Merge pull request #153 from mcveanlab/DEploid-r

DEploid-r version v0.3-beta.1
DEploid-dev · Oct 14, 2016 · 0255a63 · 0255a63
2 parents c0d75c3 + 57feebf
commit 0255a63
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Showing 37 changed files with 688 additions and 386 deletions.
diff --git a/.gitignore b/.gitignore
@@ -22,6 +22,10 @@
 *.a
 *.lib
 
+# Backup file generated while rewriting r scripts
+utilities/dataExplore.r.bak
+utilities/interpretDEploid.r.bak
+
 # Executables
 *.exe
 *.out
@@ -79,3 +83,6 @@ vcf.*
 *.gcov
 libbash_test.info
 test_coverage/
+
+# Doxyfile
+docs/doxygen/Doxyfile
diff --git a/.travis.yml b/.travis.yml
@@ -18,7 +18,7 @@ before_script:
 script:
   - make
   - make check
-  - ./tests/test_binary.sh
+  - if [ $TRAVIS_OS_NAME == linux ]; then ./tests/test_binary.sh; fi
   - ./tests/testPOS.sh
   - ./tests/test_binaryVcfVsTxt.sh
   - ./tests/test-against-previous-version.sh

diff --git a/src/dEploid.cpp b/src/dEploid.cpp
@@ -6,7 +6,7 @@
  *
  * This file is part of dEploid.
  *
- * scrm is free software: you can redistribute it and/or modify
+ * dEploid is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
@@ -18,8 +18,8 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-*/
+ *
+ */
 
 #include <iostream> // std::cout
 #include "mcmc.hpp"
@@ -30,17 +30,16 @@ using namespace std;
 
 int main( int argc, char *argv[] ){
     try {
-
-        DEploidIO dEploidIO;
-        (void)dEploidIO.core( argc, argv );
+        DEploidIO dEploidIO(argc, argv);
+        std::ostream *output = &std::cout;
 
         if ( dEploidIO.version() ){
-            dEploidIO.printVersion();
+            dEploidIO.printVersion(*output);
             return EXIT_SUCCESS;
         }
 
         if ( dEploidIO.help() ){
-            dEploidIO.printHelp();
+            dEploidIO.printHelp(*output);
             return EXIT_SUCCESS;
         }
 
@@ -58,12 +57,14 @@ int main( int argc, char *argv[] ){
         }
 
         McmcSample * mcmcSample = new McmcSample();
+        MersenneTwister rg(dEploidIO.randomSeed());
 
-        McmcMachinery mcmcMachinery(&dEploidIO, panel, mcmcSample);
-        mcmcMachinery.runMcmcChain();
+        McmcMachinery mcmcMachinery(&dEploidIO, panel, mcmcSample, &rg);
+        mcmcMachinery.runMcmcChain(true);
 
         dEploidIO.write(mcmcSample, panel);
 
+        rg.clearFastFunc();
         if ( panel ){
             delete panel;
         }

diff --git a/src/dEploidIO.cpp b/src/dEploidIO.cpp
@@ -6,7 +6,7 @@
  *
  * This file is part of dEploid.
  *
- * scrm is free software: you can redistribute it and/or modify
+ * dEploid is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
@@ -18,21 +18,40 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
 */
 
 #include "dEploidIO.hpp"
 #include "utility.hpp"  // normailize by sum
 #include <cassert>       // assert
 #include <iomanip>      // std::setw
 #include <ctime>
+#include <iterator>
 
 
 DEploidIO::DEploidIO(){
     this->init();
 }
 
 
+DEploidIO::DEploidIO(const std::string &arg) {
+    this->init();
+    std::istringstream iss(arg);
+    copy(std::istream_iterator<std::string>(iss),
+         std::istream_iterator<std::string>(),
+         std::back_inserter(argv_));
+    this->argv_i = argv_.begin();
+    this->core();
+}
+
+
+DEploidIO::DEploidIO(int argc, char *argv[]) {
+    this->init();
+    argv_ = std::vector<std::string>(argv + 1, argv + argc);
+    this->argv_i = argv_.begin();
+    this->core();
+}
+
+
 DEploidIO::~DEploidIO(){
     if ( this->excludedMarkers != NULL ){
         delete this->excludedMarkers;
@@ -45,10 +64,7 @@ DEploidIO::~DEploidIO(){
 }
 
 
-void DEploidIO::core(int argc, char *argv[]) {
-    argv_ = std::vector<std::string>(argv + 1, argv + argc);
-    this->argv_i = argv_.begin();
-
+void DEploidIO::core() {
     if ( argv_.size() == 0 ) {
         this->set_help(true);
         return;
@@ -394,41 +410,47 @@ void DEploidIO::readNextStringto( string &readto ){
 }
 
