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Merge branch 'master' into 1.39.0

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2 parents f3cad7b + 8f163fa commit 2db84668fe7778a3e55341a20ef65f561c34c4d8 @mothur-westcott mothur-westcott committed on GitHub Jan 19, 2017
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2 .gitignore
@@ -9,11 +9,13 @@ xcuserdata
project.xcworkspace
*.xcuserdata
TARGET_BUILD_DIRTARGET_BUILD_DIR
+DerivedData
*.xcuserdata
*.xml
nbproject/
mothur
Mothur.1
+DerivedData/
*.stdout
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4 Makefile
@@ -15,8 +15,8 @@ USEBOOST ?= yes
BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"7/20/2016\""
-VERSION = "\"1.38.0\""
+RELEASE_DATE = "\"8/9/2016\""
+VERSION = "\"1.38.1\""
ifeq ($(strip $(64BIT_VERSION)),yes)
CXXFLAGS += -DBIT_VERSION
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12 Mothur.xcodeproj/project.pbxproj
@@ -3384,8 +3384,8 @@
GCC_MODEL_TUNING = G5;
GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.38.1\\\"\"",
- "RELEASE_DATE=\"\\\"09/26/2016\\\"\"",
+ "VERSION=\"\\\"1.39.0\\\"\"",
+ "RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3419,8 +3419,8 @@
GCC_MODEL_TUNING = G5;
GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.38.1\\\"\"",
- "RELEASE_DATE=\"\\\"09/26/2016\\\"\"",
+ "VERSION=\"\\\"1.39.0\\\"\"",
+ "RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3504,8 +3504,8 @@
GCC_MODEL_TUNING = "";
GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.38.1\\\"\"",
- "RELEASE_DATE=\"\\\"09/26/2016\\\"\"",
+ "VERSION=\"\\\"1.39.0\\\"\"",
+ "RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_VERSION = "";
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2 README.md
@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/mothur/mothur.svg?branch=v.1.37.0)](https://travis-ci.org/mothur/mothur)
+[![Build Status](https://travis-ci.org/mothur/mothur.svg?branch=master)](https://travis-ci.org/mothur/mothur)
# README
View
6 source/commandfactory.cpp
@@ -556,7 +556,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
else if(commandName == "classify.svm") { command = new ClassifySvmSharedCommand(optionString); }
- else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
+ //else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
@@ -729,7 +729,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
- else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(optionString); }
+ //else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(optionString); }
else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
@@ -889,7 +889,7 @@ Command* CommandFactory::getCommand(string commandName){
else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); }
else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
- else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
+ //else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
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2 source/commands/chimeraperseuscommand.h
@@ -398,7 +398,7 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
}
catch(exception& e) {
- pDataArray->m->errorOut(e, "ChimeraUchimeCommand", "MyPerseusThreadFunction");
+ pDataArray->m->errorOut(e, "ChimeraPersuesCommand", "MyPerseusThreadFunction");
exit(1);
}
}
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2 source/commands/chimerauchimecommand.cpp
@@ -602,7 +602,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) {
}
}
catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
+ m->errorOut(e, "ChimeraUchimeCommand", "ChimeraUchimeCommand");
exit(1);
}
}
View
4 source/commands/chimerauchimecommand.h
@@ -186,7 +186,6 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
for (int i = pDataArray->start; i < pDataArray->end; i++) {
int start = time(NULL); if (pDataArray->m->control_pressed) { if (pDataArray->hasCount) { delete cparser; } { delete parser; } return 0; }
-
int error;
long long numSeqs = 0;
if (pDataArray->hasCount) {
@@ -521,7 +520,8 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
if (pDataArray->hasCount && pDataArray->dups) { outCountList.close(); }
pDataArray->count = totalSeqs;
- if (pDataArray->hasCount) { delete cparser; } { delete parser; }
+ if (pDataArray->hasCount) { delete cparser; }
+ else { delete parser; }
return totalSeqs;
}
View
1 source/commands/clustercommand.cpp
@@ -412,7 +412,6 @@ int ClusterCommand::runVsearchCluster(){
try {
//look for vsearch exe
string path = m->mothurProgramPath;
-
string vsearchCommand;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vsearchCommand = path + "vsearch"; // format the database, -o option gives us the ability
View
3 source/commands/clustersplitcommand.cpp
@@ -1861,8 +1861,9 @@ bool ClusterSplitCommand::findVsearch(){
if (cutoffNotSet) { m->mothurOut("\nYou did not set a cutoff, using 0.03.\n"); cutoff = 0.03; }
//look for vsearch exe
+
string path = m->mothurProgramPath;
-
+
string vsearchCommand;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vsearchCommand = path + "vsearch"; // format the database, -o option gives us the ability
View
32 source/commands/makefilecommand.cpp
@@ -145,9 +145,7 @@ int MakeFileCommand::execute(){
//find all .fastq files
string tempFile = inputDir + "fileList.temp";
- string findCommand = "find \"" + inputDir.substr(0, inputDir.length()-1) + "\" -maxdepth 1 -name \"*." + typeFile + "\" > \"" + tempFile + "\"";
- if (m->debug) { m->mothurOut(findCommand + "\n"); }
- system(findCommand.c_str());
+ fillAccnosFile(tempFile);
//read in list of files
vector<string> fastqFiles;
@@ -334,4 +332,32 @@ vector< vector<string> > MakeFileCommand::findGroupNames(vector< vector<string>
//**********************************************************************************************************************
+int MakeFileCommand::fillAccnosFile(string tempFile){
+ try {
+
+ string findCommand = "";
+ tempFile = "\"" + tempFile + "\"";
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ findCommand = "find \"" + inputDir.substr(0, inputDir.length()-1) + "\" -maxdepth 1 -name \"*." + typeFile + "\" > " + tempFile;
+ if (m->debug) { m->mothurOut(findCommand + "\n"); }
+ system(findCommand.c_str());
+#else
+ //use ls command
+
+ findCommand = "ls *." + typeFile + " > " + tempFile;
+ if (m->debug) { m->mothurOut(findCommand + "\n"); }
+ system(findCommand.c_str());
+#endif
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFileCommand", "fillAccnosFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
View
2 source/commands/sharedcommand.cpp
@@ -476,6 +476,8 @@ int SharedCommand::createSharedFromBiom() {
//read data
vector<SharedRAbundVector*> lookup = readData(matrixFormat, thisLine, matrixElementType, groupNames, otuNames.size());
+
+ eliminateZeroOTUS(lookup);
m->mothurOutEndLine(); m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
lookup[0]->printHeaders(out);
View
5 source/commands/sparcccommand.cpp
@@ -610,7 +610,6 @@ vector<vector<float> > SparccCommand::createProcesses(vector<vector<float> >& sh
exit(1);
}
}
-
//**********************************************************************************************************************
vector<vector<float> > SparccCommand::driver(vector<vector<float> >& sharedVector, vector<vector<float> >& origCorrMatrix, int numPerms){
try {
@@ -634,7 +633,9 @@ vector<vector<float> > SparccCommand::driver(vector<vector<float> >& sharedVecto
else if(observedValue < 0 && randValue < observedValue){ pValues[j][k]++; }//pvalues of small rho values
}
}
- if((i+1) % (int)(numPermutations * 0.05) == 0){ cout << i+1 << endl; }
+
+ float done = ceil(numPermutations * 0.05);
+ if((i+1) % (int)(done) == 0){ cout << i+1 << endl; }
}
return pValues;

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