrepseqsArray)/sizeof(string));
+               string distsharedArray[] =  {"line","label","calc","groups"};
+               commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
                
-               string getOTURepArray[] =  {"fasta","list","line","label","name"};
+               string getOTURepArray[] =  {"fasta","list","line","label","name", "group"};
                commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
                
                string treeGroupsArray[] =  {"line","label","calc","groups"};
@@ -294,7 +294,7 @@ void ValidParameters::initCommandParameters() {
                string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
                commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
-               string AlignArray[] =  {"fasta","phylip","clustal","nexus", "template", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+               string AlignArray[] =  {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
                commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
                
                string quitArray[] = {};