check style

.ci/checkedList

@@ -1,3 +1,5 @@
+src/dEploidIO-operation.cpp
+src/dEploidIO-workflow.cpp
 src/mcmc.hpp
 src/dEploid.cpp
 src/variantIndex.cpp
@@ -22,4 +24,3 @@ tests/unittest/test_runner.cpp
 tests/unittest/test_utilities.cpp
 src/export/dEploidIOExportPosteriorProb.cpp
 src/export/writeMcmcRelated.cpp
-src/dEploidIO-workflow.cpp

.gitignore

@@ -80,6 +80,8 @@ PG400*
 PG0*
 txt.*
 vcf.*
+data/
+docs/
 
 # coverage test
 *.gcda

Makefile.am

@@ -28,6 +28,7 @@ common_src = src/random/fastfunc.cpp \
 			 src/panel.cpp \
 			 src/utility.cpp \
 			 src/dEploidIO.cpp \
+			 src/dEploidIO-operation.cpp \
 			 src/dEploidIO-workflow.cpp \
 			 src/updateHap.cpp \
 			 src/txtReader.cpp \

src/dEploid.cpp

@@ -32,12 +32,12 @@ int main(int argc, char *argv[]) {
         std::ostream *output = &std::cout;
 
         if ( dEploidIO.version() ) {
-            dEploidIO.printVersion(*output);
+            dEploidIO.operation_printVersion(*output);
             return EXIT_SUCCESS;
         }
 
         if ( dEploidIO.help() ) {
-            dEploidIO.printHelp(*output);
+            dEploidIO.operation_printHelp(*output);
             return EXIT_SUCCESS;
         }
 

src/dEploidIO-operation.cpp

@@ -0,0 +1,144 @@
+/*
+ * dEploid is used for deconvoluting Plasmodium falciparum genome from
+ * mix-infected patient sample.
+ *
+ * Copyright (C) 2016-2017 University of Oxford
+ *
+ * Author: Sha (Joe) Zhu
+ *
+ * This file is part of dEploid.
+ *
+ * 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.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * 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 <iomanip>        // std::setw
+#include "dEploidIO.hpp"
+
+
+void DEploidIO::operation_printVersion(std::ostream& out) {
+    out << endl
+        << "dEploid " << VERSION
+        << endl
+        << "Git commit (DEploid): " << dEploidGitVersion_ << endl
+        << "Git commit (Lasso): " << lassoGitVersion_ << endl;
+}
+
+
+void DEploidIO::operation_printHelp(std::ostream& out) {
+    out << endl
+        << "dEploid " << VERSION << endl
+        << endl;
+    out << "Contact: Joe Zhu <[email protected]>" << 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) << "-vcf STR"            << "  --  "
+        << "VCF file path." << 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 << setw(20) << "-ibd"                << "  --  "
+        << "Use DEploid-IBD" << endl;
+    out << setw(20) << "-lasso"              << "  --  "
+        << "Use DEploid-LASSO" << endl;
+    out << setw(20) << "-best"               << "  --  "
+        << "Use DEploid-Best-practice" << endl;
+    out << endl;
+    out << "Note: Please `man docs/_build/man/dEploid.1' for the manual."
+        << 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;
+    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-C-ibd -panel data/testData/labStrains.test.panel.txt "
+        << "-ibd" << 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-C-best -panel data/testData/labStrains.test.panel.txt "
+        << "-best" << endl;
+    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf.gz "
+        << "-exclude data/testData/labStrains.test.exclude.txt.gz "
+        << "-plaf data/testData/labStrains.test.PLAF.txt.gz -o PG0390-C-best "
+        << "-panel data/testData/labStrains.test.panel.txt.gz -best" << 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-CPanelExclude "
+        << "-panel data/testData/labStrains.test.panel.txt "
+        << "-painting PG0390-CPanelExclude.hap" << endl;
+    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf "
+        << "-plaf data/testData/labStrains.test.PLAF.txt "
+        << "-o PG0390-CNopanel -noPanel -k 2 -nSample 250 -rate 8 -burn 0.67 "
+        << "-ibd "  << endl;
+    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf "
+        << "-plaf data/testData/labStrains.test.PLAF.txt "
+        << "-o PG0390-CNopanel -initialP 0.2 0.8 -ibdPainting"  << 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-CLassoExclude "
+        << "-panel data/testData/labStrains.test.panel.txt "
+        << "-initialP 0.2 0.8 -writePanel -lasso" << endl;
+    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf.gz "
+        << "-sample PG0390-C -plafFromVcf "
+        << "-exclude data/testData/labStrains.test.exclude.txt.gz "
+        << "-o PG0390-C-best "
+        << "-panel data/testData/labStrains.test.panel.txt.gz -best" << endl;
+}
+