 
-void DEploidIO::printVersion(){
-    cout << endl
-         << "dEploid " << VERSION
-         << endl
-         << "Git commit: " << dEploidGitVersion_ << endl;
+void DEploidIO::printVersion(std::ostream& out){
+    out << endl
+        << "dEploid " << VERSION
+        << endl
+        << "Git commit: " << dEploidGitVersion_ << endl;
+}
+
+void DEploidIO::printHelp(std::ostream& out){
+    out << endl
+        << "dEploid " << VERSION
+        << endl
+        << endl;
+    out << "Usage:"
+        << endl;
+    out << setw(20) << "-h or -help"         << "  --  " << "Help. List the following content."<<endl;
+    out << setw(20) << "-v or -version"      << "  --  " << "DEploid version."<<endl;
+    out << setw(20) << "-ref STR"            << "  --  " << "File path of reference allele count."<<endl;
+    out << setw(20) << "-alt STR"            << "  --  " << "File path of alternative allele count."<<endl;
+    out << setw(20) << "-plaf STR"           << "  --  " << "File path of population level allele frequencies."<<endl;
+    out << setw(20) << "-panel STR"          << "  --  " << "File path of the reference panel."<<endl;
+    out << setw(20) << "-exclude STR"        << "  --  " << "File path of sites to be excluded."<<endl;
+    out << setw(20) << "-o STR"              << "  --  " << "Specify the file name prefix of the output."<<endl;
+    out << setw(20) << "-p INT"              << "  --  " << "Out put precision (default value 8)."<<endl;
+    out << setw(20) << "-k INT"              << "  --  " << "Number of strain (default value 5)."<<endl;
+    out << setw(20) << "-seed INT"           << "  --  " << "Random seed."<<endl;
+    out << setw(20) << "-nSample INT"        << "  --  " << "Number of MCMC samples."<<endl;
+    out << setw(20) << "-rate INT"           << "  --  " << "MCMC sample rate."<<endl;
+    out << setw(20) << "-noPanel"            << "  --  " << "Use population level allele frequency as prior."<<endl;
+    out << setw(20) << "-forbidUpdateProp"   << "  --  " << "Forbid MCMC moves to update proportions."<<endl;
+    out << setw(20) << "-forbidUpdateSingle" << "  --  " << "Forbid MCMC moves to update single haplotype."<<endl;
+    out << setw(20) << "-forbidUpdatePair"   << "  --  " << "Forbid MCMC moves to update pair haplotypes."<<endl;
+    out << setw(20) << "-initialP FLT ..."   << "  --  " << "Initialize proportions."<<endl;
+    out << endl;
+    out << "Examples:" << endl;
+    out << endl;
+    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf -plaf data/testData/labStrains.test.PLAF.txt -o PG0390-CNopanel -noPanel"<< endl;
+    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf -exclude data/testData/labStrains.test.exclude.txt -plaf data/testData/labStrains.test.PLAF.txt -o PG0390-CNopanelExclude -noPanel"<< endl;
 }
 
-void DEploidIO::printHelp(){
-    cout << endl
-         << "dEploid " << VERSION
-         << endl
-         << endl;
-    cout << "Usage:"
-         << endl;
-    cout << setw(20) << "-h or -help"         << "  --  " << "Help. List the following content."<<endl;
-    cout << setw(20) << "-v or -version"      << "  --  " << "DEploid version."<<endl;
-    cout << setw(20) << "-ref STR"            << "  --  " << "File path of reference allele count."<<endl;
-    cout << setw(20) << "-alt STR"            << "  --  " << "File path of alternative allele count."<<endl;
-    cout << setw(20) << "-plaf STR"           << "  --  " << "File path of population level allele frequencies."<<endl;
-    cout << setw(20) << "-panel STR"          << "  --  " << "File path of the reference panel."<<endl;
-    cout << setw(20) << "-exclude STR"        << "  --  " << "File path of sites to be excluded."<<endl;
-    cout << setw(20) << "-o STR"              << "  --  " << "Specify the file name prefix of the output."<<endl;
-    cout << setw(20) << "-p INT"              << "  --  " << "Out put precision (default value 8)."<<endl;
-    cout << setw(20) << "-k INT"              << "  --  " << "Number of strain (default value 5)."<<endl;
-    cout << setw(20) << "-seed INT"           << "  --  " << "Random seed."<<endl;
-    cout << setw(20) << "-nSample INT"        << "  --  " << "Number of MCMC samples."<<endl;
-    cout << setw(20) << "-rate INT"           << "  --  " << "MCMC sample rate."<<endl;
-    cout << setw(20) << "-noPanel"            << "  --  " << "Use population level allele frequency as prior."<<endl;
-    cout << setw(20) << "-forbidUpdateProp"   << "  --  " << "Forbid MCMC moves to update proportions."<<endl;
-    cout << setw(20) << "-forbidUpdateSingle" << "  --  " << "Forbid MCMC moves to update single haplotype."<<endl;
-    cout << setw(20) << "-forbidUpdatePair"   << "  --  " << "Forbid MCMC moves to update pair haplotypes."<<endl;
-    cout << setw(20) << "-initialP FLT ..."   << "  --  " << "Initialize proportions."<<endl;
-    cout << endl;
-    cout << "Examples:" << endl;
-    cout << endl;
-    cout << "./dEploid -vcf data/testData/PG0390-C.test.vcf -plaf data/testData/labStrains.test.PLAF.txt -o PG0390-CNopanel -noPanel"<< endl;
-    cout << "./dEploid -vcf data/testData/PG0390-C.test.vcf -exclude data/testData/labStrains.test.exclude.txt -plaf data/testData/labStrains.test.PLAF.txt -o PG0390-CNopanelExclude -noPanel"<< endl;
+
+std::ostream& operator<< (std::ostream& stream, const DEploidIO& dEploidIO) {
+  for (std::string arg : dEploidIO.argv_) stream << " " << arg;
+  return stream;
 }
diff --git a/src/dEploidIO.hpp b/src/dEploidIO.hpp
@@ -6,7 +6,7 @@
  *
  * This file is part of dEploid.
  *
- * scrm is free software: you can redistribute it and/or modify
+ * dEploid is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
@@ -18,8 +18,8 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-*/
+ *
+ */
 
