From 95a40cd0031da456c064727fffbd3787bfd7257a Mon Sep 17 00:00:00 2001
From: Joe Zhu <sha.joe.zhu@gmail.com>
Date: Thu, 4 Aug 2016 16:57:38 +0100
Subject: [PATCH] by default, do no print out recombination probabilities

---
 src/dEploidIO.cpp                 | 3 +++
 src/dEploidIO.hpp                 | 4 ++++
 src/export/dEploidIOExport.cpp    | 6 ++++--
 tests/unittest/test_dEploidIO.cpp | 1 +
 4 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/dEploidIO.cpp b/src/dEploidIO.cpp
index 7245a7f8..9c556928 100644
--- a/src/dEploidIO.cpp
+++ b/src/dEploidIO.cpp
@@ -63,6 +63,7 @@ void DEploidIO::core(int argc, char *argv[]) {
 
 
 void DEploidIO::init() {
+    this->setDoExportRecombProb ( false );
     this->setRandomSeedWasSet( false );
     this->initialPropWasGiven_ = false;
     this->initialProp.clear();
@@ -295,6 +296,8 @@ void DEploidIO::parse (){
             if ( this->constRecombProb_ < 0 || this->constRecombProb_ > 1){
                 throw ( OutOfRange ("-recomb", *argv_i) );
             }
+        } else if ( *argv_i == "-printRecomb" ) {
+            this->setDoExportRecombProb( true );
         } else if ( *argv_i == "-forbidSame" ) {
             this->setForbidCopyFromSame( true );
         } else if ( *argv_i == "-rate" ) {
diff --git a/src/dEploidIO.hpp b/src/dEploidIO.hpp
index 9d5e900d..7b74ddd8 100644
--- a/src/dEploidIO.hpp
+++ b/src/dEploidIO.hpp
@@ -138,6 +138,10 @@ class DEploidIO{
     void setDoExportVcf( const bool exportVcf ){ this->doExportVcf_ = exportVcf; }
     bool doExportVcf() const { return this->doExportVcf_; }
 
+    bool doExportRecombProb_;
+    void setDoExportRecombProb( const bool exportRecombProb ){ this->doExportRecombProb_ = exportRecombProb; }
+    bool doExportRecombProb() const { return this->doExportRecombProb_; }
+
     // Parameters
     double missCopyProb_;
     double averageCentimorganDistance_;// = 15000.0,
diff --git a/src/export/dEploidIOExport.cpp b/src/export/dEploidIOExport.cpp
index 8b756c62..84063e29 100644
--- a/src/export/dEploidIOExport.cpp
+++ b/src/export/dEploidIOExport.cpp
@@ -29,7 +29,7 @@ void DEploidIO::write( McmcSample * mcmcSample, Panel * panel ){
     this->writeLLK( mcmcSample );
     this->writeHap( mcmcSample );
     this->writeVcf( mcmcSample );
-    this->writeRecombProb( panel ); // issue $98
+    this->writeRecombProb( panel );
 
     // Get End time before writing the log
     this->getTime(false);
@@ -42,7 +42,8 @@ void DEploidIO::write( McmcSample * mcmcSample, Panel * panel ){
 }
 
 
-void DEploidIO::writeRecombProb ( Panel * panel ){  // issue $98
+void DEploidIO::writeRecombProb ( Panel * panel ){
+    if ( !doExportRecombProb() ) return;
 
     if ( panel != NULL ){
         ofstreamExportRecombProb.open( strExportRecombProb.c_str(), ios::out | ios::app | ios::binary );
@@ -171,6 +172,7 @@ void DEploidIO::writeHap( McmcSample * mcmcSample ){
 
 
 void DEploidIO::writeVcf( McmcSample * mcmcSample ){
+    if ( !doExportVcf() ) return;
 
     ofstreamExportTmp.open( strExportVcf.c_str(), ios::out | ios::app | ios::binary );
     // VCF HEADER
diff --git a/tests/unittest/test_dEploidIO.cpp b/tests/unittest/test_dEploidIO.cpp
index 77f579bf..d2234fec 100644
--- a/tests/unittest/test_dEploidIO.cpp
+++ b/tests/unittest/test_dEploidIO.cpp
@@ -40,6 +40,7 @@ class TestIO : public CppUnit::TestCase {
 
     void testInitialization(){
         CPPUNIT_ASSERT_EQUAL( this->input_->randomSeedWasSet(), false );
+        CPPUNIT_ASSERT_EQUAL( this->input_->doExportRecombProb(), false );
         CPPUNIT_ASSERT_EQUAL( this->input_->initialPropWasGiven(), false );
         CPPUNIT_ASSERT_EQUAL( this->input_->excludeSites() , false );
         CPPUNIT_ASSERT( this->input_->excludedMarkers == NULL);