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old mode 100644 new mode 100755 diff --git a/src/codeCogs/randomSample.hpp b/src/codeCogs/randomSample.hpp old mode 100644 new mode 100755 diff --git a/src/codeCogs/stirling.h b/src/codeCogs/stirling.h old mode 100644 new mode 100755 diff --git a/src/codeCogs/xsub_ln_add1.h b/src/codeCogs/xsub_ln_add1.h old mode 100644 new mode 100755 diff --git a/src/dEploid.cpp b/src/dEploid.cpp old mode 100644 new mode 100755 diff --git a/src/dEploidIO-operation.cpp b/src/dEploidIO-operation.cpp old mode 100644 new mode 100755 diff --git a/src/dEploidIO-workflow.cpp b/src/dEploidIO-workflow.cpp old mode 100644 new mode 100755 diff --git a/src/dEploidIO.cpp b/src/dEploidIO.cpp old mode 100644 new mode 100755 index 7834a3db..db1cb58c --- a/src/dEploidIO.cpp +++ b/src/dEploidIO.cpp @@ -209,7 +209,7 @@ void DEploidIO::finalize() { this->setBestPracticeParameters(); } - if ( this->doIbdPainting() | this->doComputeLLK() | this->doIbdViterbiPainting() ) { + if ( this->doIbdPainting() || this->doComputeLLK() || this->doIbdViterbiPainting() ) { if (!initialPropWasGiven()) { throw InitialPropUngiven(""); } @@ -625,7 +625,7 @@ void DEploidIO::checkInput() { // set k strain by proportion length } } - if (this->useBestPractice() & (!this->usePanel())){ + if (this->useBestPractice() && (!this->usePanel())){ throw FlagsConflict("-best" , string("-noPanel. Reference panel is") + string("required for using best-practices.")); } @@ -731,7 +731,7 @@ void DEploidIO::readPanel() { if ( this->usePanel() == false ) { return; } - if ( this->doIbdPainting() | this->doComputeLLK() ) { + if ( this->doIbdPainting() || this->doComputeLLK() ) { return; } diff --git a/src/dEploidIO.hpp b/src/dEploidIO.hpp old mode 100644 new mode 100755 diff --git a/src/dEploid_completion.sh b/src/dEploid_completion.sh old mode 100644 new mode 100755 diff --git a/src/debug/mcmcDebug.cpp b/src/debug/mcmcDebug.cpp old mode 100644 new mode 100755 diff --git a/src/debug/vcfReaderDebug.cpp b/src/debug/vcfReaderDebug.cpp old mode 100644 new mode 100755 diff --git a/src/exceptions.hpp b/src/exceptions.hpp old mode 100644 new mode 100755 index 3bb85d25..40e4e8d0 --- a/src/exceptions.hpp +++ b/src/exceptions.hpp @@ -39,7 +39,8 @@ struct ShouldNotBeCalled : std::exception{ ShouldNotBeCalled() { } virtual ~ShouldNotBeCalled() throw() {} virtual const char* what() const noexcept { - return "Should not reach here"; + static const std::string msg = "Should not reach here"; + return msg.c_str(); } }; @@ -75,7 +76,8 @@ struct OutOfVectorSize : std::exception{ OutOfVectorSize() { } virtual ~OutOfVectorSize() throw() {} virtual const char* what() const noexcept { - return "Out of vector size!"; + static const std::string msg = "Out of vector size!"; + return msg.c_str(); } }; diff --git a/src/export/dEploidIOExport.cpp b/src/export/dEploidIOExport.cpp old mode 100644 new mode 100755 diff --git a/src/export/dEploidIOExportPosteriorProb.cpp b/src/export/dEploidIOExportPosteriorProb.cpp old mode 100644 new mode 100755 diff --git a/src/export/writeMcmcRelated.cpp b/src/export/writeMcmcRelated.cpp old mode 100644 new mode 100755 diff --git a/src/global.hpp b/src/global.hpp old mode 100644 new mode 100755 diff --git a/src/gzstream/COPYING.LIB b/src/gzstream/COPYING.LIB old mode 100644 new mode 100755 diff --git a/src/gzstream/README b/src/gzstream/README old mode 100644 new mode 100755 diff --git a/src/gzstream/gzstream.cpp b/src/gzstream/gzstream.cpp old mode 100644 new mode 100755 diff --git a/src/gzstream/gzstream.h b/src/gzstream/gzstream.h old mode 100644 new mode 100755 diff --git a/src/gzstream/index.html b/src/gzstream/index.html old mode 100644 new mode 100755 diff --git a/src/gzstream/logo.gif b/src/gzstream/logo.gif old mode 100644 new mode 100755 diff --git a/src/gzstream/test_gunzip.C b/src/gzstream/test_gunzip.C old mode 100644 new mode 100755 diff --git a/src/gzstream/test_gzip.C b/src/gzstream/test_gzip.C old mode 100644 new mode 100755 diff --git a/src/gzstream/version b/src/gzstream/version old