Merge pull request #100 from mcveanlab/issue98

Issue98
DEploid-dev · Aug 4, 2016 · baf3286 · baf3286
2 parents 9db56f5 + 95a40cd
commit baf3286
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Showing 4 changed files with 12 additions and 2 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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);