src/dEploidIO-workflow.cpp

@@ -104,8 +104,6 @@ void DEploidIO::workflow_ibd() {
     this->paintIBD();
     this->writeHap(mcmcSample->hap, "final");
     delete mcmcSample;
-
-
 }
 
 
@@ -281,9 +279,9 @@ void DEploidIO::workflow_best() {
       this->writeHap(hap, "final");
       this->writeVcf(hap, dEploidLassoIO.initialProp, "final");
     }
-    if (this->inferBestPracticeP() &
-        (this->initialProp.size() > 1)) {
-      this->paintIBD();
+
+    if (this->inferBestPracticeP() & (this->initialProp.size() > 1)) {
+        this->paintIBD();
     }
 }
 

src/dEploidIO.cpp

@@ -25,7 +25,6 @@
 #include <ctime>
 #include <iterator>
 #include <cassert>        // assert
-#include <iomanip>        // std::setw
 #include "utility.hpp"    // normailize by sum
 #include "updateHap.hpp"  // chromPainting
 #include "dEploidIO.hpp"
@@ -652,61 +651,6 @@ void DEploidIO::readNextStringto( string &readto ) {
 }
 
 
-void DEploidIO::printVersion(std::ostream& out) {
-    out << endl
-        << "dEploid " << VERSION
-        << endl
-        << "Git commit (DEploid): " << dEploidGitVersion_ << endl
-        << "Git commit (Lasso): " << lassoGitVersion_ << endl;
-}
-
-void DEploidIO::printHelp(std::ostream& out) {
-    out << endl
-        << "dEploid " << VERSION << endl
-        << endl;
-    out << "Contact: Joe Zhu <[email protected]>" << 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) << "-vcf STR"            << "  --  " << "VCF file path."<<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 << setw(20) << "-ibd"                << "  --  " << "Use DEploid-IBD"<<endl;
-    out << setw(20) << "-lasso"              << "  --  " << "Use DEploid-LASSO"<<endl;
-    out << setw(20) << "-best"               << "  --  " << "Use DEploid-Best-practice"<<endl;
-    out << endl;
-    out << "Note: Please `man docs/_build/man/dEploid.1' for the manual." << 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;
-    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-C-ibd -panel data/testData/labStrains.test.panel.txt -ibd" << 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-C-best -panel data/testData/labStrains.test.panel.txt -best" << endl;
-    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf.gz -exclude data/testData/labStrains.test.exclude.txt.gz -plaf data/testData/labStrains.test.PLAF.txt.gz -o PG0390-C-best -panel data/testData/labStrains.test.panel.txt.gz -best" << 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-CPanelExclude -panel data/testData/labStrains.test.panel.txt -painting PG0390-CPanelExclude.hap" << endl;
-    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf -plaf data/testData/labStrains.test.PLAF.txt -o PG0390-CNopanel -noPanel -k 2 -nSample 250 -rate 8 -burn 0.67 -ibd " <<endl;
-    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf -plaf data/testData/labStrains.test.PLAF.txt -o PG0390-CNopanel -initialP 0.2 0.8 -ibdPainting" <<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-CLassoExclude -panel data/testData/labStrains.test.panel.txt -initialP 0.2 0.8 -writePanel -lasso" << endl;
-    out << "./dEploid -vcf data/testData/PG0390-C.test.vcf.gz -sample PG0390-C -plafFromVcf -exclude data/testData/labStrains.test.exclude.txt.gz -o PG0390-C-best -panel data/testData/labStrains.test.panel.txt.gz -best" << endl;
-}
-
 