mode 100644 new mode 100755 diff --git a/src/ibd.cpp b/src/ibd.cpp old mode 100644 new mode 100755 diff --git a/src/ibd.hpp b/src/ibd.hpp old mode 100644 new mode 100755 diff --git a/src/log-double.hpp b/src/log-double.hpp old mode 100644 new mode 100755 diff --git a/src/logsum.hpp b/src/logsum.hpp old mode 100644 new mode 100755 diff --git a/src/mcmc.cpp b/src/mcmc.cpp old mode 100644 new mode 100755 index c71e420b..6a581370 --- a/src/mcmc.cpp +++ b/src/mcmc.cpp @@ -340,7 +340,7 @@ void McmcMachinery::runMcmcChain( bool showProgress, bool useIBD, bool notInR, b this->mcmcSample_->siteOfOneMissCopyOne[atSiteI] /= (double)this->maxIteration_; } - if ( notInR & ((jobbrief == "lassoK") | (jobbrief == "ibd") | (jobbrief == "classic")) ) { // notInPython + if ( notInR & ((jobbrief == "lassoK") || (jobbrief == "ibd") || (jobbrief == "classic")) ) { // notInPython this->dEploidIO_->writeMcmcRelated(this->mcmcSample_, jobbrief, useIBD); } diff --git a/src/mcmc.hpp b/src/mcmc.hpp old mode 100644 new mode 100755 diff --git a/src/panel.cpp b/src/panel.cpp old mode 100644 new mode 100755 diff --git a/src/panel.hpp b/src/panel.hpp old mode 100644 new mode 100755 diff --git a/src/param.hpp b/src/param.hpp old mode 100644 new mode 100755 diff --git a/src/random/fastfunc.cpp b/src/random/fastfunc.cpp old mode 100644 new mode 100755 diff --git a/src/random/fastfunc.hpp b/src/random/fastfunc.hpp old mode 100644 new mode 100755 index f0775d91..899564f7 --- a/src/random/fastfunc.hpp +++ b/src/random/fastfunc.hpp @@ -29,6 +29,7 @@ #include #include #include +#include // Number of interpolation points. If this is changed, several constants in fastlog must also be changed. diff --git a/src/random/mersenne_twister.cpp b/src/random/mersenne_twister.cpp old mode 100644 new mode 100755 diff --git a/src/random/mersenne_twister.hpp b/src/random/mersenne_twister.hpp old mode 100644 new mode 100755 diff --git a/src/random/random_generator.cpp b/src/random/random_generator.cpp old mode 100644 new mode 100755 diff --git a/src/random/random_generator.hpp b/src/random/random_generator.hpp old mode 100644 new mode 100755 diff --git a/src/txtReader.cpp b/src/txtReader.cpp old mode 100644 new mode 100755 diff --git a/src/txtReader.hpp b/src/txtReader.hpp old mode 100644 new mode 100755 diff --git a/src/updateHap.cpp b/src/updateHap.cpp old mode 100644 new mode 100755 diff --git a/src/updateHap.hpp b/src/updateHap.hpp old mode 100644 new mode 100755 diff --git a/src/utility.cpp b/src/utility.cpp old mode 100644 new mode 100755 diff --git a/src/utility.hpp b/src/utility.hpp old mode 100644 new mode 100755 diff --git a/src/variantIndex.cpp b/src/variantIndex.cpp old mode 100644 new mode 100755 diff --git a/src/variantIndex.hpp b/src/variantIndex.hpp old mode 100644 new mode 100755 diff --git a/src/vcfReader.cpp b/src/vcfReader.cpp old mode 100644 new mode 100755 diff --git a/src/vcfReader.hpp b/src/vcfReader.hpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_dEploidIO.cpp b/tests/unittest/test_dEploidIO.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_ibd.cpp b/tests/unittest/test_ibd.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_mcmc.cpp b/tests/unittest/test_mcmc.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_panel.cpp b/tests/unittest/test_panel.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_runner.cpp b/tests/unittest/test_runner.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_txtReader.cpp b/tests/unittest/test_txtReader.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_updatePairHap.cpp b/tests/unittest/test_updatePairHap.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_updateSingleHap.cpp b/tests/unittest/test_updateSingleHap.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_utilities.cpp b/tests/unittest/test_utilities.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_vcfReader.cpp b/tests/unittest/test_vcfReader.cpp old mode 100644 new mode 100755 diff --git a/tests/unittest/test_workflow.cpp b/tests/unittest/test_workflow.cpp old mode 100644 new mode 100755