1.20.0

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 9699584ca4e8a856ad85470accae4b08b121f1c8..d3030bbf67a6f8fdc9d3ab411e011148abba012c 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -2153,8 +2153,8 @@
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.19.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"5/9/2011\\\"\"",
+                                       "VERSION=\"\\\"1.20.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"6/20/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 375964c306651e93c07966d464b02cf24acb187c..af427d8b6445e39185661bf51782bec1efc54fe6 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -65,7 +65,7 @@ string ChimeraUchimeCommand::getHelpString(){
                helpString += "The abskew parameter can only be used with template=self. Minimum abundance skew. Default 1.9. Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query).\n";
                helpString += "The chimealns parameter allows you to indicate you would like a file containing multiple alignments of query sequences to parents in human readable format. Alignments show columns with differences that support or contradict a chimeric model.\n";
                helpString += "The minh parameter - mininum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.\n";
-               helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease --min h, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n";
+               helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease minh, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n";
                helpString += "The xn parameter - weight of a no vote. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.\n";
                helpString += "The dn parameter - pseudo-count prior on number of no votes. Default 1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2.\n";
                helpString += "The xa parameter - weight of an abstain vote. Default 1. So far, results do not seem to be very sensitive to this parameter, but if you have a good training set might be worth trying. Reasonable values might range from 0.1 to 2.\n";

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index a9bffc6eca25d3ad78ce7b01d96e196ba6308bfb..a7890b878a7f1210137e683e4a1311a02439eb49 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -147,9 +147,9 @@ int CountSeqsCommand::execute(){
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                ofstream out;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + ".seq.count";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "seq.count";
                m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName);
-               out << "Representative Sequence\t total\t";
+               out << "Representative_Sequence\ttotal\t";
                
                GroupMap* groupMap;
                if (groupfile != "") { 

diff --git a/pcacommand.cpp b/pcacommand.cpp
index 5eed4566a74565c5641720dd519ae4df77e90b31..8dee743e07bd4fb546d907e41fd7ab97f6f71664 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -319,7 +319,6 @@ int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
                vector< vector<double> > matrix(numSamples);
                vector<double> colMeans(numOTUs);
                
-                               
                //fill matrix with shared relative abundances, re-center
                for (int i = 0; i < lookupFloat.size(); i++) {
                        matrix[i].resize(numOTUs, 0);
@@ -427,7 +426,7 @@ void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vecto
                }
                pcaData << endl;
                
-               for(int i=0;i<numEigenValues;i++){
+               for(int i=0;i<name_list.size();i++){
                        pcaData << name_list[i] << '\t';
                        for(int j=0;j<numEigenValues;j++){
                                pcaData << G[i][j] << '\t';