 #include <stdlib.h>     /* strtol, strtod */
 #include <fstream>
@@ -48,14 +48,17 @@ class DEploidIO{
  friend class TestMcmcMachinery;
 #endif
  friend class McmcMachinery;
+ friend class RMcmcSample;
   public:
     DEploidIO();
+    DEploidIO(const std::string &arg);
+    DEploidIO(int argc, char *argv[]);
     ~DEploidIO ();
 
-    void core(int argc, char *argv[]);
-    void printHelp();
+    void core();
+    void printHelp(std::ostream& out);
     bool help() const { return help_; }
-    void printVersion();
+    void printVersion(std::ostream& out);
     bool version() const { return version_; }
 
     bool initialPropWasGiven() const { return initialPropWasGiven_; }
@@ -65,6 +68,8 @@ class DEploidIO{
     string panelFileName_;
 
     size_t nLoci() const { return this->nLoci_; }
+    size_t kStrain() const { return this->kStrain_;}
+    size_t nMcmcSample() const { return this->nMcmcSample_; }
     double averageCentimorganDistance() const { return this->averageCentimorganDistance_; }
     double Ne() const { return this->Ne_; }
     double constRecombProb() const { return this->constRecombProb_; }
@@ -80,6 +85,10 @@ class DEploidIO{
 
     // Log
     void write (McmcSample * mcmcSample, Panel * panel );
+    bool randomSeedWasSet() const {return this->randomSeedWasSet_; }
+
+    friend std::ostream& operator<< (std::ostream& stream, const DEploidIO& dEploidIO);
+    size_t randomSeed() const { return randomSeed_;}
 
   private:
 
@@ -91,10 +100,8 @@ class DEploidIO{
     string excludeFileName_;
     string prefix_;
     size_t randomSeed_;
-    size_t randomSeed() const { return randomSeed_;}
     bool randomSeedWasSet_;
     void setRandomSeedWasSet(const bool random){ this->randomSeedWasSet_ = random; }
-    bool randomSeedWasSet() const {return this->randomSeedWasSet_; }
 
 
     bool initialPropWasGiven_;

diff --git a/src/debug/mcmcDebug.cpp b/src/debug/mcmcDebug.cpp
@@ -6,7 +6,7 @@
  *
  * This file is part of dEploid.
  *
- * scrm is free software: you can redistribute it and/or modify
+ * dEploid is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
@@ -18,8 +18,8 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-*/
+ *
+ */
 
 #include "mcmc.hpp"
 //#include "utility.hpp"

diff --git a/src/debug/vcfReaderDebug.cpp b/src/debug/vcfReaderDebug.cpp
@@ -6,7 +6,7 @@
  *
  * This file is part of dEploid.
  *
- * scrm is free software: you can redistribute it and/or modify
+ * dEploid is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
@@ -18,8 +18,8 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-*/
+ *
+ */
 
 #include "global.h"
 #include <iostream>      // std::cout

diff --git a/src/exceptions.hpp b/src/exceptions.hpp
@@ -6,7 +6,7 @@
  *
  * This file is part of dEploid.
  *
- * scrm is free software: you can redistribute it and/or modify
+ * dEploid is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
@@ -18,8 +18,8 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-*/
+ *
+ */
 
 
 #include <string>  /* string */

diff --git a/src/export/dEploidIOExport.cpp b/src/export/dEploidIOExport.cpp
@@ -6,7 +6,7 @@
  *
  * This file is part of dEploid.
  *
- * scrm is free software: you can redistribute it and/or modify
+ * dEploid is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
@@ -18,8 +18,8 @@
  *
  * You should have received a copy of the GNU General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-*/
+ *
+ */
 
 #include "dEploidIO.hpp"
 #include "mcmc.hpp"