 std::ostream& operator<< (std::ostream& stream, const DEploidIO& dEploidIO) {
   for (std::string arg : dEploidIO.argv_) stream << " " << arg;

src/dEploidIO.hpp

@@ -63,9 +63,10 @@ class DEploidIO{
 
     ChooseK chooseK;
 
-    void printHelp(std::ostream& out);
+    void operation_printHelp(std::ostream& out);
+    void operation_printVersion(std::ostream& out);
+
     bool help() const { return help_; }
-    void printVersion(std::ostream& out);
     bool version() const { return version_; }
     // Painting related
     void chromPainting ();

tests/unittest/test_dEploidIO.cpp

@@ -222,22 +222,22 @@ class TestIO : public CppUnit::TestCase {
         DEploidIO dEploidIO1(1, argv);
         CPPUNIT_ASSERT_EQUAL((size_t)0, dEploidIO1.argv_.size());
         CPPUNIT_ASSERT_EQUAL(true, dEploidIO1.help());
-        CPPUNIT_ASSERT_NO_THROW(dEploidIO1.printHelp(*output));
+        CPPUNIT_ASSERT_NO_THROW(dEploidIO1.operation_printHelp(*output));
 
         char *argv1[] = { "./dEploid", "-h" };
         CPPUNIT_ASSERT_NO_THROW(DEploidIO(2, argv1));
         DEploidIO dEploidIO2(2, argv1);
         CPPUNIT_ASSERT_EQUAL((size_t)1, dEploidIO2.argv_.size());
         CPPUNIT_ASSERT_EQUAL(true, dEploidIO2.help());
-        CPPUNIT_ASSERT_NO_THROW(dEploidIO2.printHelp(*output));
+        CPPUNIT_ASSERT_NO_THROW(dEploidIO2.operation_printHelp(*output));
         CPPUNIT_ASSERT_NO_THROW(DEploidIO(string("-help")));
 
         char *argv2[] = { "./dEploid", "-help" };
         CPPUNIT_ASSERT_NO_THROW(DEploidIO(2, argv2));
         DEploidIO dEploidIO3(2, argv2);
         CPPUNIT_ASSERT_EQUAL((size_t)1, dEploidIO3.argv_.size());
         CPPUNIT_ASSERT_EQUAL(true, dEploidIO3.help());
-        CPPUNIT_ASSERT_NO_THROW(dEploidIO3.printHelp(*output));
+        CPPUNIT_ASSERT_NO_THROW(dEploidIO3.operation_printHelp(*output));
     }
 
 
@@ -247,13 +247,13 @@ class TestIO : public CppUnit::TestCase {
         CPPUNIT_ASSERT_NO_THROW(DEploidIO(2, argv1));
         DEploidIO dEploidIO1(2, argv1);
         CPPUNIT_ASSERT_EQUAL(true, dEploidIO1.version());
-        CPPUNIT_ASSERT_NO_THROW(dEploidIO1.printVersion(*output));
+        CPPUNIT_ASSERT_NO_THROW(dEploidIO1.operation_printVersion(*output));
 
         char *argv2[] = { "./dEploid", "-version" };
         CPPUNIT_ASSERT_NO_THROW(DEploidIO(2, argv2));
         DEploidIO dEploidIO2(2, argv2);
         CPPUNIT_ASSERT_EQUAL(true, dEploidIO2.version());
-        CPPUNIT_ASSERT_NO_THROW(dEploidIO2.printVersion(*output));
+        CPPUNIT_ASSERT_NO_THROW(dEploidIO2.operation_printVersion(*output));
     }